title: NCI-H226_Passage 10 xenograft_R5

description:
NCI-H226 P10 T5
Gene expression data from NCI-H226 Passage 10 xenograft.

source_name: NCI-H226, passage 10 xenograft

value: squamous carcinoma lung


title: prostate_cancer_primary_231

status: Public on Jul 01 2013

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

country: USA

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using fRMA package (v.1.4.0) and Bioconductor (v.2.8). The data matrix (available on Series records) contains quantile normalized PSR (probe selection regions) level expression values from fRMA.
probe group file: HuEx-1_0-st-v1.r2.pgf

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 2.0 (NuGEN)

growth_protocol: not applicable

extract_protocol: RNA was extracted from four 10 um FFPE sections. The highest Gleason grade was macrodissected from surrounding non-neoplastic cells, guided by an H&E stained slide for tumor identification. RNA was extracted and purified using the Roche HighPure FFPE kit.

treatment_protocol: not applicable

tag: gleason score

tag: metastatic event


title: prostate_cancer_primary_230


title: NCI-H23_Passage 1 xenograft_R2

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description:
NCI-H23 P01 T2
Gene expression data from NCI-H23 Passage 1 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

label: Biotin

source_name: NCI-H23, passage 1 xenograft

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).

tag: originating cell line

tag: tumor type

value: adenocarcinoma NSCLC lung

tag: in vivo passage


title: NCI-H23_Passage 1 xenograft_R1

description:
NCI-H23 P01 T1
Gene expression data from NCI-H23 Passage 1 xenograft.


title: NCI-H23_Passage 1 xenograft_R3

description:
NCI-H23 P01 T3
Gene expression data from NCI-H23 Passage 1 xenograft.


title: prostate_cancer_primary_232


title: NCI-H226_Passage 10 xenograft_R3

description:
NCI-H226 P10 T3
Gene expression data from NCI-H226 Passage 10 xenograft.


title: prostate_cancer_primary_229


title: NCI-H226_Passage 10 xenograft_R4

description:
NCI-H226 P10 T4
Gene expression data from NCI-H226 Passage 10 xenograft.


title: NCI-H226_Passage 10 xenograft_R2

description:
NCI-H226 P10 T2
Gene expression data from NCI-H226 Passage 10 xenograft.


title: prostate_cancer_primary_228


title: prostate_cancer_primary_226


title: prostate_cancer_primary_225


title: prostate_cancer_primary_227


title: prostate_cancer_primary_224


title: NCI-H226_Passage 4 xenograft_R4

description:
NCI-H226 P04 T4
Gene expression data from NCI-H226 Passage 4 xenograft.

source_name: NCI-H226, passage 4 xenograft


title: prostate_cancer_primary_223


title: NCI-H226_Passage 10 xenograft_R1

description:
NCI-H226 P10 T1
Gene expression data from NCI-H226 Passage 10 xenograft.


title: prostate_cancer_primary_222


title: NCI-H226_Passage 1 xenograft_R2

description:
NCI-H226 P01 T2
Gene expression data from NCI-H226 Passage 1 xenograft.

source_name: NCI-H226, passage 1 xenograft


title: NCI-H226_Passage 4 xenograft_R2

description:
NCI-H226 P04 T2
Gene expression data from NCI-H226 Passage 4 xenograft.


title: NCI-H226_Passage 4 xenograft_R1

description:
NCI-H226 P04 T1
Gene expression data from NCI-H226 Passage 4 xenograft.


title: prostate_cancer_primary_220


title: prostate_cancer_primary_219


title: prostate_cancer_primary_218


title: NCI-H226_Passage 1 xenograft_R1

description:
NCI-H226 P01 T1
Gene expression data from NCI-H226 Passage 1 xenograft.


title: NCI-H226_Passage 4 xenograft_R5

description:
NCI-H226 P04 T5
Gene expression data from NCI-H226 Passage 4 xenograft.


title: prostate_cancer_primary_217


title: NCI-H226_Passage 4 xenograft_R3

description:
NCI-H226 P04 T3
Gene expression data from NCI-H226 Passage 4 xenograft.


title: prostate_cancer_primary_216


title: NCI-H226_originating cell line_R2

description:
NCI-H226 P0 T2
Gene expression data from NCI-H226 originating cell line.

source_name: NCI-H226, originating cell line


title: prostate_cancer_primary_215


title: MOLT-4_Passage 10 xenograft_R5

description:
MOLT-4 P10 T5
Gene expression data from MOLT-4 Passage 10 xenograft.

source_name: MOLT-4, passage 10 xenograft

value: acute lymphoblastic leukemia


title: NCI-H226_originating cell line_R1

description:
NCI-H226 P0 T1
Gene expression data from NCI-H226 originating cell line.


title: NCI-H226_originating cell line_R3

description:
NCI-H226 P0 T3
Gene expression data from NCI-H226 originating cell line.


title: prostate_cancer_primary_221


title: prostate_cancer_primary_214


title: MOLT-4_Passage 10 xenograft_R4

description:
MOLT-4 P10 T4
Gene expression data from MOLT-4 Passage 10 xenograft.


title: MOLT-4_Passage 10 xenograft_R3

description:
MOLT-4 P10 T3
Gene expression data from MOLT-4 Passage 10 xenograft.


title: MOLT-4_Passage 10 xenograft_R2

description:
MOLT-4 P10 T2
Gene expression data from MOLT-4 Passage 10 xenograft.


title: MOLT-4_Passage 10 xenograft_R1

description:
MOLT-4 P10 T1
Gene expression data from MOLT-4 Passage 10 xenograft.


title: prostate_cancer_primary_212


title: prostate_cancer_primary_208


title: prostate_cancer_primary_209


title: prostate_cancer_primary_211


title: prostate_cancer_primary_210


title: MOLT-4_Passage 4 xenograft_R2

description:
MOLT-4 P04 T2
Gene expression data from MOLT-4 Passage 4 xenograft.

source_name: MOLT-4, passage 4 xenograft


title: prostate_cancer_primary_207


title: prostate_cancer_primary_204


title: prostate_cancer_primary_206


title: prostate_cancer_primary_205


title: MOLT-4_Passage 4 xenograft_R3

description:
MOLT-4 P04 T3
Gene expression data from MOLT-4 Passage 4 xenograft.


title: MOLT-4_Passage 4 xenograft_R5

description:
MOLT-4 P04 T5
Gene expression data from MOLT-4 Passage 4 xenograft.


title: MOLT-4_Passage 4 xenograft_R4

description:
MOLT-4 P04 T4
Gene expression data from MOLT-4 Passage 4 xenograft.


title: MOLT-4_Passage 1 xenograft_R3

description:
MOLT-4 P01 T3
Gene expression data from MOLT-4 Passage 1 xenograft.

source_name: MOLT-4, passage 1 xenograft


title: prostate_cancer_primary_201


title: prostate_cancer_primary_200


title: prostate_cancer_primary_199


title: MOLT-4_Passage 1 xenograft_R1

description:
MOLT-4 P01 T1
Gene expression data from MOLT-4 Passage 1 xenograft.


title: MOLT-4_Passage 1 xenograft_R5

description:
MOLT-4 P01 T5
Gene expression data from MOLT-4 Passage 1 xenograft.


title: MOLT-4_Passage 1 xenograft_R4

description:
MOLT-4 P01 T4
Gene expression data from MOLT-4 Passage 1 xenograft.


title: MOLT-4_Passage 4 xenograft_R1

description:
MOLT-4 P04 T1
Gene expression data from MOLT-4 Passage 4 xenograft.


title: prostate_cancer_primary_198


title: prostate_cancer_primary_203


title: prostate_cancer_primary_202


title: prostate_cancer_primary_197


title: MOLT-4_Passage 1 xenograft_R2

description:
MOLT-4 P01 T2
Gene expression data from MOLT-4 Passage 1 xenograft.


title: MDA-N_Passage 10 xenograft_R3

description:
MDA-N P10 T3
Gene expression data from MDA-N Passage 10 xenograft.

source_name: MDA-N, passage 10 xenograft

value: MDA-N

value: adenocarcinoma HER2/ERBB2 transfectant of MDA-MB-435 melanoma


title: MOLT-4_originating cell line_R2

description:
MOLT-4 P0 T2
Gene expression data from MOLT-4 originating cell line.

source_name: MOLT-4, originating cell line


title: MDA-N_Passage 10 xenograft_R5

description:
MDA-N P10 T5
Gene expression data from MDA-N Passage 10 xenograft.


title: MDA-N_Passage 10 xenograft_R2

description:
MDA-N P10 T2
Gene expression data from MDA-N Passage 10 xenograft.


title: MDA-N_Passage 10 xenograft_R4

description:
MDA-N P10 T4
Gene expression data from MDA-N Passage 10 xenograft.


title: MOLT-4_originating cell line_R1

description:
MOLT-4 P0 T1
Gene expression data from MOLT-4 originating cell line.


title: MDA-N_Passage 10 xenograft_R1

description:
MDA-N P10 T1
Gene expression data from MDA-N Passage 10 xenograft.


title: prostate_cancer_primary_196


title: MDA-N_Passage 4 xenograft_R5

description:
MDA-N P04 T5
Gene expression data from MDA-N Passage 4 xenograft.

source_name: MDA-N, passage 4 xenograft


title: MOLT-4_originating cell line_R3

description:
MOLT-4 P0 T3
Gene expression data from MOLT-4 originating cell line.


title: MDA-N_Passage 4 xenograft_R4

description:
MDA-N P04 T4
Gene expression data from MDA-N Passage 4 xenograft.


title: prostate_cancer_primary_195


title: MDA-N_Passage 4 xenograft_R1

description:
MDA-N P04 T1
Gene expression data from MDA-N Passage 4 xenograft.


title: prostate_cancer_primary_194


title: prostate_cancer_primary_193


title: MDA-N_Passage 4 xenograft_R2

description:
MDA-N P04 T2
Gene expression data from MDA-N Passage 4 xenograft.


title: prostate_cancer_primary_192


title: prostate_cancer_primary_191


title: prostate_cancer_primary_190


title: MDA-N_Passage 4 xenograft_R3

description:
MDA-N P04 T3
Gene expression data from MDA-N Passage 4 xenograft.


title: prostate_cancer_primary_189


title: prostate_cancer_primary_188


title: prostate_cancer_primary_187


title: prostate_cancer_primary_186


title: prostate_cancer_primary_185


title: prostate_cancer_primary_184


title: prostate_cancer_primary_183


title: prostate_cancer_primary_182


title: MDA-N_Passage 1 xenograft_R4

description:
MDA-N P01 T4
Gene expression data from MDA-N Passage 1 xenograft.

source_name: MDA-N, passage 1 xenograft


title: MDA-N_Passage 1 xenograft_R5

description:
MDA-N P01 T5
Gene expression data from MDA-N Passage 1 xenograft.


title: MDA-N_Passage 1 xenograft_R1

description:
MDA-N P01 T1
Gene expression data from MDA-N Passage 1 xenograft.


title: prostate_cancer_primary_180


title: MDA-N_Passage 1 xenograft_R2

description:
MDA-N P01 T2
Gene expression data from MDA-N Passage 1 xenograft.


title: prostate_cancer_primary_179


title: MDA-N_originating cell line_R2

description:
MDA-N P0 T2
Gene expression data from MDA-N originating cell line.

