title: NFCs

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

description: sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R and  J-Express software (Molmine, Bergen, Norway).  Quantile normalisation makes different arrays comparable by making sure that the distribution of intensities are the same across arrays. The normalisation distribution is chosen by averaging each quantile across chips.

source_name: glioblastoma stem like cells

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

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.

tag: cell type

value: NFC cultures-spheres


title: 600246

status: Public on Nov 26 2015

type: genomic

city: London

first: Robert

last: Brown

address: Du Cane Road, The Hammersmith Hospital-4th floor

country: United Kingdom

institute: Imperial College London

description:
chipid: 5552218043_B
tumour sample 7

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2

MISSING RAW DATA EXPLANATION: The raw data was not kept after conversion into beta values because of limitations of storage capacity.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from tumour sample 7

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions. Tumour DNA was bisulphite converted using the EZ-96 DNA Methylation™ Kit (Zymo) as per manufacturers protocol

tag: status

value: Case

tag: ChIP

tag: tumour nuclei(%)

tag: site

value: Ovarian

tag: histology

value: Serous

tag: grade


title: 600184

description:
chipid: 5552234033_E
tumour sample 5

source_name: genomic DNA from tumour sample 5


title: 600268

description:
chipid: 5552234033_L
tumour sample 8

source_name: genomic DNA from tumour sample 8


title: T0996 sph-3

type: RNA

city: Oslo

country: Norway

institute: Oslo University Hospital

description: replicate of sample 4

label: biotin

molecule: total RNA

value: GSC culture-spheres

tag: treatment


title: 600170

description:
chipid: 5552200032_E
tumour sample 4

source_name: genomic DNA from tumour sample 4


title: 600240

description:
chipid: 5552234033_F
tumour sample 6

source_name: genomic DNA from tumour sample 6


title: 600132

description:
chipid: 5552234033_A
tumour sample 2

source_name: genomic DNA from tumour sample 2


title: T0996 sph-7

description: sample


title: T09111 tissue

description: sample

value: GBM-tissue


title: R. sphaeroides 2.4.1 (trans) vs. R. sphaeroides 2.4.1 (exp low) 1

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description:
1 trans vs exp (low)
biological sample 1-3

hyb_protocol: Total RNA of three independent experiments (biological replicates 1-3 or 4-6) of two different growth phases were pooled and hybridized to one array. Two arrays were hybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: LOESS normalization log2 ratio (Cy3/Cy5) with Limma package (v.3.14.3; release date: 2012/11/29) for Bioconductor in R

organism: Cereibacter sphaeroides 2.4.1

source_name: transition phase_low aeration

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

treatment_protocol: R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases

tag: growth phase

value: transition phase

tag: aeration condition

value: low aeration

source_name: exponential phase_low aeration

value: exponential phase


title: C2R1 vs C1R1

city: Madrid

first: Alicia

last: Bravo

address: Calle Ramiro de Maeztu, 9

department: Centro de Investigaciones Biologicas

country: Spain

institute: CSIC

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

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

organism: Enterococcus faecalis OG1RF

source_name: mafR deletion mutant strain

label_protocol: Two-color microarray-based Prokaryote Analysis (FairPlay III Labeling) Protocol v.1.3 (Agilent)

growth_protocol: Bacteria were grown in Brain Heart Infusion (BHI) medium, at 37ºC, without aeration

extract_protocol: Total RNA was isolated using the RNeasy mini Kit (QIAGEN). Cultures were processed as specified by the suppliers, except that cells were resuspended in buffer L (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1 mg/ml lysozyme, 160 units/ml mutanolysin) and incubated at 37ºC for 10 min. An additional DNase I digestion step was performed.

treatment_protocol: Bacteria were grown to an optical density at 650 nm of 0.4

tag: genotype/variation

value: mafR deletion mutant

source_name: wild-type strain

value: wild-type


title: 600160

description:
chipid: 5552234033_C
tumour sample 3

source_name: genomic DNA from tumour sample 3


title: T0965 tissue

description: sample


title: CAST4 sph

description: sample


title: T09111 sph

description: sample


title: C1R2 vs C2R2


title: R. sphaeroides 2.4.1 (trans) vs. R. sphaeroides 2.4.1 (exp low) 2

description:
2 trans vs exp (low)
biological sample 4-6

growth_protocol: R. sphaeroides strains grown under low aeration or aerobic conditions


title: myoblasts treated with  palmitate (0.1 mmol/l)- rep3

status: Public on Nov 25 2015

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description: Biological replicate 3 of 4. Control: myoblasts cells, untreated, harvested after 3 day of proliferation.

hyb_protocol: The cRNA was fragmented and hybridized to Agilent whole mouse genome oligonucleotide microarray (4 × 44K slide format) at 37 ºC for 17 hours (protocol Version 5.7, March 2008).

scan_protocol: After washing the slides were scanned with a DNA microarray Agilent Technologies Scanner G2505C US10353831.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were processed using GeneSpring 12GX (Agilent). Total detected entities were filtered by flags (present, marginal) and coeffi. In statistical analysis of differential gene expression unpaired t-test testing the null hypothesis of no differential expression between the control and experimental group was used. The statistical significance was set at P≤0.05. Moreover, the Benjamini-Hochberg FDR (False discovery rate) test with the significance level p≤0.05 was employed. Absolute fold change cut-off for ontological analyses  was 1.6. For interaction network analysis were used all entities with significant changes in expression.

organism: Mus musculus

source_name: C2C12 myoblasts- 48-h exposure to palmitate (final concentration 0.1 mmol/l) added to 5%FBS/DMEM

label_protocol: The total RNA (1 μg) was extracted, amplified and labeled in accordance with the protocol for Agilent Gene Expression oligo microarrays

growth_protocol: Research work was carried out on the murine myogenic C2C12 cell line (satellite cells from thigh muscle), purchased from the European Collection of Animal Cell Culture (ECACC). This cell line undergoes proliferation and differentiation in response to growth factors present in the extracellular environment, thus, it is a useful model to study the mechanisms controlling myogenesis (Yaffe and Saxel 1977).   Mouse C2C12 myoblasts were maintained free of contamination at the exponential phase of growth in DMEM supplemented with 10% FBS (Foetal Bovine Serum) and an antibiotic-antimycotic mixture (Life Technologies), in controlled humidified air supplemented with 5% CO2, at 37oC. The growing medium was changed every other day.

extract_protocol: Total RNA was extracted and purified from C2C12 cells using the Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol. The isolated RNA samples were dissolved in RNase-free water. The quantity of the isolated RNA was measured using Nano-Drop (NanoDrop Technologies, USA). The RNA samples were treated with DNase I to eliminate DNA contamination and subsequently purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany). Subsequently, the RNA samples were analyzed on a BioAnalyzer (Agilent, USA) to measure the final RNA quality and integrity.

treatment_protocol: After reaching ~40% confluence, the proliferating myoblasts were subjected to 48-h exposure to palmitate (final concentration 0.1 mmol/l) added to 5%FBS/DMEM, according to experimental protocol described previously (Lee et al. 2009). The control cultures were maintained in 5% FBS/DMEM, containing the same amounts of ethanol and FFA-free bovine serum albumin as the experimental medium. To preserve the characteristics of C2C12 cell line, the cells were split up to a maximum of 7 times.

tag: cell line

tag: age

value: 3th day of proliferation

tag: tissue

value: myoblasts

tag: tratment

value: palmitate (0.1 mmol/l)- treated

source_name: C2C12 myoblasts- 3th day of proliferation in [10%HS/24h/3d]

value: CTRL- untreated


title: myoblasts treated with  palmitate (0.1 mmol/l)- rep2

description: Biological replicate 2 of 4. Control: myoblasts cells, untreated, harvested after 3 day of proliferation.


title: 400130

description:
chipid: 5552234033_J
tumour sample 1

source_name: genomic DNA from tumour sample 1


title: Stat3wt/wt/MIC_9597_bio rep6

city: Montreal

first: William

middle: Joseph

last: Muller

state: Quebec

address: 1160 Pine ave Ouest

department: Biochemistry

country: Canada

institute: McGill University

description: Gene expression data from Stat3wt/wt/MIC mammary tumors

hyb_protocol: The fragmented and labeled DNA target was hybridized on a Mouse Gene 2.0 ST (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm.

scan_protocol: GeneChips were scanned GeneChip® scanner 3000 (Affymetrix).

data_processing: Microarray raw intensities were normalized using RMA method via Expression console software and absolute expression values were obtained

source_name: Stat3wt/wt/MIC tumor

label_protocol: A tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample was done from 1µg of total RNA using the Affymetrix FlashTag™ Biotin HSR Labeling Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA). An ELISA QC Assay was done to confirm that the labeling kit performed appropriately.

growth_protocol: Transgenic mice were induced at 8-10 weeks of age with doxycyclin and allowed to develop mammary tumors up to ethical tumor burden before sacrifice.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Tumors were flash frozen with liquid nitrogen

tag: strain

value: FVB

value: Mammary tumor

tag: genotype

value: 6 months


title: Stat3flx/flx/MIC_5943_bio rep6

description: Gene expression data from Stat3flx/flx/MIC mammary tumors

source_name: Stat3flx/flx/MIC tumor

value: 14 months


title: Stat3wt/wt/MIC_2256_bio rep1


title: myoblasts treated with  palmitate (0.1 mmol/l)- rep4

description: Biological replicate 4 of 4. Control: myoblasts cells, untreated, harvested after 3 day of proliferation.


title: myoblasts treated with  palmitate (0.1 mmol/l)- rep1

description: Biological replicate 1 of 4. Control: myoblasts cells, untreated, harvested after 3 day of proliferation.


title: Stat3flx/flx/MIC_5936_bio rep4

value: 13 months


title: Stat3flx/flx/MIC_5940_bio rep5


title: Stat3wt/wt/MIC_9601_bio rep8


title: CAST3 sph

description: sample

source_name: glioblastoma stem like cells

tag: cell type


title: Sperm_control_rep7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Ctrl_14
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.4.0.38) including median polish and Sketch-Quantile normalisation.

