title: Treated HAND brain 7, biological rep1

status: Public on Sep 25 2011

first: Alejandra

last: Borjabad

address: 432 West 58th, Street

department: Medicine

institute: St.Luke's-Roosevelt Hospital Center

description: gene expression data for portmortem brain tissue uninfected patients

hyb_protocol: The samples were hybridized to Affymetrix Human Genome 133 plus 2.0 arrays.  Washing and staining of all arrays were carried out in the Affymetrix fluidics module as per the manufacturer's protocol.

scan_protocol: The detection and quantitation of target hybridization was performed with an Affymetrix GeneChip Scanner.

data_processing: The .cel data files generated by the Affymetrix microarray hybridization platform were analyzed by the ArrayAssist software (Stratagene, Santa Clara, CA).  Probe level analysis was performed using the Robust Microarray Average (RMA) algorithm.

source_name: Homo sapiens postmortem brain tissue

label_protocol: Biotin labeling using NuGen Encore Biotin Module.

extract_protocol: RNA was isolated from human brain tissue by RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: antiretroviral treated

value: postmortem brain

value: HIV1 with HIV-1-associated neurocognitive disorders


title: Cohyb_H1_D0 vs D21_GE_A

status: Public on Sep 26 2011

type: RNA

city: Houston

first: Robert

middle: A

last: Waterland

state: TX

address: 1100 Bates St.,

country: USA

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol (version 6.5, 2010)

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

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Homo sapiens

source_name: RNA extracted from undifferentiated hESCs

label_protocol: Amplified cRNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol (version 6.5, 2010)

extract_protocol: Total RNA was extracted by Qiagen Rneasy Mini Kit (Cat. No. 74104)

tag: cell type

value: embryonic stem cell

tag: cell line

tag: differentian stage

source_name: RNA extracted from hESCs with 21 days after undirected differentiation


title: Treated HAND brain 5, biological rep1

city: New York

state: NY

label: biotin

tag: treatment

tag: tissue

tag: disease state


title: Treated HAND brain 5, biological rep2


title: Treated HAND brain 4, biological rep2


title: Cohyb_H1_D0 vs D21_Methy_A

type: genomic

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization. Probe ratios within one SmaI interval were averaged and the median of the P value log10 ratios of the probes within one SmaI interval was calculated.

molecule: genomic DNA

source_name: genomic DNA extracted from undifferentiated hESCs

label_protocol: 2µg of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

extract_protocol: Total DNA was extracted by standard phenol-chloroform isolation

source_name: genomic DNA extracted from hESCs with 21 days after undirected differentiation


title: Chondrosarcoma case 3

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Genomic DNA extracted from chondrosarcoma biopsy was analyzed using Illumina Human Omni-Quad v1.0 BeadChip (Illumina).

hyb_protocol: Hybridization was done according to the manufacturer's instructions (Illumina).

scan_protocol: Scanning was done according to the manufacturer's instructions (Illumina).

data_processing: Data were extracted from the GenomeStudio software (Illumina), and subsequently normalized and segmented using thresholded quantile normalization (tQN) and BAFsegmentation, respectively (Staaf et al. Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics 2007, 8:382; Staaf et al. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol 2008, 9:R136). Base pair positions are indicated according to the NCBI build 36 (hg18).

label: C-Bio and A-DNP

source_name: Chondrosarcoma

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tumour biopsies using the DNeasy Tissue Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).

tag: case

tag: gender

value: Female

value: Chondrosarcoma

value: bone tumor


title: Treated HAND brain 3, biological rep1


title: Treated HAND brain 2, biological rep2


title: Treated HAND brain 3, biological rep2


title: Untreated HAND brain 8, biological rep1

value: untreated


title: Chondrosarcoma case 11

value: Male


title: Chondrosarcoma case 8


title: Treated HAND brain 2, biological rep1


title: Chondrosarcoma case 1


title: Treated HAND brain 4, biological rep1


title: Untreated HAND brain 8, biological rep2


title: Treated HAND brain 6, biological rep1


title: Untreated HAND brain 7, biological rep1


title: Chondrosarcoma case 15


title: Chondrosarcoma case 2


title: Treated HAND brain 1, biological rep1


title: Chondrosarcoma case 13


title: 96hpic_3 with array type rice from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Plant-parasitic nematodes cause profound economic losses to global agriculture with the obligate sedentary endoparasitic varieties; amongst them the cyst and Root Knot Nematode (RKN) species are the most damaging. Meloidogyne graminicola is a RKN mainly found in the monocotyledous plants. In the compatible interaction with Oryza sativa, M. graminicola induces the characteristic formation of hook-like galls resulting from the redifferentiation of root cells into multinucleate giant cells. In order to understand the global transcriptome changes occurring during infection, several recent microarray studies on root knots have demonstrated complex changes in host plant gene expression in response to infection. However, to our knowledge, all these transcriptome studies were performed on dicotyledous plants. A histological study enabled us to observe hyperplasia and hypertrophy of the surrounding cells leading to the formation of hook-like galls. We also investigated the plant response to M. graminicola by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at an early stage (2dpi) and a latter stage (4dpi) of gall development.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - Media: Hydroponic in ¼ Hoagland’s solution - hygrometry:  70% - Temperature 23°C - Light: 9 h/15 h light/dark regime at 80 mol m-2 s-1 during the light period 50% 36 watt GE Polylux XLRTM Fluorescent tubes (General Electric Company) and 50 % 36 watt Gro-Lux Fluorescent tubes (Sylvania)

treatment_protocol: Name:4 dai M.  graminicola  - time course study - pathogen infection,meloidogyne incognita:. nematode inoculation

tag: harvest date

tag: infection

value: Meloidogyne graminicola

value: root

tag: time

value: 96 hpi


title: Treated HAND brain 7, biological rep2


title: Untreated HAND brain 6, biological rep1


title: Untreated HAND brain 5, biological rep2


title: 96hpib_2 with array type rice from Affymetrix


title: temoinc_3 with array type rice from Affymetrix

treatment_protocol: no treatment

value: control


title: Untreated HAND brain 3, biological rep1


title: Untreated HAND brain 7, biological rep2


title: Untreated HAND brain 4, biological rep1


title: 48hpib_2 with array type rice from Affymetrix

treatment_protocol: Name:2 dai M.  graminicola - time course study - pathogen infection,meloidogyne incognita:. nematode inoculation

value: 48 hpi


title: 96hpia_1 with array type rice from Affymetrix


title: 48hpia_1 with array type rice from Affymetrix


title: temoinb_2 with array type rice from Affymetrix

growth_protocol: roots - - Media: Hydroponic in ¼ Hoagland’s solution - hygrometry:  70% - Temperature 23°C - Light: 9 h/15 h light/dark regime at 80 mol m-2 s-1 during the light period 50% 36 watt GE Polylux XLRTM Fluorescent tubes (General Electric Company) and 50 % 36 watt Gro-Lux Fluorescent tubes (Sylvania)


title: Chondrosarcoma case 12

description: Genomic DNA extracted from chondrosarcoma biopsy was analyzed using Illumina Human CNV370-Quad v3.0 BeadChip (Illumina).


title: Untreated HAND brain 3, biological rep2


title: Untreated HAND brain 5, biological rep1


title: 144hpi_1 with array type rice from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: Plant-parasitic nematodes cause heavy economic losses to global agriculture. The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. M. incognita infection to dicotyledous plants is extensively studied but it is also important to study their interaction with monocotyledous plants, in particular with cereals. In our growing conditions, as of day 6, histological studies revealed a profound rice tissue reorganisation around nematodes, notably characterized by the plant feeding site formation. We are investigating the molecular plant response to M. incognita by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at this early stage (6dpi) of gall development

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003) using R-2.6.2 version and AFFYMETRIX bioconductor packages (Gentleman and Carey, 2002).

extract_protocol: 144hpi_1:6ug. Qiagen_RNeasy kit

treatment_protocol: Name:M.incognita - nematode inoculation - pathogen infection,meloidogyne incognita:time 24hour . -6 days old rice seedlings were inoculated with 300 J2-stage juveniles M. incognita.

tag: variety

value: Nipponbare

value: galls from 45 infected plants


title: Untreated HAND brain 2, biological rep1


title: Chondrosarcoma case 9


title: temoin_1 with array type rice from Affymetrix

extract_protocol: temoin_1:16ug. Qiagen_RNeasy kit

value: uninfected meristematic root fragments


title: 144hpi_3 with array type rice from Affymetrix

extract_protocol: 144hpi_3:35ug. Qiagen_RNeasy kit


title: Chondrosarcoma case 10


title: temoina_1 with array type rice from Affymetrix


title: Untreated HAND brain 1, biological rep2


title: 48hpic_3 with array type rice from Affymetrix


title: temoin_3 with array type rice from Affymetrix

extract_protocol: temoin_3:35ug. Qiagen_RNeasy kit


title: Control brain 6, biological rep1

value: uninfected


title: Chondrosarcoma case 7


title: Control brain 6, biological rep2

value: postmortem brain


title: Untreated HAND brain 6 biological rep2

value: HIV1 with HIV-1-associated neurocognitive disorders


title: Control brain 4, biological rep2


title: Untreated HAND brain 1, biological rep1


title: 144hpi_2 with array type rice from Affymetrix

extract_protocol: 144hpi_2:17ug. Qiagen_RNeasy kit


title: Control brain 4, biological rep1


title: Chondrosarcoma case 4


title: Control brain 2, biological rep1


title: Control brain 3, biological rep1


title: Chondrosarcoma case 6


title: Control brain 1, biological rep1


title: Control brain 5, biological rep2


title: temoin_2 with array type rice from Affymetrix

extract_protocol: temoin_2:17ug. Qiagen_RNeasy kit


title: Control brain 5, biological rep1


title: AB5 (Illumina human -6 V2)

status: Public on Sep 24 2011

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description:
A375SM cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina Human-6 BeadChip v.2(48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. Quantile normalization.