source_name: MDA-N, originating cell line


title: prostate_cancer_primary_178


title: MDA-MB-435_Passage 10 xenograft_R3

description:
MDA-MB-435 P10 T3
Gene expression data from MDA-MB-435 Passage 10 xenograft.

source_name: MDA-MB-435, passage 10 xenograft

value: melanoma


title: MDA-MB-435_Passage 10 xenograft_R2

description:
MDA-MB-435 P10 T2
Gene expression data from MDA-MB-435 Passage 10 xenograft.


title: prostate_cancer_primary_177


title: MDA-N_originating cell line_R1

description:
MDA-N P0 T1
Gene expression data from MDA-N originating cell line.


title: prostate_cancer_primary_176


title: prostate_cancer_primary_175


title: MDA-MB-435_Passage 1 xenograft_R3

description:
MDA-MB-435 P01 T3
Gene expression data from MDA-MB-435 Passage 1 xenograft.

source_name: MDA-MB-435, passage 1 xenograft


title: MDA-MB-435_Passage 10 xenograft_R1

description:
MDA-MB-435 P10 T1
Gene expression data from MDA-MB-435 Passage 10 xenograft.


title: MDA-MB-435_Passage 1 xenograft_R5

description:
MDA-MB-435 P01 T5
Gene expression data from MDA-MB-435 Passage 1 xenograft.


title: prostate_cancer_primary_173


title: MDA-MB-435_Passage 1 xenograft_R2

description:
MDA-MB-435 P01 T2
Gene expression data from MDA-MB-435 Passage 1 xenograft.


title: MDA-MB-435_Passage 1 xenograft_R4

description:
MDA-MB-435 P01 T4
Gene expression data from MDA-MB-435 Passage 1 xenograft.


title: prostate_cancer_primary_170


title: prostate_cancer_primary_171


title: MDA-MB-435_Passage 4 xenograft_R2

description:
MDA-MB-435 P04 T2
Gene expression data from MDA-MB-435 Passage 4 xenograft.

source_name: MDA-MB-435, passage 4 xenograft


title: MDA-N_Passage 1 xenograft_R3

description:
MDA-N P01 T3
Gene expression data from MDA-N Passage 1 xenograft.


title: prostate_cancer_primary_169


title: prostate_cancer_primary_168


title: MDA-MB-435_Passage 4 xenograft_R5

description:
MDA-MB-435 P04 T5
Gene expression data from MDA-MB-435 Passage 4 xenograft.


title: MDA-MB-435_Passage 4 xenograft_R1

description:
MDA-MB-435 P04 T1
Gene expression data from MDA-MB-435 Passage 4 xenograft.


title: prostate_cancer_primary_174


title: prostate_cancer_primary_172


title: prostate_cancer_primary_213


title: prostate_cancer_primary_167


title: MDA-MB-435_Passage 4 xenograft_R3

description:
MDA-MB-435 P04 T3
Gene expression data from MDA-MB-435 Passage 4 xenograft.


title: prostate_cancer_primary_166


title: MDA-MB-435_originating cell line_R2

description:
MDA-MB-435 P0 T2
Gene expression data from MDA-MB-435 originating cell line.

source_name: MDA-MB-435, originating cell line


title: MDA-MB-435_Passage 4 xenograft_R4

description:
MDA-MB-435 P04 T4
Gene expression data from MDA-MB-435 Passage 4 xenograft.


title: prostate_cancer_primary_164

source_name: primary prostate cancer FFPE tissue sample


title: MDA-MB-435_originating cell line_R1

description:
MDA-MB-435 P0 T1
Gene expression data from MDA-MB-435 originating cell line.


title: prostate_cancer_primary_165


title: MDA-MB-435_Passage 1 xenograft_R1

description:
MDA-MB-435 P01 T1
Gene expression data from MDA-MB-435 Passage 1 xenograft.


title: MDA-MB-231T_Passage 4 xenograft_R3

description:
MDA-MB-231T P04 T3
Gene expression data from MDA-MB-231T Passage 4 xenograft.

source_name: MDA-MB-231T, passage 4 xenograft

value: adenocarcinoma, breast grown from mouse mammary fat pad


title: prostate_cancer_primary_161


title: prostate_cancer_primary_160


title: MDA-MB-231T_Passage 10 xenograft_R3

description:
MDA-MB-231T P10 T3
Gene expression data from MDA-MB-231T Passage 10 xenograft.

source_name: MDA-MB-231T, passage 10 xenograft


title: prostate_cancer_primary_162


title: MDA-MB-231T_Passage 4 xenograft_R4

description:
MDA-MB-231T P04 T4
Gene expression data from MDA-MB-231T Passage 4 xenograft.


title: prostate_cancer_primary_159


title: MDA-MB-231T_Passage 4 xenograft_R2

description:
MDA-MB-231T P04 T2
Gene expression data from MDA-MB-231T Passage 4 xenograft.


title: MDA-MB-231T_Passage 10 xenograft_R5

description:
MDA-MB-231T P10 T5
Gene expression data from MDA-MB-231T Passage 10 xenograft.


title: prostate_cancer_primary_163


title: prostate_cancer_primary_157


title: prostate_cancer_primary_156


title: MDA-MB-231T_Passage 4 xenograft_R1

description:
MDA-MB-231T P04 T1
Gene expression data from MDA-MB-231T Passage 4 xenograft.


title: MDA-MB-231T_Passage 10 xenograft_R2

description:
MDA-MB-231T P10 T2
Gene expression data from MDA-MB-231T Passage 10 xenograft.


title: MDA-MB-231T_Passage 1 xenograft_R5

description:
MDA-MB-231T P01 T5
Gene expression data from MDA-MB-231T Passage 1 xenograft.

source_name: MDA-MB-231T, passage 1 xenograft


title: MDA-MB-231T_Passage 1 xenograft_R4

description:
MDA-MB-231T P01 T4
Gene expression data from MDA-MB-231T Passage 1 xenograft.


title: MCF7_Passage 10 xenograft_R5

description:
MCF7 P10 T5
Gene expression data from MCF7 Passage 10 xenograft.

source_name: MCF7, passage 10 xenograft

value: adenocarcinoma breast


title: prostate_cancer_primary_158


title: MDA-MB-231T_Passage 10 xenograft_R4

description:
MDA-MB-231T P10 T4
Gene expression data from MDA-MB-231T Passage 10 xenograft.


title: MDA-MB-231T_originating cell line_R2

description:
MDA-MB-231T P0 T2
Gene expression data from MDA-MB-231T originating cell line.

source_name: MDA-MB-231T, originating cell line


title: MDA-MB-231T_Passage 1 xenograft_R2

description:
MDA-MB-231T P01 T2
Gene expression data from MDA-MB-231T Passage 1 xenograft.


title: MDA-MB-231T_originating cell line_R1

description:
MDA-MB-231T P0 T1
Gene expression data from MDA-MB-231T originating cell line.


title: MDA-MB-231T_Passage 1 xenograft_R1

description:
MDA-MB-231T P01 T1
Gene expression data from MDA-MB-231T Passage 1 xenograft.


title: prostate_cancer_primary_155


title: prostate_cancer_primary_154


title: MDA-MB-231T_Passage 1 xenograft_R3

description:
MDA-MB-231T P01 T3
Gene expression data from MDA-MB-231T Passage 1 xenograft.


title: prostate_cancer_primary_153


title: prostate_cancer_primary_152


title: prostate_cancer_primary_151


title: spo5

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

country: Japan

institute: University of Tokyo

description: the spo5 mutant under meiosis

hyb_protocol: Hybridization was performed by Filgen, Japan.

scan_protocol: Scanning was performed by Filgen, Japan.

data_processing: Data processing was performed by Filgen, Japan.

organism: Schizosaccharomyces pombe

label_protocol: Labeling was performed by Filgen, Japan.

growth_protocol: Cells of the wild-type (JY882) and spo5∆ (MA482) fission yeast strains were grown to the mid-log phase in liquid MM and shifted to nitrogen-free MM–N at 25ºC. The cells were harvested 6 h after this shift, the tempereture was raised to 34ºC.

extract_protocol: total RNA was extracted by the hot phenol method.

tag: strain

tag: genotype


title: wt

description: wild-type Schizosaccharomyce pombe under meiosis

value: wild-type


title: prostate_cancer_primary_150


title: prostate_cancer_primary_149


title: B. bifidum PRL2010 growth in MRS_1

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C.  5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95°C. Hybridization was performed at 45Â°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner. Laser was set at 33% power and PMT at 650.

data_processing: Data extraction was carried out using CombiMstrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software. All teh procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com).

organism: Bifidobacterium bifidum

source_name: B.bifidum PRL2010 growth in MRS broth

label_protocol: Five µg of the same pool of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.

extract_protocol: Total RNA was isolated using the macaloid acid method and then treated with DNase. Briefly, cell pellets were resuspended in 1 ml of QUIAZOL and placed in a tube containing 0.8 g of glass beads (diameter, 106 um). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to a previously described method (Sambrook et al., 1989).

tag: growth condition

value: in MRS broth


title: B. bifidum PRL2010 growth in mouse feed_2

source_name: B.bifidum PRL2010 growth in mouse feed

growth_protocol: B. bifidum PRL2010 cultures were grown at 37°C in mouse feed

value: in mouse feed


title: B. bifidum PRL2010 growth in mouse feed_1


title: MCF7_Passage 10 xenograft_R3

description:
MCF7 P10 T3
Gene expression data from MCF7 Passage 10 xenograft.


title: MCF7_Passage 10 xenograft_R4

description:
MCF7 P10 T4
Gene expression data from MCF7 Passage 10 xenograft.


title: B. bifidum PRL2010 growth in MRS_2


title: MCF7_Passage 10 xenograft_R2

description:
MCF7 P10 T2
Gene expression data from MCF7 Passage 10 xenograft.


title: prostate_cancer_primary_148


title: B. bifidum PRL2010 in contact with HT29_2

source_name: B.bifidum PRL2010 growth in contact with HT29 cell lines

value: in contact with HT29 cell lines


title: B. bifidum PRL2010 in contact with HT29_1


title: B. bifidum PRL2010 growth in DMEM_1

source_name: B.bifidum PRL2010 growth in DMEM medium

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Dulbecco's modified Eagle medium (DMEM) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.

value: in DMEM medium


title: B. bifidum PRL2010 growth in DMEM_2


title: MCF7_Passage 10 xenograft_R1

description:
MCF7 P10 T1
Gene expression data from MCF7 Passage 10 xenograft.


title: B. bifidum PRL2010 growth in vivo condition_2

source_name: B.bifidum PRL2010 growth in vivo condition

value: in vivo condition


title: B. bifidum PRL2010 growth in vivo condition_3


title: B. bifidum PRL2010 growth in vivo condition_1


title: prostate_cancer_primary_147


title: MCF7_Passage 4 xenograft_R3

description:
MCF7 P04 T3
Gene expression data from MCF7 Passage 4 xenograft.

source_name: MCF7, passage 4 xenograft


title: B. bifidum PRL2010 growth in vivo condition_4


title: prostate_cancer_primary_146


title: MCF7_Passage 4 xenograft_R4

description:
MCF7 P04 T4
Gene expression data from MCF7 Passage 4 xenograft.


title: MCF7_Passage 4 xenograft_R1

description:
MCF7 P04 T1
Gene expression data from MCF7 Passage 4 xenograft.