source_name: Sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen).

growth_protocol: Animals housed under spf conditions.

extract_protocol: miRNeasy Micro Kit (Qiagen) including DNase treatment.

treatment_protocol: As described in the paper. Briefly, starting at 9 weeks of age, male C57BL/6Ntac mice were either treated with dexamethasone at a concentration of 2 mg/kg body weight (D4902, Sigma-Aldrich, USA) dissolved in (2-Hydroxypropyl)-β-cyclodextrin solution (H5784, Sigma-Aldrich, USA) at 10 mg/ml and further diluted 50-fold in sterile saline (final dexamethasone concentration 0.2 mg/ml)) or were treated with vehicle (Veh), (2-Hydroxypropyl)-β-cyclodextrin solution 50-fold diluted in sterile saline. Every mouse received a total of 15 injections within 33 days.

tag: strain/background

value: WT

value: 15 weeks

tag: gender

value: male

value: sperm

value: vehicle control

tag: treatment duration

value: 33 days


title: Stat3wt/wt/MIC_9598_bio rep7


title: Stat3wt/wt/MIC_2260_bio rep3


title: Stat3wt/wt/MIC_6219_bio rep5


title: Stat3wt/wt/MIC_2348_bio rep4


title: Sperm_control_rep4

description:
Ctrl_05
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: Sperm_control_rep6

description:
Ctrl_07
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: Stat3flx/flx/MIC_5921_bio rep3


title: Stat3flx/flx/MIC_2128_bio rep1

value: 11 months


title: Stat3flx/flx/MIC_2248_bio rep2


title: Sperm_control_rep2

description:
Ctrl_03
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: Sperm_control_rep3

description:
Ctrl_04
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: TIMP-4 HeLa cells 2-24h

city: Mexico City

first: Jorge

last: Melendez-Zajgla

address: Periferico Sur 4809 Col. Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

description: Gene expression data from HeLa cells grown for 24h upon serum starvation plus hrTIMP-4 treatment

hyb_protocol: 2.5mg labeled cDNA were hybridized for 16h at 45 C on Affymetrix Human Gene ST 1.0 on GeneChip Hybridization Owen 640. GeneChips were washed and stained in the Affymetrix Fluidic station 450.

scan_protocol: GeneChips were scanned with GeneChip scanner 3000 7G.

data_processing: The data was analyzed with Partek Genomic Suite version 6.6 using RMA as normalization method and following Partek's standard gene expression pipeline. Significantly up- and down-regulated genes were sorted using a p value with FDR < 0.05 and a fold change of >1.1 and <-1.1

source_name: HeLa cell line_TIMP-4

label_protocol: Fragmented single-stranded DNA was labeled according to the standard Affymetrix protocol (GeneChip WT terminal labeling and hybridazation user manual for use with the Ambion WT expression Kit P/N 702808 Rev.4)

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

value: human cervical  adenocarcinoma

value: HeLa


title: Sperm_control_rep1

description:
Ctrl_01
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: TIMP-4 HeLa cells 3-24h


title: Sperm_dexamethasone_rep8

description:
Dex_16
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.

source_name: Sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days

value: dexamethasone


title: Sperm_control_rep5

description:
Ctrl_06
Gene expression data from sperms derived from C57BL/6Ntac mice treated with vehicle for 33 days.


title: TIMP-4 HeLa cells 1-24h


title: Sperm_dexamethasone_rep7

description:
Dex_15
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Sperm_dexamethasone_rep4

description:
Dex_10
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Sperm_dexamethasone_rep6

description:
Dex_12
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Sperm_dexamethasone_rep5

description:
Dex_11
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Control HeLa cells 2-24h

description: Gene expression data from HeLa cells grown for 24h upon serum starvation

source_name: HeLa cell line_control


title: Normal scalp sample, Scalp_N_30

city: New York

first: Juan

last: Ruano

state: NY

address: 1230 York ave

country: USA

institute: Rockefeller University

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Subject 30

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

extract_protocol: Qiagen RNeasy Kit protocol

tag: disease state

value: Control subject, normal scalp sample

value: scalp


title: Control HeLa cells 3-24h


title: Normal scalp sample, Scalp_N_28

source_name: Subject 28


title: Normal scalp sample, Scalp_N_23

source_name: Subject 23


title: Sperm_dexamethasone_rep3

description:
Dex_09
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Normal scalp sample, Scalp_N_26

source_name: Subject 26


title: Normal scalp sample, Scalp_N_25

source_name: Subject 25


title: Normal scalp sample, Scalp_N_24

source_name: Subject 24


title: Scalp lesional sample, Scalp_LS_18

source_name: Subject 18

value: psoriatic patient, lesional scalp sample


title: Sperm_dexamethasone_rep2

description:
Dex_08
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.


title: Scalp lesional sample, Scalp_LS_20

source_name: Subject 20


title: Normal scalp sample, Scalp_N_27

source_name: Subject 27


title: Scalp lesional sample, Scalp_LS_19

source_name: Subject 19


title: Scalp lesional sample, Scalp_LS_17

source_name: Subject 17


title: Scalp lesional sample, Scalp_LS_14

source_name: Subject 14


title: Normal scalp sample, Scalp_N_21

source_name: Subject 21


title: Stat3wt/wt/MIC_2259_bio rep2

description: Gene expression data from Stat3wt/wt/MIC mammary tumors

source_name: Stat3wt/wt/MIC tumor

value: FVB

value: Mammary tumor


title: Control HeLa cells 1-24h


title: Normal scalp sample, Scalp_N_29

source_name: Subject 29


title: Normal scalp sample, Scalp_N_22

source_name: Subject 22


title: Scalp lesional sample, Scalp_LS_16

source_name: Subject 16


title: Scalp lesional sample, Scalp_LS_15

source_name: Subject 15


title: Scalp lesional sample, Scalp_LS_12

source_name: Subject 12


title: Scalp lesional sample, Scalp_LS_13

source_name: Subject 13


title: Scalp non-lesional sample, Scalp_NL_12

value: psoriatic patient, non-lesional scalp sample


title: Sperm_dexamethasone_rep1

description:
Dex_02
Gene expression data from sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days.

source_name: Sperms derived from C57BL/6Ntac mice treated with dexamethasone for 33 days


title: Scalp lesional sample, Scalp_LS_11

source_name: Subject 11


title: Scalp lesional sample, Scalp_LS_10

source_name: Subject 10


title: Scalp lesional sample, Scalp_LS_9

source_name: Subject 9


title: Scalp non-lesional sample, Scalp_NL_10


title: Scalp non-lesional sample, Scalp_NL_11


title: Scalp lesional sample, Scalp_LS_8_3

source_name: Subject 8


title: Dystrophic single fibers from diaphragm, replicate 3

type: mixed

city: Bergisch Gladbach

first: Silvia

last: Rueberg

state: NRW

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

institute: Miltenyi Biotec GmbH

description:
dia_mdx_f_03
6830012

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of the hybridized miRXplore ™ microarrays were done with the ScanArrayLite4000 Microarray Scanner (Packard-Biosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos. Valid data of up to 4 reps only was used for the normalized ratios.

molecule: other

organism: synthetic construct

source_name: Universal Reference

label_protocol: 2 µg of respective total RNA as well as 1 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix were hybridized in a dual colour approach to microarrays.

extract_protocol: Synthetic RNA oligonucleotides.

tag: vendor

value: Miltenyi Biotec GmbH

tag: sample description

value: synthethic miRNA pool of 950 miRNA sequences from human, mouse, rat, and virus