organism:
Homo sapiens
Mus musculus

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: Human cancer A375SM cells xenografted into mouse brain


title: AS1 (Illumina human -6 V2)

description:
A375SM cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer A375SM cells xenografted into mouse skin


title: AB1 (Illumina human -6 V2)

source_name: A375SM cells xenografted into mouse brain


title: AS2 (Illumina human -6 V2)

source_name: A375SM cells xenografted into mouse skin


title: AS4 (Illumina human -6 V2)


title: AS5 (Illumina human -6 V2)


title: AB4 (Illumina human -6 V2)


title: AB2 (Illumina human -6 V2)


title: AB3 (Illumina human -6 V2)


title: BR_N_PC (Illumina human -6 V2)

description:
PC14 cells mixed with normal mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer PC14 cells mixed with normal mouse brain


title: PS4 (Illumina human -6 V2)

description:
PC14Br4 cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer PC14Br4 cells xenografted into mouse skin


title: PS3 (Illumina human -6 V2)

source_name: PC14Br4 cells xenografted into mouse skin


title: AS3 (Illumina human -6 V2)


title: PS2 (Illumina human -6 V2)


title: Clp Yra1 depleted

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: NIMBLEGEN ARRAY USED IN THIS SAMPLE WAS A CUSTOM ORDER WHICH HAD THE SAME 378,684 50mers AS IN cat. no. C4214-00-01 BUT PRINTED 3 TIMES ON THE SAME SLIDE.

hyb_protocol: labelling and hybridization was done by Nimblegen

scan_protocol: scanning was done by Nimblegen

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Saccharomyces cerevisiae

source_name: Clp1  ChIP DNA

growth_protocol: cells were grown in SC 2%raffinose+galactose to O.D. ~ 0.2 at 25º then shifted to SC 2% glucose for 8 hr

extract_protocol: cells were cross-linked 1% formaldehyde 15 min-2 hr. and processed for ChIP as described in Schroeder et al Genes Dev.

tag: strain

value: DBY1272-2 (W303 background)

tag: chip antibody

value: rabbit anti Clp1 (Johnson et al NSMB. 2011 in press)

source_name: Input DNA

tag: sample type

value: Input DNA


title: PS1 (Illumina human -6 V2)


title: Chondrosarcoma case 14

value: Female

value: Chondrosarcoma

value: bone tumor


title: PL1 (Illumina human -6 V2)

description:
PC14Br4 cells xenografted into mouse lung
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer PC14Br4 cells xenografted into mouse lung


title: Pcf11 Yra1 depleted

source_name: Pcf11 ChIP DNA

label_protocol: labelling and hybridization was done by Nimblegen

value: rabbit anti-Pcf11 (Johnson et al Mol Cell. 33:215, 2009)


title: Pcf11 W303


title: PB3 (Illumina human -6 V2)

description:
PC14Br4 cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer PC14Br4 cells xenografted into mouse brain


title: PB2 (Illumina human -6 V2)

source_name: PC14Br4 cells xenografted into mouse brain


title: Chondrosarcoma case 16


title: Clp1-HA WT

source_name: Clp1-HA ChIP DNA

growth_protocol: cells were grown in YPD to O.D. ~ 0.8 at 25º

value: DBY1223 (S288C background)

value: anti-HA 12CA5 (Roche)


title: Clp1 W303

source_name: Clp1 ChIP DNA


title: PL2 (Illumina human -6 V2)

source_name: PC14Br4 cells xenografted into mouse lung


title: Chondrosarcoma case 5

value: Male


title: Sub2

source_name: Sub2 ChIP DNA

value: rabbit anti Sub2 (Johnson et al Mol Cell. 33:215, 2009)


title: MS1 (Illumina human -6 V2)

description:
MDA-MB231Br3 cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer MDA-MB231Br3 cells xenografted into mouse skin


title: MF5 (Illumina human -6 V2)

description:
MDA-MB231Br3 cells xenografted into mouse Fatpad
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer MDA-MB231Br3 cells xenografted into mouse Fatpad


title: MS2 (Illumina human -6 V2)

source_name: MDA-MB231Br3 cells xenografted into mouse skin


title: MF2 (Illumina human -6 V2)

source_name: MDA-MB231Br3 cells xenografted into mouse Fatpad


title: PB1 (Illumina human -6 V2)


title: MF4 (Illumina human -6 V2)


title: Yra1

source_name: Yra1ChIP DNA

value: rabbit anti Yra1 (Johnson et al Mol Cell. 33:215, 2009)


title: MS4 (Illumina human -6 V2)


title: MB1 (Illumina human -6 V2)

description:
MDA-MB231Br3 cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer MDA-MB231Br3 cells xenografted into mouse brain


title: MS3 (Illumina human -6 V2)


title: MB3 (Illumina human -6 V2)

source_name: MDA-MB231Br3 cells xenografted into mouse brain


title: KC3 (Illumina human -6 V2)

description:
KM12M cells xenografted into mouse cecum
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer KM12M cells xenografted into mouse cecum


title: MB4 (Illumina human -6 V2)


title: MF1 (Illumina human -6 V2)


title: MB5 (Illumina human -6 V2)


title: KS4 (Illumina human -6 V2)

description:
KM12M cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

source_name: KM12M cells xenografted into mouse skin

value: Human cancer KM12M cells xenografted into mouse skin


title: MB2 (Illumina human -6 V2)


title: KC2 (Illumina human -6 V2)

source_name: KM12M cells xenografted into mouse cecum


title: KS1 (Illumina human -6 V2)


title: KS2 (Illumina human -6 V2)


title: KB2 (Illumina human -6 V2)

description:
KM12M cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

value: Human cancer KM12M cells xenografted into mouse brain


title: KC1 (Illumina human -6 V2)


title: Astrocytes-1

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

data_processing: Array data processing were performed on Illumina BeadStudio software.

organism: Mus musculus

source_name: Mouse Astrocytes Cell

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

value: Mouse Astrocytes

tag: mrna ratio of hs/mm (human)

tag: mrna ratio of hs/mm (mouse)


title: KB3 (Illumina human -6 V2)

source_name: KM12M cells xenografted into mouse brain

tag: cell type


title: MDA231_Astro(19)-1 (Illumina human -6 V2)

source_name: Mixed samples of MDAMB231 Breast Cancer Cell and Mouse Astrocytes

value: MDAMB231 and mouse astrocytes


title: KB4 (Illumina human -6 V2)


title: MDA231_Astro(37)_t4 (Illumina human -6 V2)


title: KB1 (Illumina human -6 V2)


title: MDA231_Astro(55)_s1 (Illumina human -6 V2)


title: MDA231_Astro(37)_t3 (Illumina human -6 V2)


title: MDA231_Astro(91)-1 (Illumina human -6 V2)


title: MDA231_Astro(73)_t1 (Illumina human -6 V2)


title: MDA231_Astro(55)_s2 (Illumina human -6 V2)


title: MDA231_Astro(73)_t2 (Illumina human -6 V2)


title: MDA231-1 (Illumina human -6 V2)

source_name: MDAMB231 Breast Cancer Cell


title: BR1 (Illumina Mouse -6 V1.1)

description:
normal mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina Mouse-6 BeadChip v.1.1(46K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

source_name: normal mouse brain

value: normal mouse brain


title: BR_PCM (Illumina Mouse -6 V1.1)

description:
PC14 cells mixed with normal mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

value: Human cancer PC14 cells mixed with normal mouse brain


title: BR3 (Illumina Mouse -6 V1.1)


title: MF3 (Illumina human -6 V2)


title: BR2 (Illumina Mouse -6 V1.1)


title: AS3 (Illumina Mouse -6 V1.1)

description:
A375SM cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

value: Human cancer A375SM cells xenografted into mouse skin


title: AS4 (Illumina Mouse -6 V1.1)

source_name: A375SM cells xenografted into mouse skin


title: PC_BRM1 (Illumina Mouse -6 V1.1)

source_name: PC14 cells mixed with normal mouse brain


title: AS5 (Illumina Mouse -6 V1.1)


title: AS2 (Illumina Mouse -6 V1.1)


title: KS3 (Illumina human -6 V2)


title: PC_BRM2 (Illumina Mouse -6 V1.1)


title: PC_BRM3 (Illumina Mouse -6 V1.1)


title: AB2 (Illumina Mouse -6 V1.1)

description:
A375SM cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

value: Human cancer A375SM cells xenografted into mouse brain


title: AB5 (Illumina Mouse -6 V1.1)

source_name: A375SM cells xenografted into mouse brain


title: AB3 (Illumina Mouse -6 V1.1)


title: AB4 (Illumina Mouse -6 V1.1)


title: PS3 (Illumina Mouse -6 V1.1)

description:
PC14Br4 cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

value: Human cancer PC14Br4 cells xenografted into mouse skin


title: AS1 (Illumina Mouse -6 V1.1)


title: PL3 (Illumina human -6 V2)

value: Human cancer PC14Br4 cells xenografted into mouse lung


title: PL3 (Illumina Mouse -6 V1.1)

description:
PC14Br4 cells xenografted into mouse lung
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: PS1 (Illumina Mouse -6 V1.1)

source_name: PC14Br4 cells xenografted into mouse skin


title: MS4 (Illumina Mouse -6 V1.1)

description:
MDA-MB231Br3 cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: PB2 (Illumina Mouse -6 V1.1)

description:
PC14Br4 cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

value: Human cancer PC14Br4 cells xenografted into mouse brain


title: PS2 (Illumina Mouse -6 V1.1)


title: PL1 (Illumina Mouse -6 V1.1)

source_name: PC14Br4 cells xenografted into mouse lung


title: PB1 (Illumina Mouse -6 V1.1)