title: prostate_cancer_primary_181


title: MCF7_Passage 4 xenograft_R5

description:
MCF7 P04 T5
Gene expression data from MCF7 Passage 4 xenograft.


title: MCF7_Passage 1 xenograft_R4

description:
MCF7 P01 T4
Gene expression data from MCF7 Passage 1 xenograft.

source_name: MCF7, passage 1 xenograft


title: MCF7_Passage 1 xenograft_R3

description:
MCF7 P01 T3
Gene expression data from MCF7 Passage 1 xenograft.


title: prostate_cancer_primary_144


title: MCF7_Passage 4 xenograft_R2

description:
MCF7 P04 T2
Gene expression data from MCF7 Passage 4 xenograft.


title: prostate_cancer_primary_145


title: prostate_cancer_primary_143


title: MCF7_Passage 1 xenograft_R2

description:
MCF7 P01 T2
Gene expression data from MCF7 Passage 1 xenograft.


title: prostate_cancer_primary_141


title: ES_male_TMA5_2 [Agilent Expression]

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

description: Gene expression of ES

hyb_protocol: 825 ng of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 1 ul containing 25x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer  HI-RPM was added to the fragmentation mixture and hybridized to Agilent Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned after washing on the Agilent Scanner G2505C. Grid used for scan was 1019456_D_F_20100123,  and protocol  GE1_105_Dec08 was used.

data_processing: The scanned images were analyzed with Feature Extraction Software (v 10.5.1.1) using default parameters for background subtraction and Lowess normalization.

organism: Mus musculus

source_name: ES

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was purified with AllPrep DNA/RNA micro (QIAGEN) from < 5x10E5 cells. Alternatively, total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

value: F1 hybrid beetween TgN (deGFP)20Imeg X MSM/Ms

tag: gender

value: male


title: MCF7_originating cell line_R1

description:
MCF7 P0 T1
Gene expression data from MCF7 originating cell line.

source_name: MCF7, originating cell line


title: GS-2 [Agilent Expression]

description: Gene expression of GS

source_name: GS


title: GS-1 [Agilent Expression]

description: Gene expression of GS


title: prostate_cancer_primary_140


title: Testis-2 [Agilent Expression]

description: Gene expression of adult testis

source_name: adult testis


title: ES_male_TMA5_1 [Agilent Expression]

description: Gene expression of ES


title: prostate_cancer_primary_142

source_name: primary prostate cancer FFPE tissue sample


title: MCF7_originating cell line_R2

description:
MCF7 P0 T2
Gene expression data from MCF7 originating cell line.


title: MDA-MB-231T_Passage 10 xenograft_R1

description:
MDA-MB-231T P10 T1
Gene expression data from MDA-MB-231T Passage 10 xenograft.


title: Testis-1 [Agilent Expression]

description: Gene expression of adult testis


title: MCF7_Passage 1 xenograft_R1

description:
MCF7 P01 T1
Gene expression data from MCF7 Passage 1 xenograft.


title: ES_female_no5_2 [Agilent Expression]

description: Gene expression of ES

value: female


title: ES_female_no5_1 [Agilent Expression]

description: Gene expression of ES


title: prostate_cancer_primary_139


title: prostate_cancer_primary_138


title: MALME-3M_Passage 10 xenograft_R4

description:
MALME-3M P10 T4
Gene expression data from MALME-3M Passage 10 xenograft.

source_name: MALME-3M, passage 10 xenograft

value: malignant melanoma


title: EG_male_2 [Agilent Expression]

description: Gene expression of 12.5dpc PGC

source_name: 12.5dpc PGC


title: MALME-3M_Passage 10 xenograft_R5

description:
MALME-3M P10 T5
Gene expression data from MALME-3M Passage 10 xenograft.


title: EG_male_1 [Agilent Expression]

description: Gene expression of 12.5dpc PGC


title: MALME-3M_Passage 10 xenograft_R3

description:
MALME-3M P10 T3
Gene expression data from MALME-3M Passage 10 xenograft.


title: prostate_cancer_primary_137


title: spermatogonia_2 [Agilent Expression]

description: Gene expression of spermatogonia

source_name: spermatogonia

value: BDF1 x Tg(Mvh-Venus)1Rbrc


title: prostate_cancer_primary_136


title: EG_female_2 [Agilent Expression]

description: Gene expression of 12.5dpc PGC


title: oogonia_2 [Agilent Expression]

description: Gene expression of oogonia

source_name: oogonia


title: prostate_cancer_primary_135


title: EG_female_1 [Agilent Expression]

description: Gene expression of 12.5dpc PGC


title: oogonia_1 [Agilent Expression]

description: Gene expression of oogonia


title: spermatogonia_1 [Agilent Expression]

description: Gene expression of spermatogonia


title: prostate_cancer_primary_134


title: E17.5_PGC_female_1 [Agilent Expression]

description: Gene expression of 17.5dpc PGC

source_name: 17.5dpc PGC

value: BDF1 x TgN(deGFP)18Imeg


title: E13.5_PGC_male_2 [Agilent Expression]

description: Gene expression of 13.5dpc PGC

source_name: 13.5dpc PGC


title: E17.5_PGC_female_2 [Agilent Expression]

description: Gene expression of 17.5dpc PGC


title: E17.5_PGC_male_2 [Agilent Expression]

description: Gene expression of 17.5dpc PGC


title: prostate_cancer_primary_133


title: E13.5_PGC_female_2 [Agilent Expression]

description: Gene expression of 13.5dpc PGC


title: MALME-3M_Passage 10 xenograft_R2

description:
MALME-3M P10 T2
Gene expression data from MALME-3M Passage 10 xenograft.


title: MALME-3M_Passage 10 xenograft_R1

description:
MALME-3M P10 T1
Gene expression data from MALME-3M Passage 10 xenograft.


title: prostate_cancer_primary_132


title: E10.5_PGC_male_2 [Agilent Expression]

description: Gene expression of 10.5dpc PGC

source_name: 10.5dpc PGC


title: E17.5_PGC_male_1 [Agilent Expression]

description: Gene expression of 17.5dpc PGC


title: MALME-3M_Passage 4 xenograft_R4

description:
MALME-3M P04 T4
Gene expression data from MALME-3M Passage 4 xenograft.

source_name: MALME-3M, passage 4 xenograft


title: prostate_cancer_primary_131


title: MALME-3M_Passage 4 xenograft_R3

description:
MALME-3M P04 T3
Gene expression data from MALME-3M Passage 4 xenograft.


title: E13.5_PGC_female_1 [Agilent Expression]

description: Gene expression of 13.5dpc PGC


title: E10.5_PGC_male_1 [Agilent Expression]

description: Gene expression of 10.5dpc PGC


title: prostate_cancer_primary_130


title: E10.5_PGC_female_1 [Agilent Expression]

description: Gene expression of 10.5dpc PGC


title: prostate_cancer_primary_129


title: MALME-3M_Passage 1 xenograft_R5

description:
MALME-3M P01 T5
Gene expression data from MALME-3M Passage 1 xenograft.

source_name: MALME-3M, passage 1 xenograft


title: MALME-3M_Passage 1 xenograft_R4

description:
MALME-3M P01 T4
Gene expression data from MALME-3M Passage 1 xenograft.


title: E13.5_PGC_male_1 [Agilent Expression]

description: Gene expression of 13.5dpc PGC


title: MALME-3M_Passage 4 xenograft_R1

description:
MALME-3M P04 T1
Gene expression data from MALME-3M Passage 4 xenograft.


title: E10.5_PGC_female_2 [Agilent Expression]

description: Gene expression of 10.5dpc PGC


title: cumulus_1

type: genomic

description: Biological replicate 1 of 2

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: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: cumulus

label_protocol: 2 ug of the DNA fragments labeled using the Genomic DNA Enzymatic labeling kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Genome DNA of  cells purified with AllPrep DNA/RNA micro from < 5x10E5 cells.

treatment_protocol: 2ng DNA were digested HpaII / MspI. The digested DNA was added linker and amplified (LM-PCR reaction).

tag: enzyme

value: HpaII

tag: cell type

value: cumulus

value: MspI


title: cumulus_2

description: Biological replicate 2 of 2


title: ES_female_no5_2

description: DNA methylation

hyb_protocol: The labeled DNA was precipitated, and 13 ug each of the Cy3 or Cy5 labeled DNA were combined and used for hybridization. Arrays were hybridized in Maui hybridization stations for 17 h at 42℃. Hybridization and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: After washing, the arrays were scanned on an Agilent Technologies Scanner G2505C.

data_processing: Raw data were processed using Nimblescan 2.4 ChIP data extraction.

label_protocol: Two nano gram of genomic DNA was digested with either HpaII or MspI. The digested DNA was ligated to linker-adapter and amplified by linker-mediated PCR.  The amplified DNA was labeled by random priming method with Cy3 or Cy5 nonamers separately according to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: ES cells were cultured on fedder in D-MEM with 15% fetal bovine serum, 1000 U/mL LIF, 2-mercaptoethanol, nonessential amino acids, and penicillin/streptomycin.

extract_protocol: Genome DNA was purified with AllPrep DNA/RNA micro kit (Qiagen) from < 5x10E5 cells. Alternatively, genome DNA was extracted by standard protocol: after cell lysis and proteinase K digestion, DNA was extracted by phenol/chloroform.

treatment_protocol: The feeder cells were removed.

value: ES


title: prostate_cancer_primary_128


title: prostate_cancer_primary_127


title: MALME-3M_Passage 4 xenograft_R2

description:
MALME-3M P04 T2
Gene expression data from MALME-3M Passage 4 xenograft.


title: ES_male_TMA5_1

description: DNA methylation


title: prostate_cancer_primary_126


title: MALME-3M_Passage 1 xenograft_R2

description:
MALME-3M P01 T2
Gene expression data from MALME-3M Passage 1 xenograft.


title: MALME-3M_Passage 1 xenograft_R1

description:
MALME-3M P01 T1
Gene expression data from MALME-3M Passage 1 xenograft.


title: MALME-3M_Passage 1 xenograft_R3

description:
MALME-3M P01 T3
Gene expression data from MALME-3M Passage 1 xenograft.


title: thymus-1

description: DNA methylation

value: adult testis


title: prostate_cancer_primary_125


title: ES_male_TMA5_2

description: DNA methylation


title: thymus-2

description: DNA methylation


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 8 of 10

city: New Delhi

first: Pankaj

last: Kumar

state: Delhi

address: Mall Road,

department: G N R Knowledge Center for Genome Informatics

country: India

institute: Institiue of Genomics and Integrative Biology

hyb_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).

scan_protocol: Arrays were scanned on a the Axon Genepix 4000B scanner at 5 microns for both 532nm and 635nm channels

data_processing: Scanned images were processed using NimbleScan

source_name: H4K16ac ChIP DNA from HEK293 cells

extract_protocol: DMEM high glucose with 10% FBS, culture at 37C in 5% CO2

tag: cell line

tag: antibody

source_name: Input DNA from HEK293 cells

tag: sample type

value: input


title: prostate_cancer_primary_124


title: testis-2

description: DNA methylation


title: ES_female_no5_1

description: DNA methylation


title: oogonia_2

description: DNA methylation

treatment_protocol: The VENUS-positive germ cells were purified by FACS.

value: oogonia


title: prostate_cancer_primary_123


title: M14_Passage 10 xenograft_R5

description:
M14 P10 T5
Gene expression data from M14 Passage 10 xenograft.