source_name: single fibers isolated from diaphragm

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

value: mdx

value: 3.5 months

value: diaphragm

tag: myofiber type

value: dystrophic


title: Dystrophic single fibers from quadriceps, replicate 1

description:
quad_mdx_m_01
6830019

source_name: single fibers isolated from quadriceps

value: male

value: quadriceps


title: Dystrophic single fibers from quadriceps, replicate 2

description:
quad_mdx_m_02
6830020


title: Dystrophic single fibers from quadriceps, replicate 3

description:
quad_mdx_f_03
6830018


title: Scalp non-lesional sample, Scalp_NL_9


title: Control single fibers from quadriceps, replicate 1

description:
quad_c57bl_m_01
6830013

value: wild-type

value: control


title: Dystrophic single fibers from tibialis, replicate 2

description:
tib_mdx_m_02
6830009

source_name: single fibers isolated from tibialis

value: tibialis


title: Dystrophic single fibers from tibialis, replicate 3

description:
tib_mdx_f_03
6830011


title: Dystrophic single fibers from diaphragm, replicate 1

description:
dia_mdx_m_01
6830008


title: Dystrophic single fibers from diaphragm, replicate 2

description:
dia_mdx_m_02
6830010


title: Control single fibers from quadriceps, replicate 3

description:
quad_c57bl_f_03
6830015


title: Dystrophic single fibers from tibialis, replicate 1

description:
tib_mdx_m_01
6830007


title: Control single fibers from diaphragm, replicate 3

description:
dia_c57bl_f_03
6830006


title: Scalp non-lesional sample, Scalp_NL_6

source_name: Subject 6


title: Scalp non-lesional sample, Scalp_NL_7

source_name: Subject 7


title: Scalp lesional sample, Scalp_LS_8_2


title: Scalp lesional , Scalp_LS_8_1


title: Control single fibers from tibialis, replicate 3

description:
tib_c57bl_f_03
6830005


title: Scalp non-lesional sample, Scalp_NL_8_2


title: Scalp non-lesional sample, Scalp_NL_5

source_name: Subject 5


title: Control single fibers from tibialis, replicate 2

description:
tib_c57bl_m_02
6830003


title: Scalp lesional sample, Scalp_LS_5


title: Scalp non-lesional sample, Scalp_NL_8_1


title: Control single fibers from quadriceps, replicate 2

description:
quad_c57bl_m_02
6830014


title: Scalp non-lesional sample, Scalp_NL_4

source_name: Subject 4


title: Scalp lesional sample, Scalp_LS_6


title: Scalp lesional sample, Scalp_LS_3

source_name: Subject 3


title: Scalp lesional sample, Scalp_LS_7


title: Control single fibers from tibialis, replicate 1

description:
tib_c57bl_m_01
6830001


title: Scalp non-lesional sample, Scalp_NL_2

source_name: Subject 2


title: Scalp lesional sample, Scalp_LS_2


title: Scalp non-lesional sample, Scalp_NL_3


title: Control single fibers from diaphragm, replicate 1

description:
dia_c57bl_m_01
6830002


title: Scalp lesional sample, Scalp_LS_1

source_name: Subject 1


title: normal adrenal tissue, donor 7

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 20 ug of biotinylated cRNA were hybridized for 16 hr at 45C on the Affymetrix Human Genome HGU133A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: normal adrenal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle eukaryote target Affymetrix protocol using 5-10 ug total RNA as starting template (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Tumor specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity. Tissue samples were classified according to established histopathologic criteria and verified by two independent pathologists. Total RNA was isolated from 50 to 100 mg of pediatric ACT using the RNeasy RNA Midi-Prep kit (Qiagen, Valencia, CA). Tumors were prepared in a 4 degree centigrade cold room, sliced into fine pieces using a sterile scalpel, and homogenized with 18- and 19-gauge needles in lysis Buffer RLT (Qiagen) containing beta-mercaptoethanol.

value: unknown

tag: histologic type

value: normal

tag: tumor stage

value: not applicable


title: Control single fibers from diaphragm, replicate 2

description:
dia_c57bl_m_02
6830004


title: normal adrenal tissue, donor 1


title: adrenocortical  carcinoma tumor, donor 18

source_name: adrenal tumor

value: female

value: adrenocortical carcinoma


title: normal adrenal tissue, donor 2


title: adrenocortical  carcinoma tumor, donor 13


title: adrenocortical  carcinoma tumor, donor 17


title: adrenocortical  tumor of unknown histology, donor 1


title: Scalp lesional sample, Scalp_LS_4

value: psoriatic patient, lesional scalp sample

value: scalp


title: adrenocortical  carcinoma tumor, donor 12


title: adrenocortical  carcinoma tumor, donor 8


title: adrenocortical  carcinoma tumor, donor 14


title: Scalp non-lesional sample, Scalp_NL_1

value: psoriatic patient, non-lesional scalp sample


title: adrenocortical  carcinoma tumor, donor 15


title: normal adrenal tissue, donor 5


title: adrenocortical  carcinoma tumor, donor 7


title: adrenocortical  carcinoma tumor, donor 11


title: normal adrenal tissue, donor 4


title: normal adrenal tissue, donor 3


title: adrenocortical  carcinoma tumor, donor 9


city: Shanghai

first: xin

middle: xi

last: zhao

address: Yueyang Road, 320#, new building 615

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology

description: Gene expression data from prmt6 MO mild subtype embryos

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

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

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

organism: Danio rerio

source_name: zebrafish embryo of prmt6 MO mild subtype at 6 hpf

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: Embryos were cultured at 28.5 ℃ until collection

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: prmt6 MO/cMO (0.3mM/0.3mM) was injected into one-two cell embryo with a dose of 3 nl per embryo

value: embryo

value: 6 hour after fertilization


title: adrenocortical carcinoma tumor, donor 4


description: Gene expression data from prmt6 MO normal subtype embryos

source_name: zebrafish embryo of prmt6 MO normal subtype at 6 hpf


title: adrenocortical  carcinoma tumor, donor 10


title: embryo of prmt6 MO severe subtype, biological rep 3

description: Gene expression data from prmt6 MO severe subtype embryos

source_name: zebrafish embryo of prmt6 MO severe subtype at 6 hpf


title: adrenocortical  carcinoma tumor, donor 3


title: normal adrenal tissue, donor 6


title: embryo of prmt6 MO severe subtype, biological rep 2


title: embryo of prmt6 MO severe subtype, biological rep 1


title: adrenocortical  carcinoma tumor, donor 2


title: adrenocortical  carcinoma tumor, donor 5


title: adrenocortical  adenoma tumor, donor 5

value: adrenocortical adenoma

value: not staged


title: adrenocortical  carcinoma tumor, donor 1

value: male


title: adrenocortical  carcinoma tumor, donor 6


title: embryo of cMO injection, biological rep 3

description: Gene expression data from embryos with prmt6 cMO injection

source_name: zebrafish embryo with prmt6 cMO injection at 6 hpf


title: adrenocortical  adenoma tumor, donor 4


title: adrenocortical  adenoma tumor, donor 3


title: adrenocortical  adenoma tumor, donor 2


title: adrenocortical adenoma tumor, donor 1


title: adrenocortical carcinoma tumor, donor 16


title: embryo of cMO injection, biological rep 1


title: Norm Low Sensitive

city: Moscow

first: Alina

last: Artcibasova

address: Samory Mashela, 1

country: Russia

institute: Federal Research Center of Pediatric Hematology, Oncology and Immunology

data_processing: The data were normalised using preprocessCore quantile normalisation in R. Each culture (highly and low sensitive to the virus) was normalized separately

source_name: human adult skin fibroblasts (line HAF-1608)

label_protocol: Total RNA was reverse-transcribed to cDNA and cRNA using the Ambion TotalPrep cRNA Amplification Kit (Invitrogen, USA). The cRNA concentration was quantified and adjusted to 150 ng/ml using an ND-1000 Spectrophotometer (NanoDrop Technologies, USA)

growth_protocol: The cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM, PanEco, Moscow, Russia) supplemented with 10% fetal bovine serum (FBS, PanEco), 2 mM L-glutamine and 50 ug/ml gentamicin at 37°C in 5% CO2. The cells were maintained by regular passages when confluence was reached. To obtain cells in G0 phase of cell cycle the cells of both lines were cultured in DMEM with 0.2% FBS for 48 hours.

extract_protocol: We collected the cells 3 hours after infection. Total RNA was extracted using TRIzol Reagent.

treatment_protocol: Cells HELF- 977 and HAF-1608 synchronized in G0 phase were infected with HCMV at multiplicity of infection of 3 or mock-infected. Viral inoculum was added to the cells and allowed to adsorb for 60 min at 37°C in 5% CO2. Then virus inoculum was removed and replaced with fresh medium.

tag: sensitivity

value: Low

value: adult skin fibroblasts

tag: infection


title: Infected Low Sensitive 3 hours without infection

tag: cell line

value: mock


title: Infected Low Sensitive 3 hours after infection

tag: tissue

value: HCMV at multiplicity of infection of 3


title: Control_unwounded_of_Tissue-engineered_human_cornea_replicate_1

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

description: Control unwounded of Tissue-engineered human cornea replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl (Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON)  from HCEC isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada), and cultivated on BSA, Collagen type I,Collagen type IV, Fibronectin, and Laminin matrix. Total RNA was isolated from Central, Internal and external ring of wounded tissue-engineered cornea. Unwounded tisue-engineered corneas are use as control.

value: Tissue-engineered human cornea

tag: tissue portion

value: unwounded tissue-engineered cornea

value: unknown

tag: age

value: 44 years


title: Infected Highly Sensitive 3 hours without infection

source_name: human embryonic lung fibroblast (line HELF-977)

value: Highly

value: embryonic lung fibroblast


title: Infected Highly Sensitive 3 hours after infection


title: embryo of cMO injection, biological rep 2


title: Norm Highly Sensitive


title: External_ring_of_wounded_Tissue-engineered_human_replicate_1

description: External ring of wounded Tissue-engineered human replicate 1

source_name: External ring of wounded Tissue-engineered human cornea

value: External ring of wounded Tissue-engineered cornea


title: Control_unwounded_of_Tissue-engineered_human_cornea_replicate_2

description: Control unwounded of Tissue-engineered human cornea replicate 2

value: 71 years


title: External_ring_of_wounded_Tissue-engineered_human_replicate_3

description: External ring of wounded Tissue-engineered human replicate 3


title: KWA04_Fibroblast cell_Affected

city: Boston

first: Raif

middle: S.

last: Geha

state: MA

address: 1 Blackfan Circle, Karp 10

department: Division of Immunology

institute: Boston Children's Hospital

description: Subject 19 in published pedigree A

hyb_protocol: Arrays were hybridized in the Affymetrix GeneChip Hybridization Oven 640 and washed using the Affymetrix GeneChip Fluidics Station 450 as per the Affymetrix protocol.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G as per the Affymetrix protocol.

data_processing:
The array image (DAT file) was acquired and converted to a CEL file using Affymetrix GeneChip Operating Software (GCOS v1.4).  Genotype calling was performed using Birdseed v2 within Affymetrix Genotyping Console v3.0, with a confidence threshold of 0.1.
Genotype calls (AA, AB, BB, and NoCall) for both unfiltered SNP list (all 909622 SNPs) and filtered SNP list (678442 SNPs used for haplotype comparison)

label: Biotin

source_name: Fibroblast cell

label_protocol: DNA was restriction digested, ligated to adaptors, PCR amplified, fragmented, labeled, and loaded onto arrays as per the Affymetrix protocol.

growth_protocol: Fibroblasts were grown from skin biopsies according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood or fibroblast cell lines using the Qiagen Gentra Puregene Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Picogreen assay.