source_name: PC14Br4 cells xenografted into mouse brain


title: PL2 (Illumina Mouse -6 V1.1)


title: AB1 (Illumina Mouse -6 V1.1)


title: PS4 (Illumina Mouse -6 V1.1)


title: PB3 (Illumina Mouse -6 V1.1)


title: MS1 (Illumina Mouse -6 V1.1)

source_name: MDA-MB231Br3 cells xenografted into mouse skin


title: MF3 (Illumina Mouse -6 V1.1)

description:
MDA-MB231Br3 cells xenografted into mouse Fatpad
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: MB3 (Illumina Mouse -6 V1.1)

description:
MDA-MB231Br3 cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: MB5 (Illumina Mouse -6 V1.1)


title: MS3 (Illumina Mouse -6 V1.1)


title: MF5 (Illumina Mouse -6 V1.1)

source_name: MDA-MB231Br3 cells xenografted into mouse Fatpad


title: KC3 (Illumina Mouse -6 V1.1)

description:
KM12M cells xenografted into mouse cecum
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: MS2 (Illumina Mouse -6 V1.1)


title: MF4 (Illumina Mouse -6 V1.1)


title: MF1 (Illumina Mouse -6 V1.1)


title: KC1 (Illumina Mouse -6 V1.1)


title: MB4 (Illumina Mouse -6 V1.1)


title: MB2 (Illumina Mouse -6 V1.1)


title: MF2 (Illumina Mouse -6 V1.1)


title: KC2 (Illumina Mouse -6 V1.1)


title: MB1 (Illumina Mouse -6 V1.1)


title: KS4 (Illumina Mouse -6 V1.1)

description:
KM12M cells xenografted into mouse skin
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: KS3 (Illumina Mouse -6 V1.1)


title: KS2 (Illumina Mouse -6 V1.1)


title: KB4 (Illumina Mouse -6 V1.1)

description:
KM12M cells xenografted into mouse brain
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.


title: KS1 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(19)-1 (Illumina Mouse -6 V1.1)

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the Mouse-6 beadChip ver. 1.1 were used.

extract_protocol: Total RNA was isolated from tissues with mirVana. RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)


title: MDA231_Astro(37)_t3 (Illumina Mouse -6 V1.1)


title: KB2 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(55)_s1 (Illumina Mouse -6 V1.1)


title: KB3 (Illumina Mouse -6 V1.1)


title: KB1 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(55)_s2 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(37)_t4 (Illumina Mouse -6 V1.1)


title: Astrocytes-1 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(91)-1 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(73)_t2 (Illumina Mouse -6 V1.1)


title: MDA231-1 (Illumina Mouse -6 V1.1)


title: MDA231_Astro(73)_t1 (Illumina Mouse -6 V1.1)


title: Relapse 74

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

description: Mouse MYC Relapse 74

hyb_protocol: See http://microarray.org/sfgf/meebo.do

scan_protocol: See http://microarray.org/sfgf/meebo.do

data_processing: GPR files were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, conversion to log2 ratio

source_name: Mouse MYC relapse tumor

label_protocol: See http://microarray.org/sfgf/meebo.do

growth_protocol: Cell lines were injected subcutaneously into recipient mice (7.5-10 x 10E6 cells per mouse)

extract_protocol: See http://microarray.org/sfgf/meebo.do

treatment_protocol: Doxycycline was administered to mice in drinking water (100ug/ml)

tag: immune strain/background

value: FVB

source_name: Stratagene mouse reference RNA

tag: reference rna

value: Stratagene mouse reference RNA


title: Primary 156

description: Mouse MYC Primary 156

source_name: Mouse MYC primary tumor


title: Relapse 46

description: Mouse MYC Relapse 46


title: Relapse 244

description: Mouse MYC Relapse 244


title: Relapse 183

description: Mouse MYC Relapse 183


title: Adult Mutant, biological rep1

city: Bologna

first: Elena

last: Bonora

address: via Massarenti )

department: Dept of Gynaecology

country: Italy

institute: University of Bologna

description:
NEP
Gene expression data from adult mutant.
The nep-1 allele was isolated by EMS mutagenesis.

hyb_protocol: Hybridization and staining were performed on the Affymetrix platform using standard procedures.

scan_protocol: Scanning was performed on the Affymetrix platform using standard procedures.

data_processing:
The probe-level data were converted to expression values using the robust multiarray average (RMA) procedure.

Data were filtered and analyzed using GeneSpring or dChip analysis packages. Differentially expressed genes were obtained performing either an ANOVA analysis and by using the dChip compare sample procedure requiring a 2-fold change difference and an absolute difference of 200 between the group means. False Discovery Rate (FDR) has been used to adjust p-value for multiple comparisons by 100 random permutations of the group labels.

organism: Caenorhabditis elegans

source_name: Adult mutant

label_protocol: cDNA and biotin-labeled target synthesis were performed using the Affymetrix one cycle 3’ IVT protocols.

growth_protocol: Wild-type and Nep-1 mutants were grown at 20°C on nematode growth medium (NGM) agar plates with Escherichia coli OP50 as food source, using standard methods.

extract_protocol: Total RNA was extracted from cells and worms using the Trizol method following the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA).

tag: genotype

value: Nep-1 mutant

tag: developmental stage

value: adult

value: whole body


title: Relapse 223

description: Mouse MYC Relapse 223


title: Adult Mutant, biological rep2

description:
NEP_1(2815A MUT)_adulto
Gene expression data from adult mutant.
The nep-1 allele was isolated by EMS mutagenesis.

tag: tissue


title: Relapse 40

description: Mouse MYC Relapse 40

value: SCID


title: Adult Wild-type, biological rep3

description:
WT
Gene expression data from adult wild-type.
The wild-type strain (var. Bristol) was obtained from the CGC (Caenorhabditis Genetics Center, University of Minnesota, USA).

source_name: Adult wild-type

value: Bristol

value: wild-type


title: Relapse 248

description: Mouse MYC Relapse 248


title: Primary 251

description: Mouse MYC Primary 251


title: Adult Wild-type, biological rep2

description:
N2_2(N2B WT)_adulto
Gene expression data from adult wild-type.
The wild-type strain (var. Bristol) was obtained from the CGC (Caenorhabditis Genetics Center, University of Minnesota, USA).


title: Relapse 253

description: Mouse MYC Relapse 253


title: Larval Wild-type, biological rep1

description:
N2L3
Gene expression data from larval stage L3 wild-type.
The wild-type strain (var. Bristol) was obtained from the CGC (Caenorhabditis Genetics Center, University of Minnesota, USA).

source_name: Larval wild-type

value: larval stage L3


title: Primary 157

description: Mouse MYC Primary 157


title: Larval Wild-type, biological rep2

description:
WT L3 def
Gene expression data from larval stage L3 wild-type.
The wild-type strain (var. Bristol) was obtained from the CGC (Caenorhabditis Genetics Center, University of Minnesota, USA).


title: Relapse 172

description: Mouse MYC Relapse 172


title: Adult Mutant, biological rep3

description:
NEP_2(2815B MUT)_adulto
Gene expression data from adult mutant.
The nep-1 allele was isolated by EMS mutagenesis.


title: Primary 198

description: Mouse MYC Primary 198


title: Larval Mutant, biological rep2

description:
MUTANTE L3 def
Gene expression data from larval stage L3 mutant.
The nep-1 allele was isolated by EMS mutagenesis.

source_name: Larval mutant


title: hypoxia

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

country: China

institute: Nanjing Agricultural University

description:
sample name 2
Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined, labeled with Alexa647, hybridized together (Channel 2) but was not included in the analysis.

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities (raw data with absolute values).  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.  Data was normalized by the percentile method using ch1 only. Ch2 signals were present but never used.

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.

growth_protocol: Cells are grown in RPMI supplemented with 10% FBS at 37 degree.

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from the cells.

treatment_protocol: Cells were placed inside a ~ 3% oxygen hypoxia chamber in a regular cell culture incubator for 48 hours.  Control cells were also placed in the cell culture incubator.

tag: cell line

value: epithelial ovarian cancer cells


title: Adult Wild-type, biological rep1

description:
N2_1(N2A WT)_adulto
Gene expression data from adult wild-type.
The wild-type strain (var. Bristol) was obtained from the CGC (Caenorhabditis Genetics Center, University of Minnesota, USA).


title: Larval Mutant, biological rep1

description:
BR2845L3
Gene expression data from larval stage L3 mutant.
The nep-1 allele was isolated by EMS mutagenesis.


title: control

description:
sample name 1
Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined, labeled with Alexa647, hybridized together (Channel 2) but was not included in the analysis.


title: Zebrafish-embryo_100uM-DEM-treated_2

city: Nagoya

first: Shin'ichi

last: Akiyama

state: Aichi

address: 65 Tsurumaicho

department: Department of Nephrology

country: Japan

institute: Nagoya University Graduate School of Medicine

hyb_protocol: The dual-color hybridization of the MZH chips was performed according to the manufacture’s instructions of AceGene DNA microarray (Hitachi-soft). Each experiment was repeated in triplicate.

scan_protocol: After hybridization, MZH chips were scanned using Affimetrix 428 array scanner (Affimetrix).

data_processing: Microarray data were processed from raw data image files with Affymetrix Jaguar (Affimetrix) and normalized. Processed data were subsequently imported into Excel (Microsoft) to compare expression profiles of DEM treated samples to that of control samples.

organism: Danio rerio

label_protocol: Amino-allyl-modified amplified RNA (aRNA) was synthesized in one amplification round from 1 μg of purified total RNA using the amino-allyl RNA amplification kit (Sigma-Aldrich). Subsequently, 5 μg of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 and Cy5dyes (GE Healthcare) and column purified.

growth_protocol: All embryos were incubated at 28℃.