source_name: M14, passage 10 xenograft

value: adenocarcinoma melanoma


title: MALME-3M_originating cell line_R2

description:
MALME-3M P0 T2
Gene expression data from MALME-3M originating cell line.

source_name: MALME-3M, originating cell line


title: M14_Passage 10 xenograft_R4

description:
M14 P10 T4
Gene expression data from M14 Passage 10 xenograft.


title: brain-1

description: DNA methylation

value: brain


title: oogonia_1

description: DNA methylation


title: testis-1

description: DNA methylation


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 10 of 10

label_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).


title: prostate_cancer_primary_122


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 9 of 10


title: brain-2

description: DNA methylation


title: MALME-3M_originating cell line_R1

description:
MALME-3M P0 T1
Gene expression data from MALME-3M originating cell line.


title: EG_female_1

description: DNA methylation

growth_protocol: EG cells were cultured on fedder in D-MEM with 15% fetal bovine serum, 1000 U/mL LIF, 2-mercaptoethanol, nonessential amino acids, and penicillin/streptomycin.

value: EG (12.5dpc PGC)


title: prostate_cancer_primary_121


title: spermatogonia_2

description: DNA methylation

value: spermatogonia


title: EG_male_1

description: DNA methylation


title: prostate_cancer_primary_120


title: EG_female_2

description: DNA methylation


title: prostate_cancer_primary_119


title: prostate_cancer_primary_118


title: GS-2

description: DNA methylation

growth_protocol: GS cells were cultured on fedder in StemPro medium with some supplements.

value: GS


title: M14_Passage 10 xenograft_R3

description:
M14 P10 T3
Gene expression data from M14 Passage 10 xenograft.


title: prostate_cancer_primary_117


title: E17.5_PGC_female_2

description: DNA methylation

treatment_protocol: The EGFP-positive germ cells were purified by FACS.

value: 17.5dpc PGC


title: M14_Passage 4 xenograft_R5

description:
M14 P04 T5
Gene expression data from M14 Passage 4 xenograft.

source_name: M14, passage 4 xenograft


title: EG_male_2

description: DNA methylation


title: M14_Passage 10 xenograft_R2

description:
M14 P10 T2
Gene expression data from M14 Passage 10 xenograft.


title: spermatogonia_1

description: DNA methylation


title: GS-1

description: DNA methylation


title: E13.5_PGC_female_2

description: DNA methylation

value: 13.5dpc PGC


title: E17.5_PGC_male_2

description: DNA methylation


title: E17.5_PGC_female_1

description: DNA methylation


title: M14_Passage 4 xenograft_R3

description:
M14 P04 T3
Gene expression data from M14 Passage 4 xenograft.


title: E13.5_PGC_male_2

description: DNA methylation


title: E17.5_PGC_male_1

description: DNA methylation


title: M14_Passage 4 xenograft_R4

description:
M14 P04 T4
Gene expression data from M14 Passage 4 xenograft.


title: E10.5_PGC_male_2

description: DNA methylation

value: 10.5dpc PGC


title: E13.5_PGC_female_1

description: DNA methylation


title: prostate_cancer_primary_116


title: 30 dpf sapje-like fish replicate 3

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: 30 dpf; TL Strain

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

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

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Danio rerio

source_name: 30 dpf sapje-like fish

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: Wild type, sapje, and sapje-like fish were grown in fish water on a standard shrimp diet

extract_protocol: miRVana kit (ambion); 10 fish per cohort

tag: tissue

value: whole fish

tag: age

value: 30 dpf

value: TL Strain

tag: genotype/variation

value: sapje-like


title: prostate_cancer_primary_115

source_name: primary prostate cancer FFPE tissue sample

tag: gleason score


title: prostate_cancer_primary_114

tag: metastatic event


title: 30 dpf sapje-like fish replicate 2

description: 30 dpf; TL Strain


title: E10.5_PGC_female_2

description: DNA methylation

value: HpaII

value: BDF1 x TgN(deGFP)18Imeg

value: MspI


title: E10.5_PGC_male_1

description: DNA methylation


title: 30 dpf sapje-like fish replicate 1

description: 30 dpf; TL Strain


title: 30 dpf wildtype (SLW) fish replicate 5

description: 30 dpf; TL Strain

source_name: 30 dpf wildtype fish

value: wild type (SLW)


title: 30 dpf wildtype (SLW) fish replicate 8

description: 30 dpf; TL Strain


title: prostate_cancer_primary_113


title: M14_Passage 4 xenograft_R1

description:
M14 P04 T1
Gene expression data from M14 Passage 4 xenograft.

tag: originating cell line


title: M14_Passage 1 xenograft_R5

description:
M14 P01 T5
Gene expression data from M14 Passage 1 xenograft.

source_name: M14, passage 1 xenograft

tag: tumor type


title: E13.5_PGC_male_1

description: DNA methylation


title: E10.5_PGC_female_1

description: DNA methylation


title: M14_Passage 4 xenograft_R2

description:
M14 P04 T2
Gene expression data from M14 Passage 4 xenograft.

tag: in vivo passage


title: 30 dpf wildtype (SLW) fish replicate 2

description: 30 dpf; TL Strain

tag: strain


title: M14_Passage 1 xenograft_R4

description:
M14 P01 T4
Gene expression data from M14 Passage 1 xenograft.


title: M14_Passage 1 xenograft_R3

description:
M14 P01 T3
Gene expression data from M14 Passage 1 xenograft.


title: prostate_cancer_primary_111


title: 30 dpf wildtype (SW) fish replicate 4

description: 30 dpf; TL Strain

value: wild type (SW)


title: 30 dpf wildtype (SW) fish replicate 3

description: 30 dpf; TL Strain


title: M14_Passage 1 xenograft_R2

description:
M14 P01 T2
Gene expression data from M14 Passage 1 xenograft.

value: adenocarcinoma melanoma


title: 30 dpf wildtype (SW) fish replicate 2

description: 30 dpf; TL Strain


title: 30 dpf sapje fish replicate 2

description: 30 dpf; TL Strain

source_name: 30 dpf sapje fish

value: sapje


title: 30 dpf sapje fish replicate 3

description: 30 dpf; TL Strain


title: 30 dpf sapje fish replicate 1

description: 30 dpf; TL Strain


title: prostate_cancer_primary_109


title: 5 dpf sapje-like fish replicate 2

description: 5 dpf; TL Strain

source_name: 5 dpf sapje-like fish

value: 5 dpf


title: prostate_cancer_primary_108


title: M14_Passage 1 xenograft_R1

description:
M14 P01 T1
Gene expression data from M14 Passage 1 xenograft.


title: prostate_cancer_primary_107


title: 5 dpf wildtype (SLW) fish replicate 1

description: 5 dpf; TL Strain

source_name: 5 dpf wildtype fish


title: 5 dpf sapje-like fish replicate 1

description: 5 dpf; TL Strain


title: M14_originating cell line_R2

description:
M14 P0 T2
Gene expression data from M14 originating cell line.

source_name: M14, originating cell line


title: M14_originating cell line_R1

description:
M14 P0 T1
Gene expression data from M14 originating cell line.


title: 5 dpf wildtype (SW) fish replicate 2

description: 5 dpf; TL Strain


title: M14_Passage 10 xenograft_R1

description:
M14 P10 T1
Gene expression data from M14 Passage 10 xenograft.


title: 5 dpf wildtype (SW) fish replicate 1

description: 5 dpf; TL Strain


title: prostate_cancer_primary_110


title: prostate_cancer_primary_106


title: 5 dpf sapje fish replicate 2

description: 5 dpf; TL Strain

source_name: 5 dpf sapje fish


title: prostate_cancer_primary_105


title: prostate_cancer_primary_103


title: 5 dpf wildtype (SLW) fish replicate 2

description: 5 dpf; TL Strain


title: prostate_cancer_primary_112


title: prostate_cancer_primary_102


title: prostate_cancer_primary_101


title: prostate_cancer_primary_104


title: prostate_cancer_primary_100


title: LOX IMVI_Passage 10 xenograft_R2

description:
LOX IMVI P10 T2
Gene expression data from LOX IMVI Passage 10 xenograft.

source_name: LOX IMVI, passage 10 xenograft

value: LOX IMVI

value: malignant amelanocytic melanoma


title: prostate_cancer_primary_99


title: prostate_cancer_primary_98


title: LOX IMVI_Passage 10 xenograft_R4

description:
LOX IMVI P10 T4
Gene expression data from LOX IMVI Passage 10 xenograft.


title: LOX IMVI_Passage 10 xenograft_R1

description:
LOX IMVI P10 T1
Gene expression data from LOX IMVI Passage 10 xenograft.


title: LOX IMVI_Passage 4 xenograft_R3

description:
LOX IMVI P04 T3
Gene expression data from LOX IMVI Passage 4 xenograft.

source_name: LOX IMVI, passage 4 xenograft


title: LOX IMVI_Passage 4 xenograft_R2

description:
LOX IMVI P04 T2
Gene expression data from LOX IMVI Passage 4 xenograft.


title: LOX IMVI_Passage 10 xenograft_R3

description:
LOX IMVI P10 T3
Gene expression data from LOX IMVI Passage 10 xenograft.


title: LOX IMVI_Passage 4 xenograft_R4

description:
LOX IMVI P04 T4
Gene expression data from LOX IMVI Passage 4 xenograft.


title: LOX IMVI_Passage 4 xenograft_R1

description:
LOX IMVI P04 T1
Gene expression data from LOX IMVI Passage 4 xenograft.


title: LOX IMVI_Passage 4 xenograft_R5

description:
LOX IMVI P04 T5
Gene expression data from LOX IMVI Passage 4 xenograft.


title: LOX IMVI_Passage 1 xenograft_R5

description:
LOX IMVI P01 T5
Gene expression data from LOX IMVI Passage 1 xenograft.

source_name: LOX IMVI, passage 1 xenograft


title: LOX IMVI_Passage 10 xenograft_R5

description:
LOX IMVI P10 T5
Gene expression data from LOX IMVI Passage 10 xenograft.


title: prostate_cancer_primary_97


title: prostate_cancer_primary_96


title: prostate_cancer_primary_95


title: 5 dpf sapje fish replicate 1

description: 5 dpf; TL Strain


title: LOX IMVI_Passage 1 xenograft_R4

description:
LOX IMVI P01 T4
Gene expression data from LOX IMVI Passage 1 xenograft.


title: LOX IMVI_Passage 1 xenograft_R2

description:
LOX IMVI P01 T2
Gene expression data from LOX IMVI Passage 1 xenograft.


title: prostate_cancer_primary_94


title: LOX IMVI_Passage 1 xenograft_R1

description:
LOX IMVI P01 T1
Gene expression data from LOX IMVI Passage 1 xenograft.


title: 6 Gy, 72 hr

city: Detroit

first: Steven

middle: P

last: Zielske

state: MI

address: 540 E. Canfield

department: Department of Radiation Oncology

institute: Wayne State University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to the Illumina Infinium HumanMethylation450 Beadchip using the standard Infinium HD Methylation Assay protocol.

scan_protocol: Arrays were scanned on an Illumina iScan using Illumina recommended settings.

data_processing: GenomeStudio v2011.1. Average Beta (Normalized using 'Controls' method; background subtracted). Unmethylated and methylated signal intensities (Normalized using 'Controls' method; background subtracted).

