title: CP-UT-21

value: Blood

value: Under Treatment-Droxygel (Antacid), Unidrea and Imatinib treated for 3.8 years


title: CP-NEW-9

status: Public on Jan 26 2016

type: RNA

city: Lucknow

first: Neetu

last: Singh

address: Chowk

department: Center for Advance Research

country: India

institute: King George's Medical University

hyb_protocol: Following fragmentation, 5.5 ug of single stranded cDNA were hybridized for 16 hr at 45C on Human Transcripptome Array 2.0. GeneChips were washed and stained in the Gene Chip Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console 3.0 using settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (GeneChip WT expression Array Manual,  Affymetrix).

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

treatment_protocol: All patients were commenced to Imatinib treatment alone or in combination with Hydrea/Hydroxyurea. Importantly, in some cases when patients failed to achieve time dependent molecular targets we switched to nilotinib or high dose Imatinib. Clinical outcomes included molecular response on the basis of BCR-ABL1

tag: disease state

value: CML

tag: tissue

tag: phase

value: Chronic Phase

tag: treatment

value: NEW

tag: age

value: 46 years

tag: gender

value: male


title: CP-UT-58

value: Under Treatment-Hydroxyurea , Zyloric and  Imatinib treated nine months

value: 32 years

value: female


title: RA-10

status: Public on Jan 27 2016

city: Nijmegen

first: Mathijs

last: Broeren

address: Geert Grootplein 28

department: Department of Rheumatology

country: Netherlands

institute: Radboud university medical Center

hyb_protocol: Hybridization to U133Plus 2.0 was performed according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

scan_protocol: The arrays were scanned using a GeneChip Scanner (Affymetrix)

data_processing: The arrays were analyzed using Affymetrix GeneChip Operating Software version 1.4. Array normalization and expression value calculation were performed using DNA-Chip Analyzer version 1.3. The Invariant Set Normalization method and the model-based method were used for computing expression values.

source_name: RA, synovium

label_protocol: Biotinylated cRNA was generated according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

extract_protocol: Total RNA was isolated from the synovial samples using the Rneasy kit for fibrous tissue according the manufacturer's protocol (Qiagen, Venlo, Netherlands).

value: Rheumatoid arthritis

value: synovium


title: AP-UT-86

value: Accerelated Phase

value: Under Treatment Imatinib and Nilotinib for 5 months

value: 49 years


title: AP-UT-70

value: Accelerated Phase

value: Under Treatment Imatinib and Nilotinib treated 1 year

value: 30 years


title: IkL/L anti-IgM 12h rep2

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

hyb_protocol: 10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.

data_processing: CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor (v. 2.12 with the v.3.0.1 of R) with default settings to calculate probe set signal intensities

organism: Mus musculus

source_name: IkL/L_follicular B cells_anti-IgM 12h

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from 100 ng of total RNA  in a two cycle target labeling assay

growth_protocol: FO B cells were sorted (B220+CD23hiCD21lo; >98% purity) on a FACSVantage SE option DiVa (BD Biosciences). Cells were cultured in complete medium (RPMI1640, 10% FCS, 25 mM HEPES, 1 mM sodium pyruvate, 2 mM L-glutamine, 1x non-essential amino acids, 5x10^-5 M 2-mercaptoethanol, 1% antibiotics) and stimulated or not with 10 μg/ml goat anti-mouse IgM F(ab')2 (Jackson Immunoresearch).

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro  kit

tag: strain background

value: 6 weeks

tag: genotype/variation

value: IkL/L

tag: cell type

value: cultured sorted follicular splenic B cells

tag: stimulated with

value: anti IgM for 12hrs


title: CP-UT-71

value: CML

value: Blood

value: Chronic Phase

value: Under Treatment-Initially Hydab, Uridrea and since october 2012 Imatinib 8.1 years

value: 52 years


title: IkL/L anti-IgM 12h rep1


title: IkL/L anti-IgM 3h rep2

source_name: IkL/L_follicular B cells_anti-IgM 3h

value: anti IgM for 3hrs


title: AP-NEW-73

value: NEW

value: 50 years

value: male


title: AP-UT-72

value: Under Treatment Imatinib and Nilotinib treated 6 months

value: 45 years


title: IkL/L unstimulated rep2

source_name: IkL/L_follicular B cells_unstimulated

value: none (unstimulated control)


title: WT unstimulated rep 1

source_name: WT_follicular B cells_unstimulated

value: wild type


title: WT anti-IgM 3h rep1

source_name: WT_follicular B cells_anti-IgM 3h

value: 6 weeks


title: IkL/L unstimulated rep1

value: IkL/L


title: WT unstimulated rep2

value: cultured sorted follicular splenic B cells


title: WT anti-IgM 3h rep2


title: IkL/L anti-IgM 3h rep1


title: CP-NEW-83

value: 70 years


title: WT anti-IgM 12h rep2

source_name: WT_follicular B cells_anti-IgM 12h

value: anti IgM for 12hrs


title: WT anti-IgM 12h rep1


title: PS2APP 3 months SAM14136230

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description: PS2APP 3 months SAM14136230

hyb_protocol: 750 ng of labeled cRNA was fragmented and hybridized to Agilent’s Whole Mouse Genome 4x44Kv2 arrays as described in manufacturer’s hybridization kit, against an equal amount of Cy3-labeled universal mouse reference (Stratagene).