extract_protocol: The collected zebrafish embryos were quickly homogenized with 1ml of QIAzol reagent (Qiagen), and subsequently stored at -80°C. Total RNA was extracted according to the manufacturer’s instructions. Isolated total RNA was further purified using RNAeasy mini kit (Qiagen).

treatment_protocol: Embryo were treated with culture media containing 0.1% DMSO from 96 hour post fertilization (hpf) to 108 hpf.

tag: genotype/variation

value: wild type

value: embryo

treatment_protocol: Embryo were treated with culture media containing 100 µM diethylmaleate (DEM) from 96 hour post fertilization (hpf) to 108 hpf.


title: Zebrafish-embryo_100uM-DEM-treated_1


title: Dll1-5 mutant replication 2

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of Dll1-5 mutant Replication 2

hyb_protocol: Hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 8.1.1.1

source_name: Dll1-5 Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Lines of Dll1 (Dll1-5) mutant mice neural stem cells-derived neurospheres that were prepared and maintained in EGF-supplemented, serum-free medium, as described in a previous work (Grandbarbe et al., 2003).

extract_protocol: Kit: QIAGEN, Rneasy Mini

value: 129/Sv mice crossed with C57BL/6

value: neural stem cells-derived neurospheres

value: Dll1-5 mutant

source_name: WT Control Cy5

growth_protocol: Lines of Dll1 (Dll1-5) wild type (WT) neural stem cells-derived neurospheres that were prepared and maintained in EGF-supplemented, serum-free medium, as described in a previous work (Grandbarbe et al., 2003).


title: Zebrafish-embryo_100uM-DEM-treated_4


title: Dll1-3 mutant replication 2

source_name: Dll1-3 Cy3

growth_protocol: Lines of Dll1 (Dll1-3) mutant mice neural stem cells-derived neurospheres that were prepared and maintained in EGF-supplemented, serum-free medium, as described in a previous work (Grandbarbe et al., 2003).

value: Dll1-3 mutant

growth_protocol: Lines of Dll1 (Dll1-3) of wild type (WT) neural stem cells-derived neurospheres that were prepared and maintained in EGF-supplemented, serum-free medium, as described in a previous work (Grandbarbe et al., 2003).


title: dcr1ΔC33 tiling array 3

status: Public on Sep 23 2011

city: Basel

first: Stephan

last: Emmerth

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment Sp20b_M_v04.cdf (as provided in the attached file) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file).

organism: Schizosaccharomyces pombe

source_name: dcr1ΔC33 total RNA

label_protocol: 200ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Cells were collected at OD600=0.5

extract_protocol: total RNA was extracted using the hot phenol method (Leeds, 1991): resuspend cell pellet in 1.2 ml AE Buffer (50mM NaOAc pH 5.2, 10mM EDTA), add 80 ml 25 % SDS and 1.2 ml acidic phenol, incubate for 10 minutes at 65 °C and then put on ice for 5 minutes transfer to 15 ml phase lock Falcon tubes, add 1.3 ml chloroform, mix by inverting tube, spin 10 minutes 3000 rpm at room temperature, pour the supernatant into a 15 ml Falcon tube, add 3 ml glycogen, 4 ml 100 % ethanol and 160 ml 3M NaOAc pH 5.2-5.6, spin 30 minutes 12000 rpm at 4°C, wash 2 times with 70% ethanol, air dry pellet, resuspend in 500 ul water.


title: Dll1-3 mutant replication 1

hyb_protocol: hybridization_Kit: in situ hybridization plus

source_name: WT Control Cy3

growth_protocol: Lines of Dll1 (Dll1-3) wild type (WT) neural stem cells-derived neurospheres that were prepared and maintained in EGF-supplemented, serum-free medium, as described in a previous work (Grandbarbe et al., 2003).

source_name: Dll1-3 Cy5


title: Dll1-5 mutant replication 1

description: Dye-swap (Cy3/Cy5) of Dll1-5 mutant Replication 1

source_name: Dll1-5 Cy5


title: dcr1ΔC33 tiling array 2


title: Zebrafish-embryo_100uM-DEM-treated_3


title: dcr1-SHSS tiling array 2

source_name: dcr1-SHSS total RNA


title: dcr1-SHSS tiling array 3


title: dcr1-SHSS tiling array 1


title: GFPpositive mutant H3.3 injected2

city: Los Angeles

first: Ankita

last: Das

email: ankita23@gmail.com, gcrump@usc.edu

address: 1425 San Pablo Street

department: Broad CIRM Center

institute: University of Southern California

hyb_protocol: Hybridization was performed by Nimblegen using their standard protocol

scan_protocol: Scanning was performed by Nimblegen using their standard protocol

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: sox10:GFP transgenic

label_protocol: Labeling was performed by Nimblegen using their standard protocol

growth_protocol: Sox10:GFP transgenic fish were raised in our in house facility

extract_protocol: Trizol reagent was used to make RNA and cDNA library was generated using WTA2 kit from Sigma

treatment_protocol: GFP positive and negative cells were sorted using BD Aria FACS

tag: gfp detection

value: GFP positive

tag: treatment

value: mRNAinjected

tag: phenotype

value: reduced head skeleton


title: dcr1ΔC33 tiling array 1


title: GFPpositive treated3

description: GFPpositivetreated

value: morpholino oligonucleotides


title: GFPnegative treated3

description: GFPnegativetreated

value: GFP negative


title: GFPpositive treated2

description: twistMOGFPpositive


title: GFPpositive control2

description: uninjectedGFPpositive

value: normal


title: GFPnegative control3

description: GFPnegativecontrol


title: dcr1Δ tiling array 3

source_name: dcr1Δ total RNA


title: dcr1Δ tiling array 2


title: GFPpositive control3

description: GFPpositivecontrol


title: GFPnegative control2

description: uninjectedGFPnegative


title: GFPpositive treated1

description: GFPpositivetreated


title: GFPnegative control1

description: GFPnegativecontrol


title: GFPnegative treated1

description: GFPnegativetreated


title: dcr1Δ tiling array 1


title: wild-type tiling array 3

source_name: wild-type total RNA


title: wild-type tiling array 2


title: GFPpositive mutant H3.3 injected1


title: wild-type tiling array 1


title: S0162

city: Rockville

first: Melissa

last: Rotunno

state: MD

address: 6120 Executive Blvd

department: DCEG

institute: NIH/NCI

description: Case Excluded

hyb_protocol: 10 ug fragmented cRNA were hybridized for 16 hr at 45C on GeneChip H133-A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: Gene expression data were processed and normalized using Bioconductor Affy package, based on the Robust Multichip Average (RMA) method5 for single-channel Affymetrix chips

source_name: Blood from Case Excluded

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA and following clean-up with Qiagen Rneasy Mini Kit were performed according to the manufacturers instructions

tag: case status

value: Case

tag: Stage

value: IIB

tag: morphology

value: Squamous Cell Carcinoma

tag: smoking status

value: Former


title: S0161

description: Case

source_name: Blood from Case

value: Adenocarcinoma


title: KBD -Control replicate 1

city: Xi'an

first: xiaoming

last: wu

address: Xiangningxi Road No.28

institute: Xi'anjiaotongUniversity

description: ratio of expression between control individuals and KBD  patient experiment 1

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: the microarray slides were scanned using Gene-Pix 4000B (Axon Instruments Inc., Foster City, California, USA), which used a 532nm laser for Cy3 measurement and a 635nm laser for Cy5 measurement.

data_processing: Sixteen-bit TIFF images produced by the Axon scanner were analyzed using the GenePixPro 3.0 software package (Axon Instruments Inc.).

source_name: KBD PBMCs

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Three milliliters of peripheral blood was collected from each subject into heparinized vacutainer tubes , kept in 4 ºC

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

value: peripheral blood mononuclear cells (PBMCs)

tag: diagnosis

value: Kashin-Beck disease

source_name: Control PBMCs

value: healthy


title: KBD -Control replicate 3

description: ratio of expression between control individuals and KBD  patient experiment 3


title: S0160

description: Case

value: IIIA


title: P5323

city: Stony Brook

first: Laura

middle: E.

last: Hogan

state: New York

department: Department of Pediatrics

institute: Stony Brook University

hyb_protocol: Hybridized as per manufacturer's instructions at Service XS (www.servicexs.com)

scan_protocol: Scanned as per manufacturer's instructions at Service XS (www.servicexs.com)

data_processing: Data was extracted and background normalized using the Illumina GenomeStudio Methylation (M) Module 1.0

label: Cy5 and Cy3

source_name: Remission

label_protocol: Labelled as per manufacturer's instructions at Service XS (www.servicexs.com). DNA is whole-genome amplified, hybridized to locus-specific DNA oligomers linked to individual bead types. There are two bead types that correspond to the methylated (C) and the the unmethylated (T) state. Allele-specific primer annealing is followed by single-base extension using DNP- and Biotin-labeled ddNTPs. After extension, the array is fluorescently stained, scanned, and the intensities of the unmethylated and methylated bead types measured.)

growth_protocol: Ficoll-enriched, cryopreserved paired diagnosis/relapse bone marrow samples were obtained from patients with relapsed B-precursor acute lymphoblastic leukemia.

extract_protocol: DNA was isolated using Qiagen Gentra Puregene Core Kit A (Valencia, CA).