label: Cy3 and Cy5

source_name: MDA-MB-231 cells

label_protocol: The standard Infinium HD Methylation Assay protocol was used.

extract_protocol: Qiagen EZ1 Advanced

value: female

tag: ionizing radiation treatment

value: 6 Gy, 72 hr

tag: disease state

value: breast cancer


title: LOX IMVI_Passage 1 xenograft_R3

description:
LOX IMVI P01 T3
Gene expression data from LOX IMVI Passage 1 xenograft.


title: 2 Gy, 72 hr

tag: gender

value: 2 Gy, 72 hr


title: LOX IMVI_originating cell line_R2

description:
LOX IMVI P0 T2
Gene expression data from LOX IMVI originating cell line.

source_name: LOX IMVI, originating cell line


title: 0 Gy, 72 hr

value: 0 Gy, 72 hr


title: 2 Gy, 48 hr

value: 2 Gy, 48 hr


title: 6 Gy, 48 hr

value: 6 Gy, 48 hr


title: 2 Gy, 24 hr

value: 2 Gy, 24 hr


title: 6 Gy, 4 hr

value: 6 Gy, 4 hr


title: 6 Gy, 24 hr

value: 6 Gy, 24 hr


title: prostate_cancer_primary_93


title: prostate_cancer_primary_92


title: 6 Gy, 2 hr

value: 6 Gy, 2 hr


title: KM12_Passage 10 xenograft_R5

description:
KM12 P10 T5
Gene expression data from KM12 Passage 10 xenograft.

source_name: KM12, passage 10 xenograft

value: adenocarcinoma colon


title: 0 Gy, 48 hr

value: 0 Gy, 48 hr


title: prostate_cancer_primary_91


title: 0 Gy, 24 hr

value: 0 Gy, 24 hr


title: 0 Gy, 4 hr

value: 0 Gy, 4 hr


title: KM12_Passage 10 xenograft_R4

description:
KM12 P10 T4
Gene expression data from KM12 Passage 10 xenograft.


title: 2 Gy, 8 hr

value: 2 Gy, 8 hr


title: prostate_cancer_primary_90


title: 6 Gy, 8 hr

value: 6 Gy, 8 hr


title: 2 Gy, 4 hr

value: female

value: 2 Gy, 4 hr


title: 2 Gy, 2 hr

value: 2 Gy, 2 hr

value: breast cancer


title: 0 Gy, 0 hr (3)


title: 0 Gy, 8 hr

value: 0 Gy, 8 hr


title: prostate_cancer_primary_89


title: LOX IMVI_originating cell line_R1

description:
LOX IMVI P0 T1
Gene expression data from LOX IMVI originating cell line.

value: LOX IMVI

value: malignant amelanocytic melanoma


title: 6 Gy, 1 hr

value: 6 Gy, 1 hr


title: R-U937_untreated

first: Satoshi

last: Imanishi

address: nishi-shinnjuku 6-7-1

institute: Tokyo medical univ

description:
Cell line derived from a male.
Genomic DNA from azacytidine-resistant derivative from U937.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan using the standard recommended Illumina scanner setting.

data_processing: GenomeStudio Methylation Module.

label: Alexa 555 and Alexa 647

source_name: R-U937, untreated

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from cells using the Wako DNA Extractor WB Kit according to standard instructions.

tag: azacytidine sensitivity

value: resistant

value: leukemia

tag: treatment


title: 2 Gy, 1 hr

tag: cell line

value: 2 Gy, 1 hr


title: prostate_cancer_primary_88


title: 0 Gy, 1 hr

value: 0 Gy, 1 hr


title: 0 Gy, 0 hr (1)


title: 0 Gy, 2 hr

value: 0 Gy, 2 hr


title: prostate_cancer_primary_87


title: 0 Gy, 0 hr (2)


title: KM12_Passage 10 xenograft_R2

description:
KM12 P10 T2
Gene expression data from KM12 Passage 10 xenograft.

value: adenocarcinoma colon


title: KM12_Passage 4 xenograft_R5

description:
KM12 P04 T5
Gene expression data from KM12 Passage 4 xenograft.

source_name: KM12, passage 4 xenograft


title: prostate_cancer_primary_85


title: prostate_cancer_primary_86


title: KM12_Passage 10 xenograft_R3

description:
KM12 P10 T3
Gene expression data from KM12 Passage 10 xenograft.


title: KM12_Passage 10 xenograft_R1

description:
KM12 P10 T1
Gene expression data from KM12 Passage 10 xenograft.


title: U937_untreated

description:
Cell line derived from a male.
Genomic DNA from U937.

source_name: U937, untreated

value: sensitive


title: KM12_Passage 4 xenograft_R4

description:
KM12 P04 T4
Gene expression data from KM12 Passage 4 xenograft.


title: prostate_cancer_primary_84

source_name: primary prostate cancer FFPE tissue sample


title: KM12_Passage 4 xenograft_R3

description:
KM12 P04 T3
Gene expression data from KM12 Passage 4 xenograft.


title: prostate_cancer_primary_83


title: KM12_Passage 4 xenograft_R2

description:
KM12 P04 T2
Gene expression data from KM12 Passage 4 xenograft.


title: U937_AZA 24h

description:
Cell line derived from a male.
Genomic DNA from U937 treated with azacytidine for 24 hours.

source_name: U937, AZA treated, 24hr

value: azacytidine for 24h


title: HapMap Cytosine Modification NA19222

city: Chicago

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

description: Phase 1/2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina HiScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio Methylation v1.9

source_name: lymphoblastoid cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNAs were purchased from Coriell Cell Repositories (Camden, NJ). All samples were quantitated using Molecular Probes Quanti-iT Picogreen dsDNA kit (P11496; Life TechnologiesTM, Carlsbad, CA). Random samples were chosen for additional analysis to include: nanodrop 260/280 analysis (Thermo Scientific, Wilmington, DE),  Quibit dsDNA assay analysis (Q32853; Life Technologies) and 1% TAE agarose gel analysis using Promega Blue/Orange 6x dye (G190A; Promega, Fitchburg, WI) and Gibco High DNA Mass Ladder (#10496-016; Life TechnologiesTM, Carlsbad, CA). For nanodrop analysis, all samples must have a 260/280 ratio greater than 1.7 and less than 2.0 and for the agarose gel analysis the DNA must be >100,000 bp in length.

tag: panel

value: YRI

tag: hybridization batch


title: HapMap Cytosine Modification NA19225

description: Phase 3

growth_protocol: Genomic DNAs were purchased from Coriell Cell Repositories (Camden, NJ).


title: U937_AZA 72h

description:
Cell line derived from a male.
Genomic DNA from U937 treated with azacytidine for 72 hours.

source_name: U937, AZA treated, 72hr

value: azacytidine for 72h


title: HapMap Cytosine Modification NA18511

description: Phase 3


title: KM12_Passage 1 xenograft_R5

description:
KM12 P01 T5
Gene expression data from KM12 Passage 1 xenograft.

source_name: KM12, passage 1 xenograft


title: HapMap Cytosine Modification NA19108

description: Phase 3


title: prostate_cancer_primary_81


title: HapMap Cytosine Modification NA19204

description: Phase 1/2


title: KM12_Passage 4 xenograft_R1

description:
KM12 P04 T1
Gene expression data from KM12 Passage 4 xenograft.


title: prostate_cancer_primary_82


title: KM12_Passage 1 xenograft_R4

description:
KM12 P01 T4
Gene expression data from KM12 Passage 1 xenograft.


title: HapMap Cytosine Modification NA19238

description: Phase 1/2


title: prostate_cancer_primary_79


title: HapMap Cytosine Modification NA19152

description: Phase 1/2


title: HapMap Cytosine Modification NA18856

description: Phase 1/2


title: KM12_Passage 1 xenograft_R2

description:
KM12 P01 T2
Gene expression data from KM12 Passage 1 xenograft.


title: HapMap Cytosine Modification NA19239

description: Phase 1/2


title: prostate_cancer_primary_78


title: HapMap Cytosine Modification NA19143

description: Phase 1/2


title: HapMap Cytosine Modification NA18855

description: Phase 1/2


title: HapMap Cytosine Modification NA18486

description: Phase 3


title: prostate_cancer_primary_77


title: HapMap Cytosine Modification NA07022

description: Phase 1/2

value: CEU


title: HapMap Cytosine Modification NA12264

description: Phase 1/2


title: HapMap Cytosine Modification NA19172

description: Phase 1/2


title: HapMap Cytosine Modification NA12815

description: Phase 1/2


title: prostate_cancer_primary_76


title: HapMap Cytosine Modification NA18508

description: Phase 1/2


title: HapMap Cytosine Modification NA19203

description: Phase 1/2


title: prostate_cancer_primary_80


title: prostate_cancer_primary_75


title: KM12_Passage 1 xenograft_R3

description:
KM12 P01 T3
Gene expression data from KM12 Passage 1 xenograft.


title: HapMap Cytosine Modification NA11830

description: Phase 1/2


title: HapMap Cytosine Modification NA19119

description: Phase 1/2


title: prostate_cancer_primary_74


title: HapMap Cytosine Modification NA07000

description: Phase 1/2


title: HapMap Cytosine Modification NA12249

description: Phase 1/2


title: KM12_Passage 1 xenograft_R1

description:
KM12 P01 T1
Gene expression data from KM12 Passage 1 xenograft.


title: HapMap Cytosine Modification NA18516

description: Phase 1/2


title: K-562_Passage 10 xenograft_R4

description:
K-562 P10 T4
Gene expression data from K-562 Passage 10 xenograft.

source_name: K-562, passage 10 xenograft

value: chronic myelogenous (blast crisis) leukemia


title: KM12_originating cell line_R2

description:
KM12 P0 T2
Gene expression data from KM12 originating cell line.

source_name: KM12, originating cell line


title: KM12_originating cell line_R1

description:
KM12 P0 T1
Gene expression data from KM12 originating cell line.


title: prostate_cancer_primary_73


title: KM12_originating cell line_R3

description:
KM12 P0 T3
Gene expression data from KM12 originating cell line.


title: prostate_cancer_primary_72


title: HapMap Cytosine Modification NA11831

description: Phase 1/2


title: HapMap Cytosine Modification NA18523

description: Phase 1/2


title: HapMap Cytosine Modification NA19131

description: Phase 1/2


title: HapMap Cytosine Modification NA12248

description: Phase 1/2


title: HapMap Cytosine Modification NA19210

description: Phase 1/2


title: prostate_cancer_primary_71


title: prostate_cancer_primary_69


title: K-562_Passage 10 xenograft_R2

description:
K-562 P10 T2
Gene expression data from K-562 Passage 10 xenograft.


title: K-562_Passage 10 xenograft_R1

description:
K-562 P10 T1
Gene expression data from K-562 Passage 10 xenograft.


title: HapMap Cytosine Modification NA12813

description: Phase 1/2


title: K-562_Passage 4 xenograft_R4

description:
K-562 P04 T4
Gene expression data from K-562 Passage 4 xenograft.

source_name: K-562, passage 4 xenograft


title: HapMap Cytosine Modification NA07345

description: Phase 1/2


title: prostate_cancer_primary_68


title: prostate_cancer_primary_70


title: prostate_cancer_primary_67


title: prostate_cancer_primary_66


title: HapMap Cytosine Modification NA19138

description: Phase 1/2


title: HapMap Cytosine Modification NA18498

description: Phase 3


title: HapMap Cytosine Modification NA18853

description: Phase 1/2


title: K-562_Passage 4 xenograft_R3

description:
K-562 P04 T3
Gene expression data from K-562 Passage 4 xenograft.