scan_protocol: Following hybridization, microarrays were washed, dried, and scanned on Agilent’s G2505C scanner. Agilent’s Feature Extraction 11.5 software was used to analyze acquired array images.

data_processing: Data were analyzed using the limma package from Bioconductor. ControlType weights were set to 0, spots with background signal more than 50 above the foreground signal were set to the median background intensity, background correction was performed with limma::backgroundCorrect() using the "normexp" method and an offset of 50, limma::normalizeWithinArrays() with the "loess" method,  and finally limma::normalizeBetweenArrays() with the "Aquantile" method. This gives the "test" and "reference" normalized probe intensities. Finally, for each probe an "expression ratio" was calculated, the ratio of the normalized signals in the test and reference channels.

source_name: RNA from whole cortex

label_protocol: The method for preparation of Cy-dye labeled cRNA and array hybridization was provided by Agilent. Briefly, 1 μg total RNA was converted to double-stranded cDNA and then to Cy5-labeled cRNA using Quick Amp Labeling Kit (Agilent). The labeled cRNA was purified using RNeasy mini kit (Qiagen). cRNA yield and Cy5 incorporation was determined using ND-1000 spectrophotometer.

extract_protocol: Hemicortices were rapidly frozen on dry ice and stored until a full collection was obtained. RNA was extracted using Qiazol per manufacturer instruction's, then cleaned up using RNEasy column with on-column DNase digestion (Qiagen). Quantity and quality of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

value: whole cortex

tag: genotype

value: 3 months

tag: samid

source_name: universal mouse reference (Stratagene)

label_protocol: Method for Cy-dye labeled cRNA preparation was provided by Agilent.

extract_protocol: By vendor


title: AP-UT-69

value: CML

value: Blood

value: Accelerated Phase

value: Under Treatment Imatinib treated 3 months

value: 40 years

value: female


title: WT 3 months SAM14136216

description: WT 3 months SAM14136216

value: WT


title: WT 13 months SAM14136227

description: WT 13 months SAM14136227

value: 13 months


title: WT 7 months SAM14136224

description: WT 7 months SAM14136224

value: 7 months


title: PS2APP 7 months SAM14136239

description: PS2APP 7 months SAM14136239


title: WT 3 months SAM14136218

description: WT 3 months SAM14136218


title: PS2APP 7 months SAM14136236

description: PS2APP 7 months SAM14136236


title: WT 13 months SAM14136226

description: WT 13 months SAM14136226


title: PS2APP 7 months SAM14136237

description: PS2APP 7 months SAM14136237


title: WT 7 months SAM14136223

description: WT 7 months SAM14136223


title: WT 3 months SAM14136219

description: WT 3 months SAM14136219


title: PS2APP 13 months SAM14136244

description: PS2APP 13 months SAM14136244


title: WT 3 months SAM14136215

description: WT 3 months SAM14136215


title: PS2APP 7 months SAM14136238

description: PS2APP 7 months SAM14136238


title: WT 7 months SAM14136220

description: WT 7 months SAM14136220


title: PS2APP 13 months SAM14136240

description: PS2APP 13 months SAM14136240


title: PS2APP 13 months SAM14136242

description: PS2APP 13 months SAM14136242


title: PS2APP 3 months SAM14136233

description: PS2APP 3 months SAM14136233


title: PS2APP 3 months SAM14136231

description: PS2APP 3 months SAM14136231


title: PS2APP 13 months SAM14136241

description: PS2APP 13 months SAM14136241


title: PS2APP 7 months SAM14136235

description: PS2APP 7 months SAM14136235


title: PS2APP 13 months SAM14136243

description: PS2APP 13 months SAM14136243


title: WT 7 months SAM14136222

description: WT 7 months SAM14136222


title: SAHA-2

city: Shanghai

first: Hanlin

last: Zeng

address: 555 Zuchongzhi Road

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of scineces

description: 8 hrs after 5μM SAHA treatment

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#0000212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