treatment_protocol: Leukemic bone marrow samples were used for DNA extraction without further treatment

value: bone marrow


title: P5335


title: S0158

description: Control

source_name: Blood from Control

value: Control

value: Never


title: KBD -Control replicate 2

description: ratio of expression between control individuals and KBD  patient experiment 2


title: S0154

description: Control


title: P5324

source_name: Diagnosis


title: S0156

description: Case Excluded

value: IIA


title: S0155

description: Control


title: S0157

description: Control

value: Current


title: P5294


title: S0153

description: Control


title: P5320


title: P5295


title: S0159

description: Case

value: IV


title: P5336


title: P5312


title: P5321


title: P5272


title: S0149

description: Case

value: IIIB


title: S0150

description: Control


title: S0151

description: Control


title: S0148

description: Case


title: S0147

description: Control


title: S0144

description: Control


title: P5065


title: P5062


title: P5064


title: P5313


title: S0152

description: Case

value: IA


title: P5260


title: S0145

description: Control


title: P5271


title: P5060


title: P5261


title: P5061


title: P5063


title: S0142

description: Control


title: S0143

description: Case Excluded

value: Case


title: S0146

description: Case


title: P5100


title: S0141

description: Control


title: S0136

description: Case


title: S0139

description: Control


title: P5097


title: P5054


title: P5096


title: P5055


title: P5093


title: S0138

description: Control


title: P5092


title: S0140

description: Control


title: S0133

description: Case


title: P5101


title: P5051


title: S0137

description: Control


title: S0134

description: Control


title: S0132

description: Control


title: GFPpositive control1

description: GFPpositivecontrol

value: GFP positive

value: normal


title: S0131

description: Case

value: IB


title: P5050


title: S0130

description: Control

value: Former


title: S0135

description: Control


title: P5255


title: S0124

description: Control


title: S0129

description: Control


title: S0125

description: Case

value: Adenocarcinoma


title: GFPpositive wildtype H3.3 injected1

value: mRNAinjected


title: S0128

description: Control


title: S0123

description: Control


title: P5077


title: S0127

description: Case

value: IIB


title: P5041


title: S0119

description: Case


title: S0121

description: Control


title: S0126

description: Control


title: P5068


title: P5076


title: P5253


title: S0120

description: Control


title: KBD -Control replicate 4

description: ratio of expression between control individuals and KBD  patient experiment 4

value: peripheral blood mononuclear cells (PBMCs)

value: Kashin-Beck disease

value: healthy


title: P5069

value: bone marrow


title: P5045


title: P3285


title: P5079


title: P5283


title: S0122

description: Control

value: Control


title: P5284


title: S0118

description: Control


title: P5078


title: P5279


title: P3284


title: S0112

description: Case

value: Never


title: S0115

description: Control

value: Current


title: S0116

description: Case


title: S0113

description: Case Excluded

value: Large Cell Carcinoma


title: P3279


title: S0111

description: Control


title: P5028


title: S0114

description: Control


title: P5278


title: S0117

description: Control


title: S0110

description: Case

value: IV


title: P5276


title: P3287


title: S0108

description: Control


title: P5029


title: S0107

description: Case

value: Case


title: P5330


title: S0106

description: Control


title: P5329


title: P5275


title: S0109

description: Control


title: P3288


title: P5310


title: P3278


title: P5338


title: S0104

description: Control


title: P5339


title: S0105

description: Control


title: P5309


title: S0103

description: Case

value: IIA


title: S0102

description: Case


title: S0101

description: Control


title: S0095

description: Case


title: P5273


title: S0098

description: Case


title: S0099

description: Control


title: S0094

description: Control


title: S0100

description: Case Excluded

value: Squamous Cell Carcinoma


title: P5281


title: S0092

description: Case

value: IB


title: S0093

description: Control

value: Former


title: S0088

description: Case

value: IA

value: Adenocarcinoma


title: P5274


title: S0090

description: Case

value: IIB


title: S0097

description: Case


title: S0086

description: Control


title: S0089

description: Control


title: P5067


title: S0087

description: Case Excluded


title: S0084

description: Control


title: S0091

description: Control


title: P5282


title: P5066


title: P5257


title: S0083

description: Control


title: S0081

description: Control


title: S0082

description: Control


title: S0080

description: Control


title: S0077

description: Case


title: S0076

description: Case


title: S0071

description: Control


title: S0070

description: Case


title: S0078

description: Case


title: S0074

description: Case


title: S0079

description: Control


title: S0072

description: Case


title: S0075

description: Case


title: S0068

description: Case


title: S0066

description: Control


title: S0067

description: Control


title: S0064

description: Case


title: S0061

description: Case


title: S0065

description: Control


title: S0058

description: Case


title: S0062

description: Case

value: IIIB


title: S0060

description: Control


title: S0057

description: Control


title: S0055

description: Control


title: S0069

description: Control


title: S0059

description: Case


title: S0054

description: Case

value: IIIA


title: S0056

description: Control


title: S0063

description: Case


title: S0053

description: Control


title: S0052

description: Case


title: S0048

description: Non Case Excluded

source_name: Blood from Non Case Excluded

value: Non Case


title: S0050

description: Case


title: S0085

description: Control


title: S0051

description: Case


title: SHAM

city: Columbia

first: Jennifer

last: McLarty

state: SC

address: 6349 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina-School of Medicine

description:
Control
Avg Ct_Sham
4 replicates were performed (Rat10_Sham, Rat11_Sham, Rat12_Sham, and Rat13_Sham)

scan_protocol: TaqMan arrays were run on a 7900HT Thermocycler (Applied Biosystems) using Sequence Detection Systems (SDS) software version 2.3. A single TLDA was used per Abeta or control-treated sample.

data_processing: Manual inspection of all amplification plots was performed and genes were excluded from the analysis if: Ct values were too high (above 38, indicating a gene expression too low for accurate detection), if amplification was not achieved in all samples, or if extremely high variation was found. Data analysis was performed using SDS RQ manager v1.2 (Applied Biosystems) using the delta-delta Ct method (Schmittgen TD, 2008, Nat Protocols). The endogenous control, 18s, was used for normalization. Fold Change worksheet reports test/control (i.e., (fistula/sham) or (fistula + estrogen/sham)) ratios [provided as a Series supplementary file].

label: SYBR Green

organism: Rattus norvegicus

label_protocol: Gene profiling was accessed Rat TaqMan Low Density  Inflammation Array. RT-PCR  was used to access changes in 96 inflammatory genes as described by the manufacturer's protocol. Briefly, 100 ng of total RNA  was reverse transcribed into cDNA using the reverse trascription kit by Promega obtained from the sham, fistula, and fistula + estrogen animals. The RT product was then mixed with TaquMan Master Mix and loaded on to the Rat Inflammation Low Density PCR Array containing 96 genes of interests.

growth_protocol: Eight week old male were randomly selected for  the following groups : sham, fistula and fistula + estrogen.  Three days following surgery, the LV were excised a processed for RNA isolation.

extract_protocol: LV tissue was homogenized in Trizol (Invitrogen) and chloroform was added in a ratio of 1 ml of Trizol to 0.5 ml of chloroform.  RNA was precipitated with isopropanol then purified using an Rneasy Mini Kit (Qiagen, Germantown, MD) and tested for purity. RNA concentration was determined by optical density at 260 nm. Only samples with an optical density ratio greater than 1.8 at 260/280 nm were selected. RNA was reversed transcribed to cDNA by PCR using the Promega Reverse Transcription System (Madison, WI).  The cDNA was then added to an Applied Biosystems Taqman® Low Density Inflammation Array on a 7900 HT Real–Time PCR System.

treatment_protocol: Estrogen was delivered via a time release 17β-Estradiol pellet, (21 day release pellet, Innovative Research of America, Sarasota, FL.) Pellets were implanted subcutaneously between the shoulder blades two weeks prior to fistula surgery. We have previously found that a dose of 0.02 mg/kg per day produces serum levels of ~35 pg/mL, which was comparable to the average estrogen level in female rats with ovaries (Gardner, 2008 7 /id).

tag: gender

value: male

tag: age

value: 8 weeks

tag: surgery

value: Sham Surgery

tag: time

value: 3 Days

value: Left Ventricle (LV)

tag: treatment of estrogen

value: NO


title: S0040

description: Control

value: Control


title: S0045

description: Case

value: Case

value: IV

value: Never


title: S0038

description: Case

value: Current


title: Male_Fistula

description:
Test
Avg Ct_Male Fistula
4 replicates were performed (Rat1_male_fist, Rat2_male_fist, Rat3_male_fist, and Rat 4_male_fistula)

value: Fistula Surgery


title: Male_Fistula_Estrogen

description:
Test
Avg Ct_Male Fistula+ Estrogen
4 replicates were performed (Male+Est_1, Male+Est 2, Male+Est 3, and Male+Est 4)

source_name: LV_RNA_Fistula_Surgery+Estrogen Pellet (2 wks)

value: Yes


title: S0037

description: Case

value: IB

value: Adenocarcinoma

value: Former


title: S0047

description: Case


title: S0041

description: Control


title: S0044

description: Control


title: S0096

description: Case

value: IA


title: S0034

description: Case

value: IIIB


title: S0043

description: Control


title: S0033

description: Case

value: IIB


title: S0039

description: Case Excluded

value: Small Cell Carcinoma


title: S0042

description: Case


title: S0049

description: Case


title: S0035

description: Control


title: S0032

description: Case


title: S0036

description: Control


title: S0031

description: Control


title: SAM/R-1 + CE_4

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description:
The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/R-1 with control diet

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 10 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

source_name: hippocampus, SAM/R-1, control diet, reprecate4

label_protocol: Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.

extract_protocol: Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was >9.0.

tag: background strain

value: AKR/J

value: hippocampus

value: male

tag: diet

value: control


title: S0028

description: Control

value: Control


title: S0046

description: Case

value: Case


title: S0030

description: Control


title: S0027

description: Case

value: Never


title: S0029

description: Case


title: SAM/R-1 + CE_2

source_name: hippocampus, SAM/R-1, control diet, reprecate2

tag: tissue


title: Human Control I

city: Boston

first: Douglas

last: Hayden

state: MA

address: 50 Staniford St, Suite 560

institute: Mass General Hospital

description:
Human Control I
I7_HU_MEDIA_100907.CEL

hyb_protocol: Labeled targets were hybridized to Affymetrix  MOE430 2.0 GeneChip microarrays.