value: Male

tag: clinical status

value: Affected


title: Internal_ring_of_wounded_Tissue-engineered_human_replicate_3

description: Internal ring of wounded Tissue-engineered human replicate 3

source_name: Internal ring of wounded Tissue-engineered human cornea

value: Internal ring of wounded Tissue-engineered cornea


title: Internal_ring_of_wounded_Tissue-engineered_human_replicate_1

description: Internal ring of wounded Tissue-engineered human replicate 1


title: Internal_ring_of_wounded_Tissue-engineered_human_replicate_2

description: Internal ring of wounded Tissue-engineered human replicate 2

value: 52 years


title: Central_ring_of_wounded_Tissue-engineered_human_replicate_3

description: Central ring of wounded Tissue-engineered humanreplicate 3

source_name: Central ring of wounded Tissue-engineered human cornea

value: Central ring of wounded Tissue-engineered cornea


title: Central_ring_of_wounded_Tissue-engineered_human_replicate_2

description: Central ring of wounded Tissue-engineered human replicate 2


title: UNK-344-USA_Peripheral blood_Affected

description: Subject 1 in published pedigree B

source_name: Peripheral blood


title: External_ring_of_wounded_Tissue-engineered_human_replicate_2

description: External ring of wounded Tissue-engineered human replicate 2


title: UNK-344-USAB2_Peripheral blood_Affected_rep2

description: Subject 1 in published pedigree B


title: Primary_human_corneal_epithelial_cells_Laminin_repl2

description: HCEC Laminin replicate 2

source_name: Primary human corneal epithelial cells cultivated on Laminin

tag: cell type

value: Primary human corneal epithelial cells

tag: growth protocol

value: cultivated on Laminin matrix


title: Central_ring_of_wounded_Tissue-engineered_human_replicate_1

description: Central ring of wounded Tissue-engineered human replicate 1

tag: gender


title: RALAJ_Peripheral blood_Affected

description: Subject 3 in published pedigree A

value: Female


title: Primary_human_corneal_epithelial_cells_Tenascin_C_repl1

description: HCEC Tenascin C replicate 1

source_name: Primary human corneal epithelial cells cultivated on Tenascin C

value: cultivated on Tenascin C matrix


title: Primary_human_corneal_epithelial_cells_Tenascin_C_repl2

description: HCEC Tenascin C replicate 2


title: Primary_human_corneal_epithelial_cells_Laminin_repl1

description: HCEC Laminin replicate 1


title: 109C-Saliva_Blood_Obligate carrier

description: Subject 31 in published pedigree A

data_processing:
The array image (DAT file) was acquired and converted to a CEL file using Affymetrix GeneChip Operating Software (GCOS v1.4).  Genotype calling was performed using Birdseed v2 within Affymetrix Genotyping Console v3.0, with a confidence threshold of 0.02.
primary data description:  Genotype calls (AA, AB, BB, and NoCall) and Birdseed confidence values for both unfiltered SNP list (all 909622 SNPs) and filtered SNP list (145751 SNPs used for linkage scans)

source_name: Saliva

extract_protocol: Genomic DNA was extracted from saliva, peripheral blood, or fibroblast cell lines using the QIAamp DNA Blood Mini Kit or QIAamp DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Obligate carrier


title: 111E_Blood_Healthy

description: Subject 24 in published pedigree A

value: Healthy


title: 109D_Blood_Healthy

description: Subject 12 in published pedigree A


title: 109-PreX_Blood_Affected

description: Subject 9 in published pedigree A


title: 109E-Saliva_Blood_Obligate carrier

description: Subject 32 in published pedigree A


title: 111F_Blood_Obligate carrier

description: Subject 34 in published pedigree A


title: Primary_human_corneal_epithelial_cells_Fibronectin_repl1

description: HCEC Fibronectin replicate 1

source_name: Primary human corneal epithelial cells cultivated on Fibronectin

value: cultivated on Fibronectin matrix

value: unknown


title: 104-PreX_Blood_Affected

description: Subject 19 in published pedigree A


title: Primary_human_corneal_epithelial_cells_Fibronectin_repl2

description: HCEC Fibronectin replicate 2


title: 108-Skin_Blood_Affected

description: Subject 1 in published pedigree A

source_name: Fibroblast cell line


title: 103-PreX_Blood_Affected

description: Subject 18 in published pedigree A


title: Primary_human_corneal_epithelial_cells_Collagen Type I_repl2

description: HCEC Collagen Type I  replicate 2

source_name: Primary human corneal epithelial cells cultivated on Collagen Type I

value: cultivated on Collagen Type I matrix

value: 61 years


title: Primary_human_corneal_epithelial_cells_Collagen Type IV_repl1

description: HCEC Collagen Type IV  replicate 1

source_name: Primary human corneal epithelial cells cultivated on Collagen Type IV

value: cultivated on Collagen Type IV matrix

value: 44 years


title: 111C_Blood_Obligate carrier

description: Subject 33 in published pedigree A

value: Male


title: 108G_Blood_Healthy

description: Subject 7 in published pedigree A


title: 108F_Blood_Healthy

description: Subject 8 in published pedigree A


title: Primary_human_corneal_epithelial_cells_BSA_repl6

description: HCEC BSA replicate 6

source_name: Primary human corneal epithelial cells cultivated on BSA

value: cultivated on BSA matrix


title: 109B_Blood_Healthy

description: Subject 11 in published pedigree A


title: Primary_human_corneal_epithelial_cells_BSA_repl5

description: HCEC BSA replicate 5


title: Primary_human_corneal_epithelial_cells_BSA_repl3

description: HCEC BSA replicate 3


title: 111D_Blood_Healthy

description: Subject 23 in published pedigree A


title: 108D_Blood_Obligate carrier

description: Subject 28 in published pedigree A


title: Primary_human_corneal_epithelial_cells_Collagen Type I_repl1

description: HCEC Collagen Type I  replicate 1


title: Primary_human_corneal_epithelial_cells_Collagen Type IV_repl2

description: HCEC Collagen Type IV  replicate 2

value: 45 years


title: 111B_Blood_Healthy

description: Subject 22 in published pedigree A


title: Primary_human_corneal_epithelial_cells_BSA_repl1

description: HCEC BSA replicate 1


title: HEp-2_CID70698683_5uM_2

city: Louisville

first: Donghoon

last: Chung

state: Kentucky

address: 505 Hancock Street S

department: Microbiology and Immunology

institute: UNIVERSITY OF LOUSIVILLE

description:
CD_Treatment_2
Treated2

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix PrimeView Human arrays according to the GeneChip 3' Array Hybridization User Manual from Affymetrix.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix).

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc.) and normalized using Robust Multi-Array (RMA) normalization.

source_name: HEp-2 cells, CID 70698683

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Plus Reagent Kit from 100 ng total RNA.

growth_protocol: Cells were obtained from ATCC (CCL-23) and maintained in Minimum Essential Medium with Earl's modification (MEM-E) containing 10% fetal bovine serum (FBS) and 1X GlutaMAX (Gibco 35050-061) at 37 °C with 5% CO2.

extract_protocol: Extraction was done with RNAsol RT (MRCgene) according to the manufacturer's protocol.

treatment_protocol: One million cells were seeded in a 6-well plate 18 hours prior to treatment. The cell culture medium was replaced with fresh cell culture medium with 5 microM of CID 70698683 (Treatment group) or 0.25% of DMSO (Control group). The cells were incubated 18 hours further.

tag: treatment


title: HEp-2_DMSO_Control3

description:
CD_Control_3
Mock_control3
CID 679

source_name: HEp-2 cells, control

value: DMSO


title: 108A_Blood_Obligate carrier

description: Subject 27 in published pedigree A


title: HEp-2_DMSO_Control2

description:
CD_Control_2
Mock_control2
CID 679


title: Primary_human_corneal_epithelial_cells_BSA_repl2

description: HCEC BSA replicate 2

value: 52 years


title: HEp-2_CID70698683_5uM_1

description:
CD_Treatment_1
Treated1


title: HEp-2_DMSO_Control1

description:
CD_Control_1
Mock_control1
CID 679


title: 108E_Blood_Healthy

description: Subject 6 in published pedigree A


title: Ell3 overexpressing MCF7, biological rep1

city: Seongnam-si

first: Kwang-Soo

last: Kim

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA Univ.

hyb_protocol: Following fragmentation, 12 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array.

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

data_processing:
The data were analyzed with Robust Multi-array Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method.
The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild type and Ell3 overexpressing cell lines were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen)


title: Ell3 overexpressing MCF7, biological rep2


title: 108B_Blood_Healthy

description: Subject 4 in published pedigree A


title: Ell3 overexpressing MCF7, biological rep3


title: 104A_Blood_Obligate carrier

description: Subject 30 in published pedigree A


title: Control MCF7, biological rep2

source_name: Control MCF7, biological rep2


title: Chronophin shRNA plus rescue  series 2 biological  replicate 2

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

institute: University Hospital Regensburg

hyb_protocol: gilent hybridization protocol

scan_protocol: Slides were scanned using an Agilent DNA Microarray Scanner G2505C; scan software: Agilent Scan Control Version A.8.1.3

data_processing:
Agilent Feature Extraction Version 10.5.1.1 (FE Protocol GE_105_Dec08).(Parameters: Scanning hardware = G2505A DNA microarray scanner [Agilent], Scanning software = Feature Extraction Software [Agilent])
The Limma package was used to normalize the expression log-values (M-Values) within each array using the LOESS method.  Intensity values (A-values) were normalized between arrays by quantile normalization, using the Aquantile method

source_name: Chronophin shRNA plus rescue

label_protocol: Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Version: 5.7 Agilent publication number: G4140-90050

growth_protocol: human glioma cells (GBM6840) were cultured in DMEM supplemented with 10 % FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1 µg/ml puromycin and 400 µg/ml G418

extract_protocol: Total RNA was isolated using the SV Total RNA Isolation System following the manufacturers´s instructions

treatment_protocol: Cells were transduced with a control or chronophin targeting shRNA. For rescue experiments, an RNAi-resistant human chronophin was expressed

value: Chronophin shRNA plus rescue

source_name: reference: pool of all samples


title: 111A_Blood_Healthy

description: Subject 21 in published pedigree A


title: 102-PreX_Blood_Affected

description: Subject 13 in published pedigree A

value: Affected


title: Chronophin shRNA series 2 biological replicate 1

source_name: Chronophin shRNA

value: Chronophin shRNA


title: Chronophin shRNA  series 2 biological  replicate 2


title: Primary_human_corneal_epithelial_cells_BSA_repl4

description: HCEC BSA replicate 4

value: Primary human corneal epithelial cells


title: 109A_Blood_Healthy

description: Subject 10 in published pedigree A


title: Chronophin shRNA plus rescue series 2 biological replicate 1


title: 102F _Blood_Obligate carrier

description: Subject 25 in published pedigree A

value: Female

value: Obligate carrier


title: Control shRNA biological replicate 2

source_name: Control shRNA

value: Control shRNA


title: Chronophin shRNA biological replicate 1


title: HEp-2_CID70698683_5uM_3

description:
CD_Treatment_3
Treated3


title: Control shRNA biological replicate 1


title: WholebloodAnalysis_LPS_rep4

status: Public on Nov 24 2015

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

institute: North Carolina Agricultural and Technical State University

description: Gene expression of exvivo of cow blood sample with lipopolysaccharide (100 ng/ml)  from probiotics -treated animals (Day 60)

hyb_protocol: Cy3-labelled cRNA 1.63 ug (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Bovine v2 4×44k Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan default settings for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. Data normalization and statistical analysis were performed using GeneSpring software 13.0 (Agilent). Fold changes in gene expression, t-test, gene ontology and pathway analysis were generated using the GeneSpring software.