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

source_name: MDA-MB-231 Breast cancer cell line

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

growth_protocol: DMEM/F12 medium with 10%FBS

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-18Life technologies,Carlsbad, CA, US)following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: 8hr's treatment with 5μM SAHA or DMSO

tag: cell line


title: Con-3

description: 8 hrs after DMSO treatment


title: PS2APP 3 months SAM14136232

description: PS2APP 3 months SAM14136232


title: WT 3 months SAM14136217

description: WT 3 months SAM14136217


title: SAHA-1

description: 8 hrs after 5μM SAHA treatment


title: Con-2

description: 8 hrs after DMSO treatment


title: WT 13 months SAM14136225

description: WT 13 months SAM14136225


title: 447

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

description:
Sentrix_ID : 6331441018
Sentrix_Position : H

hyb_protocol: cRNA was hybridized according to standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Raw Illumina gene expression data were processed using variance stabilization and quantile normalization with the lumi package in R, filtered to include only probes with detection call p value < 0.05 in at least seven of the arrays, followed by batch-removal using COMBAT.  Same-gene probes were consolidated to a single identifier keeping the probe with highest mean value.

source_name: Kidney

label_protocol: cRNA was generated and labeled by incorporating biotin-16-UTP.

extract_protocol: RNA was isolated using Trizol (Invitrogen), followed by RNeasy plus kit (Qiagen)

tag: batch

value: J

value: N

value: M

tag: bw(body weight in g)

tag: kw1(kidney 1 weight in g)

tag: kw2 (kidney 2 weight in g)

tag: lw (liver weight in g)

tag: kbw (kidney/body weight)

tag: lbw (liver/body weight)


title: SAHA-3

description: 8 hrs after 5μM SAHA treatment


title: 87483

description:
Sentrix_ID : 6331441018
Sentrix_Position : F

value: P


title: 87481

description:
Sentrix_ID : 6331441018
Sentrix_Position : C


title: 55274

description:
Sentrix_ID : 6331441018
Sentrix_Position : E

value: F


title: PS2APP 3 months SAM14136234

description: PS2APP 3 months SAM14136234

tag: tissue


title: 90505

description:
Sentrix_ID : 6331441018
Sentrix_Position : D

tag: age


title: 90515

description:
Sentrix_ID : 6331441018
Sentrix_Position : B

tag: gender


title: 90507

description:
Sentrix_ID : 6331441018
Sentrix_Position : G


title: 87479

description:
Sentrix_ID : 6331441016
Sentrix_Position : G

value: I


title: WT 7 months SAM14136221

description: WT 7 months SAM14136221

value: whole cortex


title: 31586

description:
Sentrix_ID : 6331441016
Sentrix_Position : H


title: Con-1

description: 8 hrs after DMSO treatment


title: Mec1_shCTR

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description:
shCTRL
5050509016_K_Grn.idat

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation

source_name: CLL Mec1 cell line transduced with control shRNA sequence

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

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

treatment_protocol: Mec1 cells were subjected to multiple cycles of infection with lentivirus carrying specific shRNAs and then maintained in culture for at least 5 passages

value: Male


title: 90510

description:
Sentrix_ID : 6331441016
Sentrix_Position : C


title: 90587

description:
Sentrix_ID : 6331441018
Sentrix_Position : A


title: 451

description:
Sentrix_ID : 6331441016
Sentrix_Position : D


title: 87473

description:
Sentrix_ID : 6331441016
Sentrix_Position : F


title: Mec1_sh23

description:
shHIF-1a
5050509016_L_Grn.idat

source_name: CLL Mec1 cell line transduced with an shRNA sequence against HIF-1a


title: Cipro vs no Cipro 2

city: Bielefeld

first: Dorit

last: Lubitz

address: Universitätsstraße 25

country: Germany

institute: University of Bielefeld

description: Cultivation in CGXII medium with 1 % glucose. Sample taken in early exponentional phase of growth. Comparison of ciprofloxacin treated C. glutamicum WT with untreated C. glutamicum WT.

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was performed with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were upregulated in WT(pEKEx3-sigH) under both 10 μM and 15 μM of IPTG concentration were taken into account for further analysis (p-value < 0.05, M value > 1).

organism: Corynebacterium glutamicum

source_name: WT with 4 µg/ml cipro

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: C. glutamicum WT was cultured in BHI medium for overnight and inoculated into 50 mL CGXII medium with 10 g/L glucose at the initial O.D. of 1. Cells were harvested in the early exponential growth phase (O.D. 600 nm of 5).