scan_protocol: Affymetrix GeneChip Scanner Model 3000 7g, and images processed with GCOS v1.4.

data_processing: The Affymetrix scanner output cel files were uploaded to Partek Genomics Suite (Partek, St. Louis, MO) for normalization (GCRMA sub-routine)

source_name: bone marrow derived macrophages

label_protocol: 1–2 µg of total RNA were used to make single-stranded antisense cDNA with the NuGEN Technologies Ovation Biotin System in accordance with the manufacturer's directions.

growth_protocol: The animal care for these studies was in accordance with institutional guidelines.  Bone marrow derived macrophages were prepared from C57/Bl6 mice as described 1.  Cells were plated in 24 well plates at 106 cells/well in Dulbecco’s modified Eagle’s Medium supplemented with glucose, L-glutamine, penicillin and streptomycin overnight at 37°C 5% CO2, after which the cells were washed three times and replaced with media containing no serum, or 5% fetal calf serum (Cell Gro), 5% mouse serum (Antibodies, Inc.), or 5% human serum (Sigma) and either media control or 25 ng/ml LPS (List).  Sera had been previously heated at 56 °C for 30 minutes to inactivate complement.  Cells were incubated for four hours after washing and media replacement, and then immediately harvested by scraping with a spatula in RLT buffer (Qiagen).

extract_protocol: Total RNA was isolated using the RNeasy kit, which included on-column DNase treatment.  Isolated RNA was quantified, and quality was assessed using an Agilent 2100 BioAnalyzer with the RNA NanoChip (Agilent).

tag: strain

tag: cell type

value: BMDM

tag: sera

value: Human

tag: experiment

value: I


title: S0025

description: Case

tag: case status


title: No Serum Control I

description:
No Serum Control I
I5_SF_media_100907.CEL

treatment_protocol: The animal care for these studies was in accordance with institutional guidelines.  Bone marrow derived macrophages were prepared from C57/Bl6 mice as described 1.  Cells were plated in 24 well plates at 106 cells/well in Dulbecco’s modified Eagle’s Medium supplemented with glucose, L-glutamine, penicillin and streptomycin overnight at 37°C 5% CO2, after which the cells were washed three times and replaced with media containing no serum, or 5% fetal calf serum (Cell Gro), 5% mouse serum (Antibodies, Inc.), or 5% human serum (Sigma) and either media control or 25 ng/ml LPS (List).  Sera had been previously heated at 56 °C for 30 minutes to inactivate complement.  Cells were incubated for four hours after washing and media replacement, and then immediately harvested by scraping with a spatula in RLT buffer (Qiagen).

value: No Serum

tag: treatment


title: Mouse Control I

description:
Mouse Control I
I8_MS_MEDIA_100907.CEL

value: Mouse


title: S0026

description: Case

tag: Stage

tag: morphology

value: Adenocarcinoma

value: Current


title: SAM/R-1 + CCH_2

description:
The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/R-1 with CCH feeding

source_name: hippocampus, SAM/R-1, CCH, reprecate2

tag: genotype/variation

value: CCH


title: S0021

description: Case

value: IIIB

tag: smoking status

value: Former


title: SAM/R-1 + CCH_3

source_name: hippocampus, SAM/R-1, CCH, reprecate3

value: AKR/J

tag: age

tag: gender


title: SAM/P-8 + CE_3

description:
The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/P-8 with control diet

source_name: hippocampus, SAM/P-8, control diet, reprecate3

value: hippocampus


title: SAM/R-1 + CE_1

source_name: hippocampus, SAM/R-1, control diet, reprecate1

value: male


title: No Serum LPS I

description:
No Serum LPS I
I2_SF_LPS_100907.CEL

value: LPS


title: SAM/P-8 + CE_4

source_name: hippocampus, SAM/P-8, control diet, reprecate4

value: control


title: SAM/R-1 + CCH_4

source_name: hippocampus, SAM/R-1, CCH, reprecate4


title: P5258

value: bone marrow


title: S0023

description: Case

source_name: Blood from Case

value: Case

value: IV


title: S0022

description: Case Excluded

source_name: Blood from Case Excluded

value: IA

value: Squamous Cell Carcinoma


title: SAM/R-1 + CCH_1

source_name: hippocampus, SAM/R-1, CCH, reprecate1


title: S0024

description: Case

value: IIIA


title: Calf Control I

description:
Calf Control I
I6_FB_MEDIA_100907.CEL

value: BMDM

value: Calf

value: Control

value: I


title: SAM/P-8 + CE_2

source_name: hippocampus, SAM/P-8, control diet, reprecate2


title: Mouse LPS I

description:
Mouse LPS I
I4_MS_LPS_100907.CEL

value: Mouse


title: Calf LPS I

description:
Calf LPS I
I1_FB_LPS_100907.CEL


title: Human LPS I

description:
Human LPS I
I3_HU_LPS_100907.CEL

value: Human


title: SAM/R-1 + CE_3

source_name: hippocampus, SAM/R-1, control diet, reprecate3

value: AKR/J


title: S0020

description: Case

value: IIB

value: Adenocarcinoma

value: Never


title: SAM/P-8 + CE_1

source_name: hippocampus, SAM/P-8, control diet, reprecate1

value: hippocampus

value: male

value: control


title: S0073

description: Case

value: Case

value: IB


title: Calf LPS H

description:
Calf LPS H
H7_FB_LPS_101007.CEL

value: LPS

value: H


title: SAM/P-8 + CCH_2

description:
The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/P-8 with CCH feeding

source_name: hippocampus, SAM/P-8, CCH, reprecate2

value: CCH


title: No Serum Control H

description:
No Serum Control H
H4_SF_MEDIA_101007.CEL

value: BMDM

value: No Serum


title: S0017

description: Case

value: IIA

value: Former


title: S0016

description: Case

value: IIIA


title: SAM/P-8 + CCH_4

source_name: hippocampus, SAM/P-8, CCH, reprecate4

value: AKR/J


title: S0018

description: Case


title: S0019

description: Case

value: Current


title: No Serum LPS H

description:
No Serum LPS H
H8_SF_LPS_101007.CEL


title: S0014

description: Case

value: Adenocarcinoma


title: Calf Control H

description:
Calf Control H
H3_FB_MEDIA_101107.CEL

value: Calf

value: Control


title: Mouse Control H

description:
Mouse Control H
H1_MS_MEDIA_101007.CEL

value: Mouse


title: S0011

description: Control

source_name: Blood from Control


title: SAM/P-8 + CCH_1

source_name: hippocampus, SAM/P-8, CCH, reprecate1

value: hippocampus

value: male


title: No Serum Control G

description:
No Serum Control G
G8_SF_MEDIA_101107.CEL

source_name: bone marrow derived macrophages

value: G


title: Human Control H

description:
Human Control H
H2_HU_MEDIA_101007.CEL

value: Human


title: SAM/P-8 + CCH_3

source_name: hippocampus, SAM/P-8, CCH, reprecate3


title: Human LPS H

description:
Human LPS H
H6_HU_LPS_101007.CEL

value: LPS

value: H


title: S0012

description: Control


title: Mouse LPS H

description:
Mouse LPS H
H5_MS_LPS_101007.CEL

value: BMDM


title: S0015

description: Case

value: Case

value: IB

value: Never


title: S0013

description: Control


title: Control – Frozen 6 day old Embryos Replicate 1

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

description: Biological Replicate 1 of 3, Control embryos vs. Frozen embryos

hyb_protocol: Hibridization was done using Agilent Gene Expression Hybridization Kit, following manufacturer's instructions. After 17 hours at 65ºC on a , hybridised slides  were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background correction and LOWESS normalization.

organism: Oryctolagus cuniculus

source_name: Control 6 day old Embryos Replicate 1

label_protocol: Total RNA (100 ng) was labelled using QuickAmp Labelling Kit (Agilent Technologies) following manufacturer's instructions. Excess dye was removed with the  RNAeasy Mini Kit (QIAGEN) and dye incorporation and concentration were determined using the microarray setting on the Nanodrop 1000.

treatment_protocol:
Vitrification: The vitrifcation procedure was carried out in two steps at 20oC. In the frst step, embryos were placed for 2 min in a vitrifcation solution consisting of 12.5% (v/v) dimethyl sulphoxide (3.5 M DMSO, Sigma) and 12.5% (v/v) ethylene glycol (4.4 M EG, Sigma) in DPBS supplemented with 0.2% (w/v) of BSA. In the second step, embryos were suspended for 1 min in a solution of 20% (v/v) DMSO and 20% (v/v) EG in DPBS supplemented with 0.2% (w/v) of BSA. Then embryos suspended in vitrifcation medium were loaded into 0.25 ml plastic straws and two sections of DPBS were added at either end of each straw separated by air bubbles. Finally, straws were sealed and plunged directly into liquid nitrogen. Devitrifcation was performed by immersing the central and final sections of the straws in a water bath at 20oC for 10-15 sec. The vitrifcation medium was eliminated employing a solution of DPBS with 0.33 M sucrose for 5 min and a wash in a solution of DBPS for another 5 min.
Slow-freezing: Embryos were placed successively for 5 min into three different solutions consisting, respectively, of 0.5M, 1M and 1.5M dimethyl sulfoxide (DMSO) in DPBS supplemented with BSA. Then, the embryos suspended in the cryopreservation medium were oaded into 0.125 mL sterile plastic straws, and submited to slow freezing 1oC/min up to -7oC. Five minutes later manual seeding were done, and then embryos were cooled at 0.3oC/min up to -35oC. After that, the straws were plunged directly into liquid nitrogen. Thawing was performed by placing the straws 10 sec in air at room temperature and then in a water bath at 20oC for 1 min. The cryopreservation medium was removed in three steps of 5 min, in which embryos were placed successively in three wash solutions consisting of 1 M, 0.5 M and 0M DMSO in DPBS supplemented with BSA.