organism: Bos taurus

source_name: Peripheral Blood, Holstein Friesian, lactating, LPS, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug (RIN>7) pooled RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total cellular RNA was extracted using the ZR whole blood RNA miniprep kit (ZYMO RESEARCH, Irvine, CA) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Total RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity and quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with high RNA integrity (RIN>7) were stored at -80oC until used for microarray analysis.

treatment_protocol: Initial (0 days) and end of study (60 day) blood samples were drawn from the jugular vein aseptically from the Probiotics-treated animals (n=5) and control animals (n=5) into ACD tubes. The blood samples were incubated for 30 minutes at 37oC with 5% CO2.  The Fastrack Microbial (Probiotics) Pack (Conklin Company, Kansas City, MO) Ingredients: Yeast culture (Saccharomyces cerevisiae), rice hulls, calcium carbonate, dried chicory root, dried Enterococcus faecium fermentation product, dried Lactobacillus acidophilus fermentation product, dried Aspergillus oryzae, fermentation extract, dried Bacillus subtilis fermentation extract. Recommended Dose for Lactating dairy cattle: Supplement at the rate of 1 to ounces per animal daily.

tag: breed

value: Holstein Friesian

value: whole blood

value: female


title: WholebloodAnalysis_LPS_rep3

source_name: Peripheral Blood, Holstein Friesian, lactating, LPS, replicate 3


title: WholebloodAnalysis_Untreated_60day_rep2

description: Gene expression of end of study (60day) cow blood sample of untreated control animals receiving only water (Control)

source_name: Peripheral Blood, Holstein Friesian, lactating, Untreated,60 day, replicate 2


title: WholebloodAnalysis_Untreated_60day_rep1

source_name: Peripheral Blood, Holstein Friesian, lactating, Untreated,60 day, replicate 1


title: WholebloodAnalysis_Untreated_60day_rep3

source_name: Peripheral Blood, Holstein Friesian, lactating, Untreated,60 day, replicate 3


title: 104B_Blood_Obligate carrier

description: Subject 29 in published pedigree A

source_name: Saliva


title: WholebloodAnalysis_LPS_rep2

source_name: Peripheral Blood, Holstein Friesian, lactating, LPS, replicate 2


title: Control MCF7, biological rep3

source_name: Control MCF7, biological rep3


title: 102E _Blood_Healthy

description: Subject 17 in published pedigree A

value: Healthy


title: WholebloodAnalysis_0day_rep3

description: Gene expression of initial (0day) cow blood sample before supplementation with probiotics

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,0 day,replicate 3


title: WholebloodAnalysis_MP_60day_rep3

description: Gene expression of end of study (60day) cow blood sample after supplementation with probiotics

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,60 day,replicate 3


title: Control MCF7, biological rep1

source_name: Control MCF7, biological rep1


title: WholebloodAnalysis_0day_rep2

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,0 day,replicate 2


title: WholebloodAnalysis_MP_60day_rep2

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,60 day,replicate 2


title: WholebloodAnalysis_Untreated_60day_rep4

source_name: Peripheral Blood, Holstein Friesian, lactating, Untreated,60 day, replicate 4


title: WholebloodAnalysis_LPS_rep1

source_name: Peripheral Blood, Holstein Friesian, lactating, LPS, replicate 1


title: WholebloodAnalysis_0day_rep1

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,0 day,replicate 1


title: WholebloodAnalysis_0day_rep4

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,0 day,replicate 4


title: 102D _Blood_Healthy

description: Subject 16 in published pedigree A


title: WholebloodAnalysis_MP_60day_rep1

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,60 day,replicate 1


title: 108C_Blood_Healthy

description: Subject 5 in published pedigree A


title: 104C_Blood_Healthy

description: Subject 20 in published pedigree A


title: 102C _Blood_Healthy

description: Subject 15 in published pedigree A


title: landi-00077: 1113-106_NA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Lung-tissue-normal

tag: tissue type

value: Normal lung


title: R4852-F

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

country: Australia

institute: UNSW

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression data was log2 transformed and quantile normalized using the Lumi Bioconductor package.

source_name: Frontal Cortex

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted from around 100mg of brain tissue using the Qiagen miRNEasy kit following the manufacturer’s protocol, including an on-column DNase I treatment. An additional DNase I (New England Biolabs) treatment was carried out in solution, in order to eliminate any contaminating genomic DNA.

tag: age (y-years; d-days)

value: Postmortem Brain Tissue

tag: disease state

value: Rett Syndrome


title: non-metastatic cell line 67NR repeat1

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: 67NR 1

hyb_protocol: miRNA were hybridized for 20 hr at 55C on Agilent Human microRNA Array.Slides were washed and stained in the Agilent recommended protocol.

scan_protocol: Slides were scanned using the Agilent Scanner.

data_processing: The data were extracted with Feature extraction using Agilent default analysis settings and No normalization performed. The sample data table contains raw data values.

label_protocol: miRNA were prepared according to the standard Agilent protocol from 100ng total RNA.

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

tag: strain background

value: Balb/C

tag: genotype/variation

value: wild type

tag: tissue source

value: spontaneous Balb/C mouse breast cancer

tag: cell line phenotype

value: non-metastatic


title: metastatic cell line 4T1 repeat2

description: 4T1 2

tag: cell line

value: metastatic


title: metastatic cell line 4T1 repeat3

description: 4T1 3


title: R4516-T

source_name: Temporal Cortex

tag: tissue


title: non-metastatic cell line 67NR repeat3

description: 67NR 3


title: R4852-T


title: non-metastatic cell line 67NR repeat2

description: 67NR 2


title: landi-00077: 1276-101_TA

scan_protocol: See mage-tab files linked to series entry for additional details

source_name: Lung-tissue-tumor

value: Lung tumor


title: R4516-F


title: metastatic cell line 4T1 repeat1

description: 4T1 1


title: non-metastatic cell line 4TO7 repeat2

description: 4TO7 2


title: R1815-T


title: R1815-F


title: landi-00077: 0059-101_TA

data_processing: See mage-tab files linked to series entry for additional details


title: landi-00077: 1061-102_T_A

label_protocol: See mage-tab files linked to series entry for additional details


title: non-metastatic cell line 4TO7 repeat3

description: 4TO7 3


title: non-metastatic cell line 168FARN repeat3

description: 168FARN 3


title: non-metastatic cell line 168FARN repeat1

description: 168FARN 1


title: landi-00077: 0007-101TA

extract_protocol: See mage-tab files linked to series entry for additional details