title: HapMap Cytosine Modification NA19114

description: Phase 3


title: HapMap Cytosine Modification NA12043

description: Phase 1/2


title: HapMap Cytosine Modification NA18501

description: Phase 1/2


title: prostate_cancer_primary_65


title: K-562_Passage 4 xenograft_R1

description:
K-562 P04 T1
Gene expression data from K-562 Passage 4 xenograft.


title: K-562_Passage 4 xenograft_R2

description:
K-562 P04 T2
Gene expression data from K-562 Passage 4 xenograft.


title: K-562_Passage 10 xenograft_R3

description:
K-562 P10 T3
Gene expression data from K-562 Passage 10 xenograft.


title: prostate_cancer_primary_64


title: HapMap Cytosine Modification NA11882

description: Phase 1/2


title: HapMap Cytosine Modification NA12873

description: Phase 1/2


title: K-562_Passage 1 xenograft_R5

description:
K-562 P01 T5
Gene expression data from K-562 Passage 1 xenograft.

source_name: K-562, passage 1 xenograft


title: prostate_cancer_primary_63


title: HapMap Cytosine Modification NA11840

description: Phase 1/2


title: HapMap Cytosine Modification NA12154

description: Phase 1/2


title: prostate_cancer_primary_62


title: HapMap Cytosine Modification NA12763

description: Phase 1/2


title: HapMap Cytosine Modification NA11832

description: Phase 1/2


title: HapMap Cytosine Modification NA19092

description: Phase 1/2


title: prostate_cancer_primary_61


title: K-562_Passage 1 xenograft_R3

description:
K-562 P01 T3
Gene expression data from K-562 Passage 1 xenograft.


title: HapMap Cytosine Modification NA18870

description: Phase 1/2


title: HapMap Cytosine Modification NA11994

description: Phase 1/2


title: HapMap Cytosine Modification NA19171

description: Phase 1/2


title: K-562_Passage 1 xenograft_R2

description:
K-562 P01 T2
Gene expression data from K-562 Passage 1 xenograft.


title: K-562_Passage 1 xenograft_R1

description:
K-562 P01 T1
Gene expression data from K-562 Passage 1 xenograft.


title: HapMap Cytosine Modification NA19223

description: Phase 1/2


title: prostate_cancer_primary_60


title: HapMap Cytosine Modification NA19192

description: Phase 1/2


title: prostate_cancer_primary_59


title: HapMap Cytosine Modification NA07034

description: Phase 1/2


title: HapMap Cytosine Modification NA19101

description: Phase 1/2


title: K-562_originating cell line_R3

description:
K-562 P0 T3
Gene expression data from K-562 originating cell line.

source_name: K-562, originating cell line


title: HapMap Cytosine Modification NA12155

description: Phase 1/2


title: prostate_cancer_primary_58


title: prostate_cancer_primary_57


title: K-562_Passage 4 xenograft_R5

description:
K-562 P04 T5
Gene expression data from K-562 Passage 4 xenograft.


title: K-562_originating cell line_R1

description:
K-562 P0 T1
Gene expression data from K-562 originating cell line.


title: HapMap Cytosine Modification NA11992

description: Phase 1/2


title: prostate_cancer_primary_56


title: HuH-7_Passage 10 xenograft_R5

description:
HuH-7 P10 T5
Gene expression data from HuH-7 Passage 10 xenograft.

source_name: HuH-7, passage 10 xenograft

value: carcinoma differentiated Hepatocellular


title: K-562_originating cell line_R2

description:
K-562 P0 T2
Gene expression data from K-562 originating cell line.


title: HapMap Cytosine Modification NA19207

description: Phase 1/2


title: HapMap Cytosine Modification NA12717

description: Phase 1/2


title: HapMap Cytosine Modification NA19102

description: Phase 1/2


title: K-562_Passage 1 xenograft_R4

description:
K-562 P01 T4
Gene expression data from K-562 Passage 1 xenograft.


title: prostate_cancer_primary_55


title: prostate_cancer_primary_54


title: HapMap Cytosine Modification NA18852

description: Phase 1/2


title: HapMap Cytosine Modification NA12044

description: Phase 1/2


title: HapMap Cytosine Modification NA19160

description: Phase 1/2


title: HuH-7_Passage 10 xenograft_R4

description:
HuH-7 P10 T4
Gene expression data from HuH-7 Passage 10 xenograft.


title: prostate_cancer_primary_53


title: HapMap Cytosine Modification NA12239

description: Phase 1/2


title: prostate_cancer_primary_52


title: HapMap Cytosine Modification NA19201

description: Phase 1/2


title: HuH-7_Passage 10 xenograft_R2

description:
HuH-7 P10 T2
Gene expression data from HuH-7 Passage 10 xenograft.


title: HapMap Cytosine Modification NA18913

description: Phase 1/2


title: HuH-7_Passage 10 xenograft_R3

description:
HuH-7 P10 T3
Gene expression data from HuH-7 Passage 10 xenograft.


title: HapMap Cytosine Modification NA06985

description: Phase 1/2


title: prostate_cancer_primary_51


title: HapMap Cytosine Modification NA06994

description: Phase 1/2


title: HapMap Cytosine Modification NA19093

description: Phase 1/2


title: HapMap Cytosine Modification NA19159

description: Phase 1/2


title: prostate_cancer_primary_50


title: HuH-7_Passage 4 xenograft_R4

description:
HuH-7 P04 T4
Gene expression data from HuH-7 Passage 4 xenograft.

source_name: HuH-7, passage 4 xenograft


title: HuH-7_Passage 10 xenograft_R1

description:
HuH-7 P10 T1
Gene expression data from HuH-7 Passage 10 xenograft.


title: HapMap Cytosine Modification NA18859

description: Phase 1/2


title: HuH-7_Passage 4 xenograft_R3

description:
HuH-7 P04 T3
Gene expression data from HuH-7 Passage 4 xenograft.


title: prostate_cancer_primary_49


title: prostate_cancer_primary_48


title: HapMap Cytosine Modification NA12760

description: Phase 1/2


title: HapMap Cytosine Modification NA19140

description: Phase 1/2


title: HuH-7_Passage 4 xenograft_R2

description:
HuH-7 P04 T2
Gene expression data from HuH-7 Passage 4 xenograft.


title: HapMap Cytosine Modification NA12761

description: Phase 1/2


title: HuH-7_Passage 4 xenograft_R5

description:
HuH-7 P04 T5
Gene expression data from HuH-7 Passage 4 xenograft.


title: HuH-7_Passage 1 xenograft_R5

description:
HuH-7 P01 T5
Gene expression data from HuH-7 Passage 1 xenograft.

source_name: HuH-7, passage 1 xenograft


title: prostate_cancer_primary_47


title: HapMap Cytosine Modification NA18858

description: Phase 1/2


title: HapMap Cytosine Modification NA12762

description: Phase 1/2


title: HapMap Cytosine Modification NA12145

description: Phase 1/2


title: HapMap Cytosine Modification NA18502

description: Phase 1/2


title: HapMap Cytosine Modification NA18499

description: Phase 3


title: HapMap Cytosine Modification NA19144

description: Phase 1/2


title: HuH-7_Passage 4 xenograft_R1

description:
HuH-7 P04 T1
Gene expression data from HuH-7 Passage 4 xenograft.


title: prostate_cancer_primary_46


title: HapMap Cytosine Modification NA12005

description: Phase 1/2


title: HapMap Cytosine Modification NA18504

description: Phase 1/2


title: prostate_cancer_primary_45


title: HapMap Cytosine Modification NA18909

description: Phase 3


title: prostate_cancer_primary_44


title: HapMap Cytosine Modification NA12234

description: Phase 1/2


title: prostate_cancer_primary_43


title: HuH-7_Passage 1 xenograft_R4

description:
HuH-7 P01 T4
Gene expression data from HuH-7 Passage 1 xenograft.


title: HapMap Cytosine Modification NA19206

description: Phase 1/2


title: HapMap Cytosine Modification NA12872

description: Phase 1/2


title: HuH-7_Passage 1 xenograft_R2

description:
HuH-7 P01 T2
Gene expression data from HuH-7 Passage 1 xenograft.


title: HuH-7_Passage 1 xenograft_R3

description:
HuH-7 P01 T3
Gene expression data from HuH-7 Passage 1 xenograft.


title: prostate_cancer_primary_41


title: HapMap Cytosine Modification NA19153

description: Phase 1/2


title: HapMap Cytosine Modification NA12716

description: Phase 1/2


title: HapMap Cytosine Modification NA11995

description: Phase 1/2


title: HapMap Cytosine Modification NA07357

description: Phase 1/2


title: HuH-7_originating cell line_R2

description:
HuH-7 P0 T2
Gene expression data from HuH-7 originating cell line.

source_name: HuH-7, originating cell line


title: HapMap Cytosine Modification NA18519

description: Phase 3


title: prostate_cancer_primary_40


title: HuH-7_Passage 1 xenograft_R1

description:
HuH-7 P01 T1
Gene expression data from HuH-7 Passage 1 xenograft.


title: HapMap Cytosine Modification NA11993

description: Phase 1/2


title: HapMap Cytosine Modification NA18505

description: Phase 1/2


title: prostate_cancer_primary_42


title: HapMap Cytosine Modification NA11839

description: Phase 1/2


title: prostate_cancer_primary_39


title: HT-29_Passage 10 xenograft_R5

description:
HT-29 P10 T5
Gene expression data from HT-29 Passage 10 xenograft.

source_name: HT-29, passage 10 xenograft

value: adenocarcinoma GR III colon


title: prostate_cancer_primary_38


title: HapMap Cytosine Modification NA18517

description: Phase 1/2


title: prostate_cancer_primary_37


title: HapMap Cytosine Modification NA19099

description: Phase 1/2


title: HapMap Cytosine Modification NA19257

description: Phase 3


title: HT-29_Passage 10 xenograft_R4

description:
HT-29 P10 T4
Gene expression data from HT-29 Passage 10 xenograft.


title: HuH-7_originating cell line_R1

description:
HuH-7 P0 T1
Gene expression data from HuH-7 originating cell line.


title: HT-29_Passage 10 xenograft_R1

description:
HT-29 P10 T1
Gene expression data from HT-29 Passage 10 xenograft.


title: HapMap Cytosine Modification NA19141

description: Phase 1/2


title: HT-29_Passage 10 xenograft_R3

description:
HT-29 P10 T3
Gene expression data from HT-29 Passage 10 xenograft.


title: HT-29_Passage 10 xenograft_R2

description:
HT-29 P10 T2
Gene expression data from HT-29 Passage 10 xenograft.


title: HapMap Cytosine Modification NA12004

description: Phase 1/2


title: prostate_cancer_primary_36


title: HapMap Cytosine Modification NA19128

description: Phase 1/2


title: prostate_cancer_primary_35


title: HapMap Cytosine Modification NA07056

description: Phase 1/2


title: HapMap Cytosine Modification NA12891

description: Phase 1/2


title: prostate_cancer_primary_34


title: HapMap Cytosine Modification NA12874

description: Phase 1/2


title: prostate_cancer_primary_33


title: HT-29_Passage 4 xenograft_R5

description:
HT-29 P04 T5
Gene expression data from HT-29 Passage 4 xenograft.