value: New Zealand White Rabbit

value: blastocyst

value: 6 days

value: Untreated

source_name: Frozen 6 day old Embryos Replicate 1

value: Frozen


title: Control – Frozen 6 day old Embryos Replicate 3

description: Biological Replicate 3 of 3, Control embryos vs. Frozen embryos

source_name: Control 6 day old Embryos Replicate 3

source_name: Frozen 6 day old Embryos Replicate 3


title: S0010

description: Control

value: Control

value: Current


title: Control – Frozen 6 day old Embryos Replicate 2

description: Biological Replicate 2 of 3, dye swap, Control embryos vs. Frozen embryos

source_name: Frozen 6 day old Embryos Replicate 2

source_name: Control 6 day old Embryos Replicate 2


title: Mouse Control G

description:
Mouse Control G
G6_MS_MEDIA_101107.CEL

value: Mouse


title: S0008

description: Control

value: Former


title: Control – Vitrified 6 day old Embryos Replicate 2

description: Biological Replicate 2 of 3, dye swap, Control embryos vs. Vitrified embryos

source_name: Vitrified 6 day old Embryos Replicate 2

value: Vitrified


title: S0007

description: Control


title: Control – Vitrified 6 day old Embryos Replicate 1

description: Biological Replicate 1 of 3, Control embryos vs. Vitrified embryos

source_name: Vitrified 6 day old Embryos Replicate 1


title: Control – Vitrified 6 day old Embryos Replicate 3

description: Biological Replicate 3 of 3, Control embryos vs. Vitrified embryos

source_name: Vitrified 6 day old Embryos Replicate 3


title: Calf Control G

description:
Calf Control G
G7_FB_MEDIA_101107.CEL

value: Calf

value: G


title: Calf LPS G

description:
Calf LPS G
G3_FB_LPS_101107.CEL

value: LPS


title: S0005

description: Control


title: S0009

description: Control


title: sucrose treatment, biological rep2

first: Francesca

last: Secchi

address: 1300 Centre St

institute: Arnold Arboretum of Harvard University

description: Gene expression data from stems collected after 90 minutes of exposure to sucrose

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affimetrix expression Console 1.1  RMA with default analysis settings.

organism: Populus trichocarpa

source_name: P.trichocarpa stems, plants subjected to sucrose infiltration

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng of total RNA (GeneChip 3'IVT Express Kit, GeneChips® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Populus trichocarpa cuttings were rooted and later on grew for four months in aerated hydroponics containers filled with modified Hoagland solution.

extract_protocol: Total RNA was extracted according to Chang et al.’s protocol (Chang et al., 1993)

treatment_protocol: plants were grown in hydroponic solution for 3 months, embolism was induced using positive pressure applied to stem (1MPa), sucrossolution was applied to hudroponic solution at the level of 1 MPa water potential

value: xylem

value: plants grown for 3 months in hydroponics from cuttings


title: S0003

description: Case

source_name: Blood from Case

value: Case

value: IIIA

value: Adenocarcinoma


title: S0006

description: Control


title: embolism treatment, biological rep1

description: Gene expression data from stems collected 90 minutes following the embolism induction

source_name: P.trichocarpa stems, plants subjected to artificial embolism


title: embolism treatment, biological rep2

value: stems collected 90 minutes following the embolism induction


title: Non-metastatic LN EC, biological rep 1

city: Clayton

first: Rae

last: Farnsworth

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

description: Gene expression data from endothelial cells isolated from draining LNs of tumors

hyb_protocol: Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.

data_processing: The raw signal intensity values were normalised using Robust Multiarray Analysis and linear modelling in AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9)

source_name: endothelial cells from lymph nodes draining non-metastatic (no VEGF-D) tumors

label_protocol: Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: To create tumors, 2.5 x 10^7 293-VEGF-D (metastatic) or 293-Apex (non-metastatic) tumor cells were injected subcutaneously into the left flank of female SCID/NOD mice. The left axillary lymph node which drains this tumor site was harvested when the tumors reached 1600-2500 mm^3 (3-4 weeks). LNs were then digested enzymatically, after which tumor cells and leukocytes were depleted via immunomagnetic selection for class I HLA and CD16/CD32 respectively. The resulting LN stromal cells were cultured briefly in EGM-2 MV growth medium with supplements (Cambrex/Lonza). Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node.

extract_protocol: RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.

value: enriched endothelial cell fraction from tumor-draining lymph nodes

value: SCID/NOD

value: female

value: 6-8 weeks

tag: sorting

value: No depletion prior to culture and endothelial cell positive selection


title: S0002

description: Case


title: Non-metastatic LN EC, biological rep 2


title: Human LPS G

description:
Human LPS G
G1_HU_LPS_101107.CEL

value: BMDM

value: Human


title: Human Control G

description:
Human Control G
G5_HU_MEDIA_101107.CEL

value: Control


title: control plants, biological rep2

description: Gene expression data from stem of control plants

source_name: P.trichocarpa stems, control plants


title: control plants, biological rep3


title: Mouse LPS G

description:
Mouse LPS G
G2_MS_LPS_101107.CEL

value: Mouse


title: sucrose treatment, biological rep3

value: stems collected after 90 minutes of exposure to sucrose


title: sucrose treatment, biological rep1


title: normal bone marrow sample 4

status: Public on Sep 22 2011

first: Changmeng

last: Cai

address: 330 Brookline Avenue

department: hematology-oncology

institute: Beth Israel Deaconess Medical Center

description: gene expression data from normal bone marrow sample #82

hyb_protocol: After fragmentation, cRNA target were hybridized to Affymetrix 133A oligonucleotide microarrays

scan_protocol: High resolution GeneArray 3000 scaner

data_processing: Expression values were derived by probe set level analysis from the raw CEL files with R statitical software and BioConductor packages and libraries.

source_name: Normal bone marrow

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

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

treatment_protocol: 22 primary cancer were hormone-naïve, while 29 metastatic cancer were castration-resistant (ADT treated).

tag: metastasis

value: normal

value: negative


title: S0004

description: Case

value: IIIB

value: Former


title: normal bone marrow sample 3

description: gene expression data from normal bone marrow sample #61


title: prostate cancer sample 51

description: gene expression data from prostate cancer sample #125

source_name: Bone metastatic prostate cancer

value: bone metastases (CRPC)

tag: androgen deprivation

value: yes

value: positive


title: No Serum LPS G

description:
No Serum LPS G
G4_SF_LPS_101107.CEL

source_name: bone marrow derived macrophages

value: No Serum

value: LPS

value: G


title: normal bone marrow sample 2

description: gene expression data from normal bone marrow sample #48


title: Metastatic (VEGF-D) LN EC, biological rep 2

source_name: endothelial cells from lymph nodes draining metastatic (VEGF-D-overexpressing) tumors

value: enriched endothelial cell fraction from tumor-draining lymph nodes

value: SCID/NOD

value: female

value: 6-8 weeks

value: Tumor cells and leukocytes depleted before culture and endothelial cell positive selection


title: control plants, biological rep1

value: xylem

value: plants grown for 3 months in hydroponics from cuttings


title: S0001

description: Case

value: Case

value: IIB

value: Adenocarcinoma


title: prostate cancer sample 48

description: gene expression data from prostate cancer sample #117

value: negative


title: Metastatic (VEGF-D) LN EC, biological rep 1


title: normal bone marrow sample 1

description: gene expression data from normal bone marrow sample #43

value: normal


title: prostate cancer sample 50

description: gene expression data from prostate cancer sample #122

value: bone metastases (CRPC)

value: yes


title: prostate cancer sample 42

description: gene expression data from prostate cancer sample #66


title: prostate cancer sample 41

description: gene expression data from prostate cancer sample #64


title: prostate cancer sample 49

description: gene expression data from prostate cancer sample #118

value: positive


title: prostate cancer sample 34

description: gene expression data from prostate cancer sample #51


title: prostate cancer sample 38

description: gene expression data from prostate cancer sample #55


title: prostate cancer sample 43

description: gene expression data from prostate cancer sample #67


title: prostate cancer sample 47

description: gene expression data from prostate cancer sample #108


title: prostate cancer sample 37

description: gene expression data from prostate cancer sample #54


title: prostate cancer sample 40

description: gene expression data from prostate cancer sample #60


title: prostate cancer sample 33

description: gene expression data from prostate cancer sample #50


title: prostate cancer sample 39

description: gene expression data from prostate cancer sample #57


title: prostate cancer sample 45

description: gene expression data from prostate cancer sample #74


title: prostate cancer sample 32

description: gene expression data from prostate cancer sample #49


title: prostate cancer sample 35

description: gene expression data from prostate cancer sample #52


title: prostate cancer sample 31

description: gene expression data from prostate cancer sample #45


title: prostate cancer sample 44

description: gene expression data from prostate cancer sample #71


title: prostate cancer sample 27

description: gene expression data from prostate cancer sample #28


title: prostate cancer sample 36

description: gene expression data from prostate cancer sample #53


title: prostate cancer sample 24

description: gene expression data from prostate cancer sample #24


title: prostate cancer sample 28

description: gene expression data from prostate cancer sample #31


title: prostate cancer sample 25

description: gene expression data from prostate cancer sample #25


title: prostate cancer sample 26

description: gene expression data from prostate cancer sample #27


title: prostate cancer sample 23

description: gene expression data from prostate cancer sample #14


title: prostate cancer sample 22

description: gene expression data from prostate cancer sample #326

source_name: Primary localized prostate cancer

value: localized prostate cancer

value: no


title: prostate cancer sample 30

description: gene expression data from prostate cancer sample #39


title: prostate cancer sample 29

description: gene expression data from prostate cancer sample #36


title: prostate cancer sample 20

description: gene expression data from prostate cancer sample #316


title: prostate cancer sample 18

description: gene expression data from prostate cancer sample #553A


title: prostate cancer sample 15

description: gene expression data from prostate cancer sample #418B


title: prostate cancer sample 19

description: gene expression data from prostate cancer sample #553B


title: prostate cancer sample 14

description: gene expression data from prostate cancer sample #419A


title: prostate cancer sample 11

description: gene expression data from prostate cancer sample #319A


title: embolism treatment, biological rep3

description: Gene expression data from stems collected 90 minutes following the embolism induction


title: prostate cancer sample 13


title: prostate cancer sample 16

description: gene expression data from prostate cancer sample #580A


title: prostate cancer sample 12

description: gene expression data from prostate cancer sample #418A


title: prostate cancer sample 5

description: gene expression data from prostate cancer sample #368


title: prostate cancer sample 7

description: gene expression data from prostate cancer sample #224A


title: prostate cancer sample 6

description: gene expression data from prostate cancer sample #371


title: prostate cancer sample 4

description: gene expression data from prostate cancer sample #361


title: prostate cancer sample 8

description: gene expression data from prostate cancer sample #224B


title: prostate cancer sample 10

description: gene expression data from prostate cancer sample #228B


title: prostate cancer sample 3

description: gene expression data from prostate cancer sample #358


title: prostate cancer sample 2

description: gene expression data from prostate cancer sample #223


title: indRKD4ox (UAS-RKD4 35S-GVG) seedlings, biological rep1

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

description: Gene expression data from DEX-inducible RKD4-overexpressing seedlings treated for 24 hrs with DEX.