title: C1541-T

value: Control


title: non-metastatic cell line 4TO7 repeat1

description: 4TO7 1


title: non-metastatic cell line 168FARN repeat2

description: 168FARN 2


title: landi-00077: 1247-109_TA


title: landi-00077: 1077-101_TA


title: C55-F

value: Female


title: Chronophin shRNA biological replicate 2

source_name: Chronophin shRNA

value: Chronophin shRNA

source_name: reference: pool of all samples


title: C1078-F


title: landi-00077: 1043-102_T_A


title: C1571-T


title: C1078-T


title: landi-00077: 1025-105_NA


title: landi-00077: 1222-101__2


title: landi-00077: 1445-101_TA


title: landi-00077: 1129-101_N_A


title: landi-00077: 1034-101_T_A


title: landi-00077: 1036-102_NA


title: landi-00077: 1119-103__NA


title: landi-00077: 1130-103_TA


title: landi-00077: 0006-103_N_A


title: landi-00077: 1095-101_NA


title: landi-00077: 1051-104_NA


title: landi-00077: 1107-101_TA


title: landi-00077: 1105-102_TA


title: landi-00077: 1442-101_NA


title: landi-00077: 1119-102_TA


title: landi-00077: 0022-101_TA


title: landi-00077: 1131-101_NA


title: landi-00077: 1001-104_NA


title: landi-00077: 1047-101_NA


title: landi-00077: 1100-103_R_N-A


title: landi-00077: 1052-101_TA


title: landi-00077: 0042-101_T_A


title: landi-00077: 1100-102_R_T-A


title: landi-00077: 1043-101_NA


title: landi-00077: 1121-103_NA


title: landi-00077: 1049-105_TA


title: landi-00077: 1126-104_TA


title: landi-00077: 1151-101_TA


title: landi-00077: 1003-103_NA


title: landi-00077: 1175-102_TA


title: landi-00077: 1120-103_N-rescane


title: landi-00077: 1421-103_NA


title: landi-00077: 1024-101_N_A


title: landi-00077: 1103-101_TA


title: landi-00077: 1019-101_T_A


title: landi-00077: 1175-101_R_T-A


title: landi-00077: 1087-104_TA


title: 102A _Blood_Obligate carrier

description: Subject 26 in published pedigree A

source_name: Saliva

value: Male

value: Obligate carrier


title: landi-00077: 1128-102_TA


title: landi-00077: 1124-108_T


title: landi-00077: 1129-102_T_A


title: landi-00077: 1126-102_T


title: landi-00077: 0042-102_TA


title: landi-00077: 1097-103_NA


title: landi-00077: 1017-105_T_A


title: landi-00077: 1411-101_TA


title: landi-00077: 1124-109_TA


title: landi-00077: 1127-103_TA


title: landi-00077: 1119-101_TA


title: landi-00077: 0146-104_N_A


title: landi-00077: 1239-104_NA


title: 102B _Blood_Healthy

description: Subject 14 in published pedigree A


title: landi-00077: 1061-101_NA


title: landi-00077: 1011-101_Tbis


title: landi-00077: 1194-103_T


title: landi-00077: 1130-102_T_A


title: landi-00077: 1148-101_TA


title: landi-00077: 1003-102_TA


title: landi-00077: 0007-103_N_A


title: landi-00077: 1089-101_TA


title: landi-00077: 1105-101_NA


title: landi-00077: 1001-106_TA


title: landi-00077: 1001-105_T


title: landi-00077: 1279-101_TA


title: landi-00077: 1040-101_TA


title: landi-00077: 1246-102_T


title: landi-00077: 1064-101_NA


title: landi-00077: 1011-103_NA


title: landi-00077: 1445-103_NA


title: landi-00077: 1283-101_NA


title: landi-00077: 1001-105_TA


title: landi-00077: 1033-103_N


title: landi-00077: 1232-101_TA


title: landi-00077: 1099-101_TA


title: landi-00077: 1247-111_NA


title: landi-00077: 0146-102_T_A


title: landi-00077: 1131-102_TA


title: landi-00077: 1099-103_NA


title: landi-00077: 1025-106_TA


title: landi-00077: 1421-102_TA


title: landi-00077: 0006-101_T_A


title: landi-00077: 0059-102_N_A


title: landi-00077: 1274-101_TA


title: landi-00077: 1417-103_NA


title: landi-00077: 1040-101T_A


title: landi-00077: 1085-108_NA


title: landi-00077: 1237-104_NA


title: landi-00077: 1182-101_TA


title: landi-00077: 1097-101_TA


title: landi-00077: 1175-103_TA


title: landi-00077: 1011-102_R_TA


title: landi-00077: 1061-103_TA


title: landi-00077: 1117-101_TA


title: landi-00077: 1156-103_NA


title: landi-00077: 1054-103_TA


title: landi-00077: 1222-N


title: landi-00077: 1479-110_NA


title: landi-00077: 1222-101__1


title: landi-00077: 1100-101_TA


title: landi-00077: 1130-101_N_A


title: landi-00077: 1135-104_TA


title: landi-00077: 1246-103_NA


title: landi-00077: 1232-102_NA


title: landi-00077: 1113-107_TA


title: landi-00077: 1068-103_T_A


title: landi-00077: 1425-102_TA


title: landi-00077: 1121-102_R_T-A


title: landi-00077: 1033-101_T2_A


title: landi-00077: 1222-101__3


title: landi-00077: 1003-103_T


title: landi-00077: 1243-103_NA


title: landi-00077: 1194-101_N


title: landi-00077: 1117-103_NA


title: WholebloodAnalysis_MP_60day_rep4

source_name: Peripheral Blood, Holstein Friesian, lactating, MP,60 day,replicate 4

value: Holstein Friesian

value: whole blood


title: landi-00077: 1038-104_NA


title: landi-00077: 1182-107_NA


title: landi-00077: 1064-103_NA


title: landi-00077: 1239-101_TA


title: landi-00077: 1107-103_NA


title: landi-00077: 1120-101_T


title: landi-00077: 1038-102_TA


title: landi-00077: 1100-103_N_A


title: landi-00077: 1128-101_N_A


title: landi-00077: 1036-101_TA


title: landi-00077: 1243-101_TA


title: landi-00077: 0022-103_TA


title: MIR618SNP1, biological rep 2

city: Antwerp

first: Sophia

last: Cammaerts

address: Universiteitsplein 1

department: Department of Molecular Genetics

country: Belgium

institute: VIB, University of Antwerp

hyb_protocol: 5.5 µg of cDNA was hybridized for 16 hr (+/- 1hr) at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix Scanner 3000 7G. The software used was AGCC ver 3.2.

data_processing: Data were RMA normalized using the Affymetrix Expression Console ver 4.0.

source_name: SH-SY5Y cells stably overexpressing mutant MIR618 gene

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100 ng of total RNA with the GeneChip WT PLUS Reagent Kit.

growth_protocol: Stable SH-SY5Y cells were cultured in Minimum Essential Medium (MEM) with 10% (vol/vol) fetal calf serum, 1X non-essential amino acids, 2mM L-glutamine, penicillin (100U/ml) /streptomycin (100µg/ml) and 3µg/ml Blasticidin S.

extract_protocol: Total RNA was extracted with mirVana miRNA Isolation Kit (Ambion, Life Technologies, CA, USA) from stable cells according to the manufacturer’s protocol. RNA was subsequently DNase treated with the TURBO DNA-free Kit (Ambion, Life Technologies) according to the supplier’s protocol. Where needed, RNA was purified and concentrated by RNA precipitation.

tag: genotype

value: MIR618 with rs2682818 genotype CC


title: landi-00077: 1240-102_NA

value: Normal lung


title: LR(M_27_49)

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (4X44K)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a scanner 4000B de Axon with Feature Extraction V 9.5.3.1 software

data_processing: The scanned images were analyzed with Feature Extraction V 9.5.3.1 (Agilent) . All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library.  The whole set of 45,220 spots were analysed. Each spot on each chip was allocated a 0-1 weight depending on various criteria on quality (routine pipeline of the Plateforme TRIX). On average, half of the spots per chip were dropped. Only spots with good quality (weight 1) for at least 70% of the chips were kept for further analysis, leading to 12,358 spots. All intensity data were log transformed, and the term “data” or “intensity” will refer to log transformed data from now on (natural logarithm). The effect of the hybridization day was removed by subtracting the mean intensity of the hybridization day. Then the mean of each chip was subtracted to make all chips comparable. A good linearity of intensity signals were observed between all samples. The resulting matrix has 12358 rows each corresponding to a unique ID (provided as data Matrix) and 147 columns (individuals).

organism: Sus scrofa

source_name: skeletal muscle Longissimus lumborum (LD)

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: The animals were raised at the French central test Station in Le Rheu (France) in 2007 and 2008.

extract_protocol: The muscle samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 250–300 mg of the fine powder was then processed for total RNA isolation and purification using RNeasy Fibrous Tissue Midi kit according to the manufacturer’s instructions (Qiagen SA France, Courtaboeuf, France). The method included a proteinase K digestion step to remove proteins and a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 300 µl of RNase-free water and stored at -80°C. RNA quality and concentration were controlled using an AGILENT 2100 bioanalyzer (RNA solutions and RNA 6000 Nano Lab- Chip Kit, Agilent Technologies France, Massy, France)

treatment_protocol: Muscle samples were biopsied from Longissimus lumborum (LD) muscle 20’ after stunning and exsanguination. Samples were immediately frozen in liquid N2 and kept at -80°C until analysis.

value: Landrace


title: MIR618WT, biological rep 3

source_name: SH-SY5Y cells overexpressing wild type MIR618 gene

value: MIR618 with rs2682818 genotype AA


title: MIR204SNP, biological rep 6

source_name: SH-SY5Y cells stably overexpressing mutant MIR204 gene

value: MIR204 with rs7861254 genotype TT


title: PI(M_8_07)

value: Pietrain


title: MIR204SNP, biological rep 4


title: MIR618WT, biological rep 2


title: MIR618SNP1, biological rep 3


title: PI(M_13_29_09)


title: LWF(M_19_38)

value: Large White Femelle


title: MIR618SNP1, biological rep 1


title: LR(M_11_47)


title: LWF(M_10_38)


title: PI(M_12_29_09)


title: MIR618WT, biological rep 1


title: MIR204SNP, biological rep 5


title: MIR204WT, biological rep 5

source_name: SH-SY5Y cells overexpressing wild type MIR204 gene

value: MIR204 with rs7861254 genotype CC


title: LRF(M_21_47_08)


title: Dchn(M_22_06)


title: PI(M_1_37_08)


title: LWF(M_21_05)


title: LWF(M_20_47)


title: LR(M_33_07)


title: PI(M_17_08_09)


title: LWF(M_30_37)


title: PI(M_1_20)


title: LR(M_15_04)


title: MIR204WT, biological rep 4


title: LRF(M_29_39_08)


title: LRF(M_28_39_08)


title: PI(M_13_05)


title: LWF(M_12_04)


title: Du(M_14_17_09)

value: Duroc


title: LWF(M_8_16)


title: LWF(M_9_50_08)


title: PI(M_10_29_09)


title: PI(M_31_49)


title: LWF(M_17_49)


title: Dchn(M_9_18_09)


title: Du(M_37_17)


title: LWF(M_17_16)


title: DuM(M_17_19)


title: LWM(M_20_17)

value: Large White Male


title: LR(M_15_38)


title: PI(M_13_31_09)


title: LWF(M_30_07)


title: LWF(M_5_04)


title: Du(M_27_38)


title: LR(M_17_47)


title: PI(M_6_31_09)


title: Du(M_31_06)


title: LR(M_05_47)


title: PI(M_2_40_08)


title: LWF(M_40_16)


title: LWM(16M)


title: LRF(M_18_37_08)


title: PI(M_3_37_08)


title: PI(M_3_29_09)


title: ChIPm1/3m48

city: Singapore

first: Yen-Hoon

last: Luah

address: Nanyang Technological University 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: 3D7_over-expression_48 hpi