source_name: HT-29, passage 4 xenograft


title: HapMap Cytosine Modification NA07055

description: Phase 1/2


title: HapMap Cytosine Modification NA18861

description: Phase 1/2


title: HapMap Cytosine Modification NA12236

description: Phase 1/2


title: HapMap Cytosine Modification NA19130

description: Phase 1/2


title: prostate_cancer_primary_32


title: HapMap Cytosine Modification NA12006

description: Phase 1/2


title: HapMap Cytosine Modification NA19098

description: Phase 1/2


title: HapMap Cytosine Modification NA12875

description: Phase 1/2


title: HT-29_Passage 4 xenograft_R4

description:
HT-29 P04 T4
Gene expression data from HT-29 Passage 4 xenograft.


title: HT-29_Passage 4 xenograft_R2

description:
HT-29 P04 T2
Gene expression data from HT-29 Passage 4 xenograft.


title: prostate_cancer_primary_30


title: HapMap Cytosine Modification NA12003

description: Phase 1/2


title: HT-29_Passage 4 xenograft_R3

description:
HT-29 P04 T3
Gene expression data from HT-29 Passage 4 xenograft.


title: HapMap Cytosine Modification NA18507

description: Phase 1/2


title: HapMap Cytosine Modification NA12751

description: Phase 1/2


title: HapMap Cytosine Modification NA18510

description: Phase 3


title: HT-29_Passage 1 xenograft_R5

description:
HT-29 P01 T5
Gene expression data from HT-29 Passage 1 xenograft.

source_name: HT-29, passage 1 xenograft


title: HT-29_Passage 4 xenograft_R1

description:
HT-29 P04 T1
Gene expression data from HT-29 Passage 4 xenograft.


title: HapMap Cytosine Modification NA18520

description: Phase 3


title: prostate_cancer_primary_28

source_name: primary prostate cancer FFPE tissue sample


title: HapMap Cytosine Modification NA11881

description: Phase 1/2


title: HT-29_Passage 1 xenograft_R4

description:
HT-29 P01 T4
Gene expression data from HT-29 Passage 1 xenograft.


title: HapMap Cytosine Modification NA19209

description: Phase 1/2


title: HapMap Cytosine Modification NA19193

description: Phase 1/2


title: prostate_cancer_primary_31


title: prostate_cancer_primary_27


title: prostate_cancer_primary_26


title: HT-29_Passage 1 xenograft_R2

description:
HT-29 P01 T2
Gene expression data from HT-29 Passage 1 xenograft.


title: prostate_cancer_primary_25


title: HapMap Cytosine Modification NA12156

description: Phase 1/2


title: HT-29_Passage 1 xenograft_R1

description:
HT-29 P01 T1
Gene expression data from HT-29 Passage 1 xenograft.


title: prostate_cancer_primary_24


title: CO ND rep.2

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

hyb_protocol: Hyb wash and stain kit (Affymetrix article no.: 900720)

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Affymetrix Expression Console (v.1.1.): RMA normalization.

source_name: wild-type_normal diet

label_protocol: Total RNA (200 ng) was amplified and labeled following the Affymetrix Whole Transcript Terminal Labeling Kit (Affymetrix article no.: 901524) and WT Expression Kit (Applied Biosystems/Life Technologies article no.: 4411974).

growth_protocol: Mouse facility, diet after 5 weeks of age, sacrificed after 22 weeks of diet

extract_protocol: RNeasy Mini Kit (Quiagen)

treatment_protocol: normal diet or high fat diet or high fat diet + butyrate

tag: strain background

value: mixed

value: wild-type

value: diet after 5 wks of age, sacrificed after 22 wks of diet

tag: diet

value: normal diet

tag: tissue

value: duodenum


title: HapMap Cytosine Modification NA06993

description: Phase 1/2

source_name: lymphoblastoid cell line


title: HapMap Cytosine Modification NA19190

description: Phase 3


title: HT-29_originating cell line_R3

description:
HT-29 P0 T3
Gene expression data from HT-29 originating cell line.

source_name: HT-29, originating cell line


title: ViRas HFD rep.2

source_name: K-Ras mutant_high fat diet

tag: genotype/variation

value: K-Ras mutant

tag: age

value: high fat diet


title: HapMap Cytosine Modification NA12892

description: Phase 1/2


title: HapMap Cytosine Modification NA19200

description: Phase 1/2


title: CO ND rep.1


title: HT-29_originating cell line_R2

description:
HT-29 P0 T2
Gene expression data from HT-29 originating cell line.

tag: originating cell line


title: HapMap Cytosine Modification NA12814

description: Phase 1/2


title: HapMap Cytosine Modification NA18871

description: Phase 1/2


title: prostate_cancer_primary_29

tag: gleason score

tag: metastatic event


title: HapMap Cytosine Modification NA12056

description: Phase 1/2


title: HapMap Cytosine Modification NA12057

description: Phase 1/2


title: prostate_cancer_primary_23


title: HapMap Cytosine Modification NA19137

description: Phase 1/2


title: HapMap Cytosine Modification NA19127

description: Phase 1/2


title: prostate_cancer_primary_22


title: HapMap Cytosine Modification NA12812

description: Phase 1/2


title: prostate_cancer_primary_21


title: prostate_cancer_primary_20


title: HapMap Cytosine Modification NA12146

description: Phase 1/2


title: prostate_cancer_primary_19


title: ViRas HFD rep.1


title: HapMap Cytosine Modification NA18912

description: Phase 1/2


title: HOP-92_Passage 10 xenograft_R5

description:
HOP-92 P10 T5
Gene expression data from HOP-92 Passage 10 xenograft.

source_name: HOP-92, passage 10 xenograft

tag: tumor type

value: large cell undifferentiated lung

tag: in vivo passage


title: CO HFD rep.1

source_name: wild-type_high fat diet


title: CO HFD rep.2


title: Kidney_TIMP2-sham_1

city: Edmonton

first: Zuocheng

last: Wang

address: 407 HMRC

country: Canada

institute: University of Alberta

description: samples are biological replicates

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MG403A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: TIMP2-/- ipsilateral kidney at 3 day post-sham operation

label_protocol: RNA (1-2µg) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) before hybridization to Mouse430A_2 GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All ipsilateral kidneys from sham and UUO treatment were snap frozen in liquid nitrogen immediately after harvest and stored at -80 ºC until extraction.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Life Technologies Inc., Burlington, ON, Canada), total RNA was extracted and purified using the RNeasy Mini kit (Qiagen Inc., Toronto, ON, Canada) (average yield 4µg/kidney sample, RNA integrity number >7).

treatment_protocol: Mice were anesthetised and the right proximal ureter was double ligated without affecting any renal nerve or vascular supply. Sham-operated control mice from each genotype underwent the exact same surgical procedure without ligation of the ureter. Ipsilateral kidneys were flash-frozen in liquid nitrogen for further RNA and protein analyses. No morphologic differences were observed in the contralateral kidneys between genotypes.

tag: strain

value: Ipsilateral kidney

tag: genotype

value: TIMP2 -/-

value: sham


title: Kidney_TIMP3-sham_3

description: samples are biological replicates

source_name: TIMP3-/- ipsilateral kidney at 3 day post-sham operation

value: TIMP3 -/-


title: HT-29_Passage 1 xenograft_R3

description:
HT-29 P01 T3
Gene expression data from HT-29 Passage 1 xenograft.


title: HapMap Cytosine Modification NA18522

description: Phase 1/2

value: YRI


title: FCL_Suspected Mito Disease_Epilepsy

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

hyb_protocol: Following fragmentation, 4.6 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Human Exon 1.0ST cartridge arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Probe-level data in CEL files was normalized by RMA method implemented in the affy package of Bioconductor to get gene-level expression measurements. Alternative CDF file of the HuEx ST1.0 platform was used as library.
probe group file: huex_chop_alt1.cdf
meta-probeset file: annotation.csv

source_name: fibroblast cell line (FCL)

label_protocol: Biotinylated amplified RNA (aRNA) was prepared from 200 ng total RNA using the standard protocol of the Ambion MessageAmp Premier Kit.

growth_protocol: Fibroblast cell lines (FCLs) were obtained from prior skin biopsies when available and/or established in the Clinical CytoGenomics Laboratory from skin biopsies performed in Mitochondrial-Genetics Diagnostic Clinic at The Children’s Hospital of Philadelphia (M.J.F.), following informed consent.

extract_protocol: Total RNA was extracted from frozen FCL pellets per standard protocol by RNeasy Mini kit (Qiagen), after cells were placed in kit lysis buffer and processed by a QIAshredder homogenizer to increase RNA yield.  RNA was analyzed by NanoDrop 1000 spectrophotometer and Agilent 2100 Bioanalyzer in the Nucleic Acid and Protein Core Facility at The Children’s Hospital of Philadelphia, with RNA integrity number (RIN) > 8 acceptable (maximum RIN is 10) for microarray analyses.

treatment_protocol: FCLs were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 1 g/L glucose and supplemented with 20% FBS (Gibco), 1 mM sodium pyruvate (CellGro), 2 mM L-glutamine, and 50 ug/mL uridine (Calbiochem).

value: fibroblast cell line

tag: respiratory chain complex deficiency in muscle

value: No Respiratory Chain Complex Deficiency

tag: gender

value: F

tag: age (years)

tag: informatic analysis group

value: Mito Disease Group


title: Kidney_TIMP2-sham_3

description: samples are biological replicates

tag: treatment


title: Kidney_WT-sham_2

description: samples are biological replicates

source_name: WT ipsilateral kidney at 3 day post-sham operation

value: WT


title: Kidney_TIMP3-sham_2

description: samples are biological replicates


title: Kidney_TIMP2-sham_2

description: samples are biological replicates


title: Kidney_WT-sham_3

description: samples are biological replicates


title: prostate_cancer_primary_18


title: HOP-92_Passage 10 xenograft_R3

description:
HOP-92 P10 T3
Gene expression data from HOP-92 Passage 10 xenograft.


title: HOP-92_Passage 10 xenograft_R4

description:
HOP-92 P10 T4
Gene expression data from HOP-92 Passage 10 xenograft.


title: Kidney_TIMP3-sham_1

description: samples are biological replicates


title: HT-29_originating cell line_R1

description:
HT-29 P0 T1
Gene expression data from HT-29 originating cell line.

value: adenocarcinoma GR III colon


title: HapMap Cytosine Modification NA19147

description: Phase 3

tag: panel

tag: hybridization batch

tag: cell line


title: HapMap Cytosine Modification NA12144

description: Phase 1/2

value: CEU


title: HapMap Cytosine Modification NA18916

description: Phase 3


title: HOP-92_Passage 10 xenograft_R2

description:
HOP-92 P10 T2
Gene expression data from HOP-92 Passage 10 xenograft.


title: HOP-92_Passage 10 xenograft_R1

description:
HOP-92 P10 T1
Gene expression data from HOP-92 Passage 10 xenograft.