hyb_protocol: Hybridization, washing, and staining procedures were conducted with the Fluidics Station 450 as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: The scanning procedure was conducted with the GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS) using default analysis settings.

organism: Arabidopsis thaliana

source_name: Transgenic Arabidopsis seedlings harboring the UAS-RKD4 and 35S-GVG transgenes, three days after germination

label_protocol: Biotin-labelled cRNA was prepared using the Affymetrix GeneChip 3' IVT Expression Kit.

growth_protocol: Sterilized Arabidopsis seeds were plated on a nutrient agar medium and grown at 23 ˚C with a 16h-light/8h-dark cycle.

extract_protocol: For each replicate, RNA was extracted from 60 seedlings using the RNeasy Plant Mini Kit (QIAGEN) accrding to the manufacturer's protocol.

treatment_protocol: Two days after germination, seedlings were transferred to a nutrient agar medium containing 1 microM of Dexamethasone (DEX).

value: UAS-RKD4 35S-GVG

tag: ecotype

value: seedlings

tag: developmental stage

value: 3 days after germination

tag: sample type

value: overexpressing RKD4


title: prostate cancer sample 9

description: gene expression data from prostate cancer sample #228A


title: indRKD4ox (UAS-RKD4 35S-GVG) seedlings, biological rep2

tag: strain

tag: tissue


title: prostate cancer sample 17

description: gene expression data from prostate cancer sample #580B


title: CD1 MEFs_rep3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with RMA as background correction, summarization & normalization method.

source_name: Mouse embryonic fibroblasts

label_protocol: Whole transcript sense target labeling assay

growth_protocol: Low passage primary MEFs were grown in DMEM (Wisent) supplemented with 10% FBS (Wisent), 10 μg/mL penicilin and streptomysin (Sigma), and 2 mM L-glutamine (Sigma). J1 ES cells and iPS cell clones were grown on arrested feeder cells under standard conditions in the presence of LIF. EOS3F-24, -28, and -29 iPS cells were mantained under 1 μg/ml puromycin selection.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: 2i conversion was performed using MEK inhibitor (2 μM) and GSK inhibitor (12 μM) from StemGent in LIF supplemented ES media.

tag: cell type

value: Mouse embryonic fibroblasts


title: CD1 MEFs_rep2


title: prostate cancer sample 1

description: gene expression data from prostate cancer sample #215


title: EOS3F-28_rep2

source_name: Full iPS cells

value: Full iPS cells


title: EOS3F-28_rep3


title: CD1 MEFs_rep1


title: Control (35S-GVG) seedlings, biological rep2

description: Gene expression data from control seedlings treated for 24 hrs with DEX.

source_name: Transgenic Arabidopsis seedlings harboring the 35S-GVG transgene, three days after germination

value: control


title: L. lactis 3 h starvation ILV10 medium replicate 3

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description: characterization of L. lactis response to isoleucine starvation

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr).. Data were normalized by the all spot’s mean with Bioplot software.

organism: Lactococcus lactis

source_name: L. lactis IL1403 3h starvation

growth_protocol: see manuscript in preparation Dressaire et al. 2008. Dynamic characterization of isoleucine starvation in Lactococcus lactis.

tag: strain IL1403

tag: 3h starvation


title: L. lactis 3 h starvation ILV10 medium replicate 2

scan_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.


title: L. lactis 1.34 h starvation ILV10 medium replicate 3

source_name: L. lactis IL1403 1.34h starvation

label_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

tag: 1.34h starvation


title: Day 3 of ES cell differentiation, untreated

city: Saint Louis

last: Gill

state: MO

address: 660 South Euclid Ave.

department: Pathology/Immunology

institute: Washington University School of Medicine

description:
ESCSnail_DKK_24h.CEL
Gene expression data from day 3 of differentiation of ES cells in DKK1

hyb_protocol: The Affymetrix operating system (Command Console) was used to manage the washing and hybridization steps.

scan_protocol: The Affymetrix operating system (Command Console) was used for scanning.  Affymetrix analysis software (Genotyping Console) was used to derive Quality Control metrics, create .cel files and scaled expression data from the scanned Expresison array image files

data_processing: The data were analyzed with dChip 2008 using default analysis settings.  All samples were normalized to a single baseline array of median intensity (87).

source_name: A2.snail, DKK treatment, day 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: ES cells were differentiated as embryoid bodies in petri dishes at a density of 15,000 cells/mL in differentiation media consisting of 10% FCS and DKK1.

extract_protocol: RNA was isolated using Qiagen RNeasy kit per the manufacture's instructions.

treatment_protocol: In DKKdox conditions, doxycycline was added for a final concentration of 250ng/mL on day 2

value: mouse embryonic stem cells

tag: cell line

tag: protocol

tag: agent

value: untreated

tag: time

value: day 3 day of differentiation


title: Day 2.5 of ES cell differentiation, untreated

description:
ESCSnail_DKK_12h.CEL
Gene expression data from day 2.5 of differentiation of ES cells in DKK1

source_name: A2.snail, DKK treatment, day 2.5

value: day 2.5 day of differentiation


title: EOS3F-29_rep1


title: L. lactis 3 h starvation ILV10 medium replicate 1

extract_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.


title: EOS3F-28_rep1


title: Day 2.5 of ES cell differentiation, dox-induced Snail

description:
ESCSnail_DKKdox_12h.CEL
Gene expression data from day 2.5 of differentiation of ES cells inducibly expressing Snail in DKK1

source_name: A2.snail, DKK+dox treatment, day 2.5

value: inducible expression of Snail

value: doxycycline

tag: dose

value: 250 ng/mL

tag: time post-dox

value: 12 hrs


title: Control (35S-GVG) seedlings, biological rep1


title: EOS3F-29_rep3


title: Day 3 of ES cell differentiation, dox-induced Snail

description:
ESCSnail_DKKdox_24h.CEL
Gene expression data from day 3 of differentiation of ES cells inducibly expressing Snail in DKK1

source_name: A2.snail, DKK+dox treatment, day 3

value: 24 hrs


title: L. lactis 1.34 h starvation ILV10 medium replicate 2


title: L. lactis 1.34 h starvation ILV10 medium replicate 1


title: EOS3F-29_rep2


title: EOS3F-24_rep2

source_name: Partial iPS cells

value: Partial iPS cells


title: Day 2.25 of ES cell differentiation, dox-induced Snail

description:
ESCSnail_DKKdox_6h.CEL
Gene expression data from day 2.25 of differentiation of ES cells inducibly expressing Snail in DKK1

source_name: A2.snail, DKK+dox treatment, day 2.25

value: 6 hrs

value: day 2.25 day of differentiation


title: L. lactis 20 min starvation ILV10 medium replicate 3

source_name: L. lactis IL1403 20 min starvation

tag: 20 min starvation


title: EOS3F-24_rep1


title: J1_ESCs_rep3

source_name: J1 Embryonic stem cells

value: J1 Embryonic stem cells


title: L. lactis 20 min starvation ILV10 medium replicate 2


title: prostate cancer sample 46

description: gene expression data from prostate cancer sample #79

source_name: Bone metastatic prostate cancer

tag: metastasis

value: bone metastases (CRPC)

tag: androgen deprivation

value: yes

value: negative


title: Day 2.25 of ES cell differentiation, untreated

description:
ESCSnail_DKK_6h.CEL
Gene expression data from day 2.25 of differentiation of ES cells in DKK1

source_name: A2.snail, DKK treatment, day 2.25

value: control


title: L. lactis 20 min starvation ILV10 medium replicate 1


title: day 5 of ES cell differentiation, dox-induced miR-200c/141

description:
ESC200c_Ntdox_day5.CEL
Gene expression data from day 5 of differentiation of ES cells inducibly expressing miR-200c/miR-141

source_name: A2.miR200c, Dox treatment, day 5

growth_protocol: ES cells were differentiated as embryoid bodies in petri dishes at a density of 15,000 cells/mL in differentiation media consisting of 10% FCS.

treatment_protocol: In Ntdox conditions, doxycycline was added for a final concentration of 500ng/mL on days 2 and 4

value: mouse embryonic stem cells

value: inducible expression of miR-200c/miR-141

value: 500 ng/mL

value: day 5 of differentiation


title: J1_ESCs_rep2


title: EOS3F-24_rep3


title: L. lactis exponential phase ILV10 medium replicate 3

source_name: L. lactis IL1403 exponential phase

tag: exponential phase