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Parasites were cultured as described previously (Trager and Jenson, 1978)

extract_protocol: Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions

treatment_protocol: Parasites were synchronized by repeated sorbitol lysis (Lambros and Vanderberg, 1979) to obtain a eight-hour growth window

value: transgenic 3D7 with over-expression of PfZnFP-G

source_name: input DNA before immunoprecipitation


title: ChIPm1/3m40

description: 3D7_over-expression_40 hpi


title: Du(M_32_16_09)


title: LR(M_34_07)


title: LWM(M_35_16)


title: LWM(17M)


title: LWF(M_3_19)


title: Du(M_31_38)


title: PI(M_24_29_09)


title: PI(M_1_40_08)


title: LWF(M_2_05)


title: LRF(M_53_47_08)


title: PI(M_06_49)


title: Du(M_31_16_09)


title: ChIPm1/3m32

description: 3D7_over-expression_32 hpi


title: LR(M_56_06)


title: Du(M_33_37)


title: LWF(M_21_06)


title: LWF(M_12_38)


title: LRF(M_39_37_08)


title: ChIPm1/3m24

description: 3D7_over-expression_24 hpi


title: LR(M_27_05)


title: ChIPm1/3m16

description: 3D7_over-expression_16 hpi


title: LWF(M_16_16)


title: LWF(M_30_47)


title: PI(M_30_49)


title: PI(M_3_07_09)


title: ChIPm1/3m08

description: 3D7_over-expression_8 hpi


title: ChIPm1/2m40

description: 3D7_over-expression_40 hpi


title: PI(M_14_31_09)


title: Du(M_30_16_09)


title: ChIPm1/2m48

description: 3D7_over-expression_48 hpi


title: LWF(M_24_05)


title: ChIPm1/2m32

description: 3D7_over-expression_32 hpi


title: ChIPm1/2m16

description: 3D7_over-expression_16 hpi


title: LWM(M_26_16)


title: LR(M_25_37)


title: ChIPm1/2m24

description: 3D7_over-expression_24 hpi


title: LWF(M_14_05)


title: LRF(M_31_49_08)


title: LWF(M_36_16)


title: PI(M_09_29_09)


title: LWM(19M)


title: ChIPm1/1m48

description: 3D7_over-expression_48 hpi


title: Du(M_30_18_09)


title: ChIPm1/2m08

description: 3D7_over-expression_8 hpi


title: LWF(M_34_47)


title: PI(M_13_40_08)


title: ChIPm1/1m40

description: 3D7_over-expression_40 hpi


title: LRF(M_24_49_08)


title: PI(M_1_07)


title: ChIPm1/1m32

description: 3D7_over-expression_32 hpi


title: ChIPm1/1m24

description: 3D7_over-expression_24 hpi


title: LWF(M_2_17)


title: PI(M_32_31_09)


title: LR(M_52_06)


title: LR(M_25_05)


title: Du(M_29_16_09)


title: ChIPm1/1m16

description: 3D7_over-expression_16 hpi


title: ChIPm1/1m08

description: 3D7_over-expression_8 hpi


title: m1R_m1_48

description: 3D7_over-expression_48 hpi

source_name: 3D7 reference RNA pool (0-48hpi)


title: m1R_m1_40

description: 3D7_over-expression_40 hpi


title: m1R_m1_32

description: 3D7_over-expression_32 hpi


title: Du(M_17_17_09)


title: m1R_m1_24

description: 3D7_over-expression_24 hpi


title: m1R_m1_08

description: 3D7_over-expression_8 hpi


title: m1R_m1_16

description: 3D7_over-expression_16 hpi


title: m1R_C40

description: 3D7_40 hpi

value: 3D7 wild-type control


title: LRF(M_36_37_08)


title: m1R_C32

description: 3D7_32 hpi


title: LWF(M_24_47)


title: LWF(M_10_16)


title: m1R_C48

description: 3D7_48 hpi


title: PI(M_4_20)


title: LR(M_18_04)


title: PI(M_26_08_09)


title: PI(M_6_39_08)


title: LWM(20M)


title: m1R_C24

description: 3D7_24 hpi


title: LWF(M_10_07)


title: LWF(M_29_47)


title: Du(M_36_38)


title: LWM(23M)


title: Du(M_3_20_09)


title: LR(M_9_04)


title: LRF(M_25_47_08)


title: Du(M_10_18_09)


title: PI(M_27_07_09)


title: LR(M_9_05)


title: LWF(M_13_38)


title: PI(M_5_06)


title: m1R_C16

description: 3D7_16 hpi


title: PI(M_15_08_09)


title: LRF(M_20_37_08)


title: PI(M_22_07)


title: Du(M_13_17_09)


title: m1R_C08

description: 3D7_8 hpi


title: LWF(M_4_04)


title: LR(M_21_37)


title: LWF(M_02_47)


title: Du(M_19_19)


title: 0(M_11_18_09)


title: PI(M_12_40_08)


title: LWM(22M)


title: LWF(M_39_16)


title: PI(M_7_31_09)


title: LWF(M_46_17)


title: LR(M_8_04)


title: Du(M_12_18_09)


title: LWF(M_24_38)


title: PI(M_11_40_08)


title: PI(M_5_29_09)


title: carotid_ligated_Has3-deficient_5

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: gene expresion ligated carotid artery

hyb_protocol: End labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol (GeneChip Whole Transcript (WT) Sense Labeling Assay User Manual, Affymetrix, Inc.)

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by GeneSpring´s ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: Has3 deficient, ligated carotid artery

label_protocol: Synthesis of biotin labeled cDNA was performed according to the manufacturer´s protocol (WT Plus Reagent Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA. After amplification by in vitro transcription and 2nd cycle synthesis, cDNA was fragmented and biotin labeled by terminal transferase

extract_protocol: Total RNA was prepared from homogenized tissue (GentleMACS™ Dissociator, Miltenyi Biotech) using the RNeasy Microarray Tissue Kit (Qiagen) according to the manufacturer´s protocol.

treatment_protocol: Neointimal hyperplasia was induced in female Has3 deficient mice and wildtype controls by ligation of the left common carotid artery. 5 days after surgery ligated carotid arteries and unligated control arteries were excised and immediately transferred to RNAlater® to remove adherent wound tissue.

value: carotid artery

value: Has3 deficient

value: female

tag: age

value: 21-22 weeks

tag: strain


title: Du(M_19_18_09)


title: PI(M_06_47)


title: carotid_ligated_wildtype_4

description: gene expresion ligated carotid artery

source_name: wildtype, ligated artery

value: wildtype


title: SH-control Sample 2 vs. DPP4 KD Sample 2

city: Bonn

first: Peter

last: Mayer

address: Kurt-Georg-Kiesinger-Allee 3

institute: BfArM

hyb_protocol: Agilent Gene Expression Hybridization Kit was used following manufacturer's protocol

scan_protocol: Fluorescence signals were detected using Agilent's DNA microarray scanner. Red color shows that the Cy5 signal is higher than the Cy3 signal

data_processing: Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: control, primary human white preadipocytes

label_protocol: sh-control samles were labelled with Cy3 and DDP4 KD samples were labelled with Cy5 using Agilent Low Input Quick Amp Labelling Kit

growth_protocol: human white preadipocytes were kept in primary culture according to standard protocols

extract_protocol: total RNA was extracted using Qiagen's RNeasy Total RNA Extraction Kit following the manufacturer's protocol

treatment_protocol: cells were transduced with a lentiviral vector carrying shRNA targeted against DPP4, resulting in DPP4 knockdown (KD) or with non-targeting negative control shRNA (sh-contol)

tag: cell type

value: primary white preadipocytes

value: control

source_name: DDP4 KD, primary human white preadipocytes

value: DDP4 KD


title: SH-control Sample 3 vs. DPP4 KD Sample 3


title: carotid_ligated_Has3-deficient_3

description: gene expresion ligated carotid artery


title: SH-control Sample 1 vs. DPP4 KD Sample 1


title: carotid_ligated_Has3-deficient_6

description: gene expresion ligated carotid artery


title: LWM(M_19_17)


title: LRF(M_28_47_08)

value: Landrace


title: LWF(M_13_04)


title: NEPHS1-GFP-_S2

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

country: Japan

institute: Kumamoto Univ.

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol:GE1_107_Sep09 and Grid: 026652_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hiPS derived kidney tissue

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: hiPS derived nephron progenitors were co-cultured with embryonic mouse spinal cords for 9 days to induce differentiated kidney tissues.

extract_protocol: Each differentiated hiPSC derived kidney cells were sorted by a FACS Aria II (Becton Dickinson). Total RNA was extracted using Rneasy Plus Micro Kit purchased from QIAGEN following manufacture's protocol.

value: hiPS derived kidney tissue

tag: fraction

value: NEPHS1-GFP negative


title: carotid_ligated_wildtype_1

description: gene expresion ligated carotid artery

tag: gender


title: carotid_ligated_wildtype_2

description: gene expresion ligated carotid artery


title: carotid_ligated_wildtype_3

description: gene expresion ligated carotid artery


title: LWF(M_3_04)

value: Large White Femelle


title: Du(M_12_17_09)


title: carotid_non-ligated_Has3-deficient_4

description: gene expresion non-ligated control carotid artery

source_name: Has3 deficient, non-ligated carotid artery


title: PI(M_10_39_08)

value: Pietrain


title: SH-control Sample 4 vs. DPP4 KD Sample 4


title: NEPHS1-GFP+_S2

value: NEPHS1-GFP positive


title: Du(M_11_17_09)

value: Duroc


title: LR(30M)


title: PI(M_31_31_09)


title: carotid_non-ligated_Has3-deficient_3


title: LRF(M_5_49_08)


title: NEPHS1-GFP-_S1


title: LWF(M_20_49)


title: carotid_non-ligated_Has3-deficient_2


title: proliferating W408 cell

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Wnt4-overexpressing subline establised from C2C12 cell, cultured in proliferation condition