title: prostate_cancer_primary_17


title: HapMap Cytosine Modification NA12750

description: Phase 1/2


title: prostate_cancer_primary_16


title: prostate_cancer_primary_15


title: prostate_cancer_primary_14


title: HapMap Cytosine Modification NA11829

description: Phase 1/2


title: prostate_cancer_primary_12


title: FCL_Definite Mito Disease_Complex I_Developmental Delay

tag: tissue

value: Complex I


title: prostate_cancer_primary_13


title: prostate_cancer_primary_11


title: Kidney_WT-sham_1

description: samples are biological replicates


title: HOP-92_Passage 4 xenograft_R5

description:
HOP-92 P04 T5
Gene expression data from HOP-92 Passage 4 xenograft.

source_name: HOP-92, passage 4 xenograft


title: Kidney_TIMP3-UUO_3

description: samples are biological replicates

source_name: TIMP3-/- ipsilateral kidney at 3 day post-UUO operation

value: unilateral ureteral obstruction


title: FCL_Suspected Mito Disease_Leigh syndrome

value: Not Determined

value: Excluded - poor quality


title: prostate_cancer_primary_10


title: HOP-92_Passage 4 xenograft_R4

description:
HOP-92 P04 T4
Gene expression data from HOP-92 Passage 4 xenograft.

value: large cell undifferentiated lung


title: Kidney_TIMP2-UUO_3

description: samples are biological replicates

source_name: TIMP2-/- ipsilateral kidney at 3 day post-UUO operation

value: Ipsilateral kidney


title: FCL_Non-Mito Disease_dysautonomia

value: Control Group


title: FCL_Suspected Mito Disease_leukoencephalopathy

value: M


title: HOP-92_Passage 4 xenograft_R3

description:
HOP-92 P04 T3
Gene expression data from HOP-92 Passage 4 xenograft.


title: prostate_cancer_primary_9


title: FCL_Definite Mito Disease_RRM2B

value: Complex IV; 93% mtDNA depletion in muscle


title: HOP-92_Passage 4 xenograft_R1

description:
HOP-92 P04 T1
Gene expression data from HOP-92 Passage 4 xenograft.


title: Kidney_TIMP3-UUO_1

description: samples are biological replicates

value: TIMP3 -/-


title: Kidney_TIMP2-UUO_2

description: samples are biological replicates

value: TIMP2 -/-


title: FCL_Healthy Control_subject 5

value: fibroblast cell line


title: FCL_Definite Mito Disease_Complex IV_autism+regression

value: Complex IV


title: HOP-92_Passage 4 xenograft_R2

description:
HOP-92 P04 T2
Gene expression data from HOP-92 Passage 4 xenograft.


title: Kidney_TIMP2-UUO_1

description: samples are biological replicates


title: FCL_Suspected Mito Disease_immune disease

value: No Respiratory Chain Complex Deficiency

value: F

value: Mito Disease Group


title: HOP-92_Passage 1 xenograft_R5

description:
HOP-92 P01 T5
Gene expression data from HOP-92 Passage 1 xenograft.

source_name: HOP-92, passage 1 xenograft


title: prostate_cancer_primary_7


title: Kidney_TIMP3-UUO_2

description: samples are biological replicates


title: HOP-92_Passage 1 xenograft_R4

description:
HOP-92 P01 T4
Gene expression data from HOP-92 Passage 1 xenograft.


title: prostate_cancer_primary_6


title: prostate_cancer_primary_8


title: Kidney_WT-UUO_2

description: samples are biological replicates

source_name: WT ipsilateral kidney at 3 day post-UUO operation

value: WT


title: Kidney_WT-UUO_1

description: samples are biological replicates


title: prostate_cancer_primary_4


title: FCL_Healthy Control_subject 4


title: FCL_Definite Mito Disease_MELAS - m.3243A>G


title: FCL_PDHc Deficiency_subject 2


title: FCL_PDHc Deficiency_subject 1


title: Kidney_WT-UUO_3

description: samples are biological replicates


title: prostate_cancer_primary_3


title: FCL_Definite Mito Disease_m.11778G>A and m.14484T>C


title: HOP-92_Passage 1 xenograft_R3

description:
HOP-92 P01 T3
Gene expression data from HOP-92 Passage 1 xenograft.


title: FCL_PC Deficiency

value: Excluded - sample outlier


title: FCL_Definite Mito Disease_m.12264C>T

value: Complexes II and III


title: FCL_Definite Mito Disease_m5537_5537insT


title: WT_2 biological rep2

city: Richmond

first: Myrna

last: Serrano

state: VA

address: 1101 East Marshall St

institute: Virginia Commonwealth University

description: Gene expression data from mice control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0002.

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

data_processing: The data were analyzed with  Affymetrix Expression Console software using Affymetrix default analysis settings and RMA as normalization method.

source_name: control mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ηg total RNA (GeneChip 3' IVT Express Kit, P/N 702646 Rev. 8, Affymetrix).

growth_protocol: Primary hepatocytes were isolated from WT and Alb/AEG-1 mice and plated on collagen-coated plates. Cells were harvested 24 hours after plating.

extract_protocol: Trizol extraction of total RNA was performed using QIAGEN columns according to the manufacturer's instruction.

treatment_protocol: No treatment.

value: hepatocyte

tag: genotype/variation

value: wild type

value: mixed strain B6/CBA


title: prostate_cancer_primary_5

source_name: primary prostate cancer FFPE tissue sample


title: WT_1 biological rep1

description: Gene expression data from mice control


title: HOP-92_originating cell line_R2

description:
HOP-92 P0 T2
Gene expression data from HOP-92 originating cell line.

source_name: HOP-92, originating cell line

tag: originating cell line

value: large cell undifferentiated lung


title: HOP-92_originating cell line_R1

description:
HOP-92 P0 T1
Gene expression data from HOP-92 originating cell line.


title: TG_3 biological rep3

description: Gene expression data from hepatocyte-specific overexpression of AEG-1

source_name: overexpression AEG-1

value: overexpression of AEG-1


title: prostate_cancer_primary_2

tag: gleason score


title: HOP-92_Passage 1 xenograft_R2

description:
HOP-92 P01 T2
Gene expression data from HOP-92 Passage 1 xenograft.


title: HOP-92_originating cell line_R3

description:
HOP-92 P0 T3
Gene expression data from HOP-92 originating cell line.


title: HOP-92_Passage 1 xenograft_R1

description:
HOP-92 P01 T1
Gene expression data from HOP-92 Passage 1 xenograft.


title: prostate_cancer_primary_1

tag: metastatic event


title: HOP-62_Passage 10 xenograft_R4

description:
HOP-62 P10 T4
Gene expression data from HOP-62 Passage 10 xenograft.

source_name: HOP-62, passage 10 xenograft

tag: tumor type

value: adenocarcinoma lung


title: TG_1 biological rep1


title: HOP-62_Passage 10 xenograft_R5

description:
HOP-62 P10 T5
Gene expression data from HOP-62 Passage 10 xenograft.

tag: in vivo passage


title: FCL_Definite Mito Disease_m.12264C>T [excluded]

value: Complexes I and III

value: M

value: Excluded - poor quality


title: FCL_Non-Mito Disease_MEF2C deletion

value: fibroblast cell line

value: Control Group


title: WT_3 biological rep3

description: Gene expression data from mice control

tag: strain


title: noLac_vs_DL-Lac

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: 1.Used script to split 8-array imagene file of Cy3 intensity into eight separate Cy3 files.  2.Used script to split 8-array imagene file of Cy5 intensity into eight separate Cy5 files.  3.For each indidivual array, a merge file was produced consisting of merging the Cy3 and Cy5 intensity files created in step 1 and 2. The merged file is provided as supplementary file for each array.  4.Background correction (Mean values). Values below 0 (higher background than foreground) were disregarded 5. LOWESS normalization was performed using the BASE plugin 6. Normalised data was further processed using an R package (limma) to get to sample to sample comparisons with p-values (false discovery rate)

organism: Lactiplantibacillus plantarum

source_name: TF101 no lactate added

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 3 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: A mutant of L. plantarum NCIMB8826 deficient for NAD-dependent L-lactate activity (TF101; Ferain et al. 1994. 176:596), and thus producing no L-lactate, was grown in MRS medium at 28°C until mid-exponential phase (OD600nm 0.75). The culture was then divided into 3 sub-cultures. Optically pure sodium L-lactate (200 mM) was added to the first sub-culture (TF101 + L-lac 200 mM). An equimolar mixture of sodium D- and L-lactate (100 mM each) was added to the second sub-culture (TF101 + L/D-lac 200 mM). The third sub-culture was not treated (TF101). The three sub-cultures were further incubated at 28°C for 1h30 (a time known to be sufficient for induction of lactate racemase activity by L-lactate).

extract_protocol: 1.Resuspend the frozen cell pellet thoroughly in TE buffer  2. Aliquot the resuspended cell pellet (400 µl per tube) in screw-cap tubes containing 500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm)  3.Freeze the tube immediately in liquid nitrogen  4.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  5.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  6.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  7.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  8.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  9.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   10.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: Cells were harvested by centrifugation (5,000xg, 10 minutes). Cell pellets were stored at -20°C until extraction.

value: control

source_name: TF101 200 mM DL-lactate added

value: L/D lac 200 mM


title: FCL_Healthy Control_subject 3

value: Not Determined

value: not obtained


title: TG_2 biological rep2


title: FCL_Suspected Mito Disease_optic atrophy

value: No Respiratory Chain Complex Deficiency

value: Mito Disease Group


title: FCL_Definite Mito Disease_Leigh syndrome

value: Complex I+III Deficiency

value: F


title: FCL_Healthy Control_subject 2


title: noLac_vs_L-lac

source_name: TF101 200 mM L-lactate added

value: L-lac 200 mM


title: FCL_Healthy Control_subject 1


title: HOP-62_Passage 10 xenograft_R2

description:
HOP-62 P10 T2
Gene expression data from HOP-62 Passage 10 xenograft.


title: Uterine epithelial cells isolated from Stat3 flox control mice on day 4 of pregnancy

city: urbana

first: Sandeep

last: Pawar

address: apt 6

department: Molecular and Integrative Physiology

description: Knocout epithelial RNA

hyb_protocol: The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining.  A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide.  Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430A 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA).  The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and  counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.

scan_protocol: The chip was scanned with a GeneChip Scanner model 3000 7G Plus.  Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file.  The quality of the image file was evaluated visually before further processing.

data_processing: The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150.

source_name: Mouse uterine epithelial cells

label_protocol: Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.  Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1.  Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA.  A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA.  The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours.  The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.

growth_protocol: Uteri were removed from Day 4 or Day 5 pregnant mice. With the aid of a dissecting microscope, each uterine horn was cut transversely into two equal segments. The tissues were then incubated in 10 ml of a solution of 0.5% bovine pancreatic trypsin (Cooper Biomedical, Malvern, PA) in Ca- and Mg-free PBS, pH 7.4 Tissues were first incubated at 4 C for 1 h and then at 37 C for 40 min. After incubation, the uterine tissue was squeezed with forceps dissociating the epithelium from the uterine pieces. The epithelial fragments in the supernatant were collected with a pipette; this procedure was repeated three or four times. The epithelial fragments were collected by centrifugation at 100 X g for 5 min. The resulting cell pellet was subjected to RNA isolation protocol.

extract_protocol: Total RNA was extracted from human endometrial stromal cells using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: The uterine epithelial cells isolated from the uteri of mice were directly used for RNA extraction, they were not subjected to any form of treatment.

tag: time

value: day 4 pregnancy

tag: cell type

value: Mouse uterine epithelial cells

tag: genotype

value: Stat3 knockout