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

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

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

source_name: mouce myoblast cell

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miR labeling kit (Toray Industries, Inc..)

growth_protocol: C2C12 and W408 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented by 10% FBS (proliferation medium:PR) or 2% horse serum (differentiation medium:DF)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: The stable Wnt4 transfectants were established as follws. After 12 to 24h of subculture, an expression vector bearing V5-tagged Wnt4 cDNA (PCMV-Wnt4-V5-PPGK-blasticidin-SV40pA) was transfected into C2C12 cells. Transfected C2C12 cells were cultured in DMEM containing 10% FBS and blasticidin. After serial passages in blasticidin containing selection medium for 4 to 5 weeks, Wnt4-expressing stable transfectants were obtained.

tag: medium

value: Proliferation medium (DMEM including 10%FBS)


title: NEPHS1-GFP+_S1


title: Biofilm Inoculum_rep2

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

institute: Montana State University

description: RNA extracted from a 72 hour biofilm, as used to inoculate a murine wound, biological replicate 2.

hyb_protocol: For each Pseudomonas genome array (#900339, Affymetrix), labeled fragmented cDNA was hybridized to the arrays at 50oC for 16 h with constant rotational mixing at 60 rpm. Washing and staining of the arrays were performed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 7G. Affymetrix GCOS v1.4 was used to generate CEL and CHP files.

data_processing: Affymetrix CEL files were imported into FlexArray v1.6.1 for QC and data analysis. The GC-RMA algorithm was applied to the arrays, which included background correction and normalization. For comparative analysis of the wound inoculums and scab, Principal Component Analysis (PCA) was used to enable visualization, assessment, and grouping of the data. Data was compared to previously published Pseudomonas transcriptomes from the top of colony biofilms, the bottom of colony biofilms, [Franklin, 2012] whole drip flow biofilms [Folsom, 2010], and planktonic cultures [Harwood, 2007].

organism: Pseudomonas aeruginosa PAO1

source_name: Biofilm

label_protocol: The RNA was reverse transcribed at 42° C overnight using 1 µl random primers, 1 µl Superase-In, 6 µl 5x first strand buffer, 3 µl 0.1 M DTT, 0.6 µl 100mM dNTPs, and 3 µl Superscript II. After synthesis, the remaining RNA was hydrolyzed by the addition of 0.5 M EDTA and 1 N sodium hydroxide. The cDNA samples were neutralized with 1 N HCl and 1 M sodium acetate. The reactions were then cleaned on MinElute columns according to the manufacturer's instructions. The resulting cDNA was fragmented with 0.6 Units DNase I per microgram cDNA for 10 minutes at 37° C. The enzyme was inactivated by heating to 98° C for 10 minutes.

growth_protocol: Pseudomonas aeruginosa PAO1 was grown overnight in LB medium at 37°C on a shaker and then diluted 1:1000 in sterile phosphate buffer solution to produce inocula for biofilm growth. For biofilm growth, polycarbonate membrane filters were cut using a 6 mm biopsy punch and sterilized with exposure to UVC light for 5 minutes on each side. The filters were inoculated with 2 μl of PAO1 and incubated at 37°C for 72 h, with transfer to fresh LB agar plates at 24 and 48 h prior to application to the wound.

extract_protocol: RNA was extracted using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA). RNA quality was verified on a Bioanalyzer 2100 Nanochip (Agilent, Santa Clara, CA). Total RNA was quantified on the NanoDrop 1000 (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: Each 72 hour biofilm was collected and stored in 1 ml of RNALater at -20oC.

tag: strain/background

value: biofilm

tag: time point

value: 72 hr

tag: sample type

value: biofilm inoculum


title: LR(M_38_07)

tag: breed


title: carotid_non-ligated_Has3-deficient_1

value: carotid artery

value: Has3 deficient

value: female


title: LWF(M_43_47_08)


title: proliferating C2C12 cell

description: Mouse myoblast cell line cultured in proliferation condition


title: differentiating C2C12 cell

description: Mouse myoblast cell line cultured in differentiation condition

value: Differentiation medium (DMEM including 2% horse serum)


title: Biofilm Inoculum_rep1

description: RNA extracted from a 72 hour biofilm, as used to inoculate a murine wound, biological replicate 1.


title: PI(M_25_29_09)


title: LWF(M_20_05)


title: carotid_non-ligated_wildtype_3

source_name: wildtype, non-ligated artery

value: wildtype

value: 21-22 weeks


title: carotid_non-ligated_wildtype_2


title: carotid_non-ligated_wildtype_4


title: DuF(M_35_17)


title: DGM-10919_M3_SAE_miRNA-2

status: Public on Nov 23 2015

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Samples were hybridized to Affymetrix miRNA 2.0 arrays according to the manufacturer's protocol.

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

data_processing: The data were analyzed with Partek Genomics Suite software version 6.6, 2012 filtering for using human miRNAs only.

source_name: small airway epithelium brushing

label_protocol: Total RNA 0.5ug was biotin labeled with the FlashTag HSR RNA laveling kit (Genisphere, Hatfield, PA).

extract_protocol: Trizol extraction and miRNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker-quitter

value: SAE


title: DGM-11047_M0_SAE_miRNA-2

value: smoker


title: DGM-11047_M3_SAE_miRNA-2


title: DGM-11008_M0_SAE_miRNA-2


title: DGM-11008_M3_SAE_miRNA-2


title: DGM-11113_M0_SAE_miRNA-2


title: DGM-11113_M3_SAE_miRNA-2


title: carotid_non-ligated_wildtype_1


title: DGM-10919_M0_SAE_miRNA-2


title: DGM-10672_M0_SAE_miRNA-2


title: DGM-10632_M0_SAE_miRNA-2

value: nonsmoker


title: DGM-10886_M0_SAE_miRNA-2


title: DGM-10672_M3_SAE_miRNA-2


title: DGM-10886_M3_SAE_miRNA-2


title: DGM-10537_M3_SAE_miRNA-2


title: DGM-10435_M3_SAE_miRNA-2


title: DGM-10435_M0_SAE_miRNA-2


title: DGM-10380_M0_SAE_miRNA-2


title: DGM-10361_M3_SAE_miRNA-2


title: DGM-10261_M0_SAE_miRNA-2


title: DGM-10361_M0_SAE_miRNA-2


title: DGM-10288_M0_SAE_miRNA-2


title: DGM-10270_M0_SAE_miRNA-2


title: DGM-10447_M0_SAE_miRNA-2


title: DGM-10537_M0_SAE_miRNA-2


title: DGM-10123_M0_SAE_miRNA-2


title: DGM-00221_M3_SAE_miRNA-2


title: DGM-10161_M0_SAE_miRNA-2


title: DGM-10254_M0_SAE_miRNA-2


title: DGM-00221_M0_SAE_miRNA-2


title: OGD activated microglial cells [miRNA]

city: Shanghai

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

institute: Fudan University Shanghai Cancer Center

hyb_protocol: The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.

scan_protocol: Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.

data_processing: The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant and median summarized.

label: FlashTag-Biotin-HSR

organism: Rattus norvegicus

source_name: Microglial cells

label_protocol: A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).

growth_protocol: Cell lines were grown in DMEM + 10% FCS

extract_protocol: Small RNAs were isolated using a miRNA Isolation Kit (Ambion, Inc.)

tag: strain background

value: Sprague Dawley

value: microglial cell

tag: exposed to

value: oxygen-glucose deprivation (OGD) for 3 h


title: Resting microglial cells [miRNA]

value: none (control)


title: FaDU-9-1-3

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: FaDu cells stably transfected with sh-MDA-9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: 10 million FaDu cells stably transfected with empty vector or Sh-MDA-9, in triplicate.

value: FaDu

tag: transfection


title: FaDU-9-1-1

treatment_protocol: 10 million FaDu cells stably transfected with empty vector or Sh-MDA-9, in triplicate.

tag: cell line


title: FaDU-9-1-2


title: LowerSICrypt_Fed_Etoposide_3h_f_Rep4

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, agilent 10x blocking reagent and kreatech Kreablock onto Agilent 4x44K V2 microarrays at 65oC for 20 min

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing: Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.

source_name: Jejunum, lower crypt, Fed Etoposide, 3h

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics) and Cy5-labeled cDNAs were hybridized to Agilent Mouse v2 4x44K microarrays (G4846A-026655).

extract_protocol: Sections were deparrafinized and dehydrated through xylene and an increasing gradient of ethanol. Laser capture microdissection was performed using the Acturus PixCell IIe, with the following settings: spot size power 80, duration 1 ms, repeat 0.2 s, target 0.150 V, current 1.82 mA. RNA was isolated from the CapSure HS LCM Caps (Applied Biosystem) using the PicoPure RNA Isolation kit (Applied Biosystems). All RNA samples were treated with DNaseI (Qiagen).

treatment_protocol: 4-6 week old, male and female Lgr5EGFP-IRES-CreERT2/+ mice were randomly assigned to one of two treatment groups.  Mice were fed or fasted for 24 h followed by injection with 80mg/kg etoposide (tail vein, i.v.) and returned to individual housed cages with moistened food pellets.  Intestines were harvested 3 h post-etoposide injection, flushed with PBS, and then flushed with ice-cold Methacarn (60% methanol, 30% chloroform, 10% acetic acid) to fix the tissue while preserving RNA integrity. Fixed intestines were rinsed with 70% ethanol, embedded in 2% agar followed by paraffin embedding.

tag: tissue

value: jejunum lower crypt

value: Female

value: 4-6 weeks


title: FaDU-C1

source_name: FaDu cells stably transfected with empty vector

value: empty vector


title: LowerSICrypt_Fed_Etoposide_3h_m_Rep2

value: Male