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: Ciprofloxacin (4 µg/ml) was added from the beginning of the growth.

tag: growth

value: Early exponential phase of growth

source_name: WT with 0 µg/ml cipro

tag: growht


title: Cipro vs no Cipro 1


title: Cipro vs no Cipro 3


title: 90588

description:
Sentrix_ID : 6331441016
Sentrix_Position : A


title: 89994

description:
Sentrix_ID : 6331441015
Sentrix_Position : F

value: H


title: WT 13 months SAM14136228

description: WT 13 months SAM14136228


title: 31588

description:
Sentrix_ID : 6331441015
Sentrix_Position : C


title: 89996

description:
Sentrix_ID : 6331441016
Sentrix_Position : B


title: 50175

description:
Sentrix_ID : 6331441015
Sentrix_Position : H


title: 55276

description:
Sentrix_ID : 6331441015
Sentrix_Position : G


title: 87480

description:
Sentrix_ID : 6331441015
Sentrix_Position : A


title: sh Ep400 [5455311040_C]

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

institute: CEA-DRF

description: SAMPLE 4

data_processing: The data were normalised using quantile normalisation with GenomeStudio

label: Biotin

source_name: Mouse ES cells

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

growth_protocol: Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and a saturating amount of leukemia inhibitory factor (LIF)

extract_protocol: Total RNA was extracted using an RNeasy Kit (Qiagen)

treatment_protocol: The pHYPER shRNA vectors were transfected in embryonic stem cells cell by electroporation. 24 h after transfection, puromycin selection was applied for an additional 48 h period, before cell collection and RNA preparation

tag: transfection

value: shRNA Ep400

tag: sample id


title: 89995

description:
Sentrix_ID : 6331441009
Sentrix_Position : E

value: G

tag: genotype


title: 50178

description:
Sentrix_ID : 6331441015
Sentrix_Position : E


title: 90511

description:
Sentrix_ID : 6331441009
Sentrix_Position : C


title: 87477

description:
Sentrix_ID : 6331441015
Sentrix_Position : D


title: 50174

description:
Sentrix_ID : 6331441009
Sentrix_Position : H


title: control, Ep400 [5455311040_E]

description: SAMPLE 2

value: control


title: sh Ep400 [5455311040_A]

description: SAMPLE 6


title: 90589

description:
Sentrix_ID : 6331441009
Sentrix_Position : G


title: sh Ep400 [5455311040_B]

description: SAMPLE 5


title: 90506

description:
Sentrix_ID : 6331441016
Sentrix_Position : E


title: control, Ep400 [5455311040_D]

description: SAMPLE 3


title: sh Chd9 [5506502022_A]

description: SAMPLE 6

value: shRNA Chd9


title: WT 13 months SAM14136229

description: WT 13 months SAM14136229

value: WT

tag: samid


title: control, Ep400 [5455311040_F]

description: SAMPLE 1


title: 55275

description:
Sentrix_ID : 6331441009
Sentrix_Position : F


title: 90517

description:
Sentrix_ID : 6331441009
Sentrix_Position : D


title: sh Chd9 [5506502022_B]

description: SAMPLE 5


title: 87485

description:
Sentrix_ID : 6331441015
Sentrix_Position : B


title: 448

description:
Sentrix_ID : 6331441009
Sentrix_Position : A


title: sh Chd9 [5506502022_C]

description: SAMPLE 4


title: 89991

description:
Sentrix_ID : 6331441005
Sentrix_Position : H


title: 50176

description:
Sentrix_ID : 6331441005
Sentrix_Position : E


title: control, Chd9 [5506502022_E]

description: SAMPLE 2


title: control, Chd9 [5506502022_D]

description: SAMPLE 3


title: 50179

description:
Sentrix_ID : 6331441005
Sentrix_Position : D


title: sh Chd8 [5452647037_A]

description: SAMPLE 6

value: shRNA Chd8


title: 55279

description:
Sentrix_ID : 6331441005
Sentrix_Position : F


title: sh Chd8 [5452647037_B]

description: SAMPLE 5


title: sh Chd8 [5452647037_C]

description: SAMPLE 4


title: 89992

description:
Sentrix_ID : 6331441005
Sentrix_Position : G


title: 90504

description:
Sentrix_ID : 6331441002
Sentrix_Position : E

value: E


title: 87476

description:
Sentrix_ID : 6331441002
Sentrix_Position : H


title: 87475

description:
Sentrix_ID : 6331441005
Sentrix_Position : A


title: control, Chd9 [5506502022_F]

description: SAMPLE 1


title: 55273

description:
Sentrix_ID : 6331441002
Sentrix_Position : G


title: control, Chd8 [5452647037_D]

description: SAMPLE 3


title: 89997

description:
Sentrix_ID : 6331441002
Sentrix_Position : F


title: control, Chd6 [9341927038_A]

description: SAMPLE 6


title: control, Chd8 [5452647037_E]

description: SAMPLE 2


title: 31587

description:
Sentrix_ID : 6331441005
Sentrix_Position : C


title: 55296

description:
Sentrix_ID : 6331441005
Sentrix_Position : B


title: 90586

description:
Sentrix_ID : 6331441002
Sentrix_Position : C


title: 87484

description:
Sentrix_ID : 6331441009
Sentrix_Position : B


title: control, Chd6 [9341927038_B]

description: SAMPLE 5


title: sh Chd6 [9341927038_D]

description: SAMPLE 3

value: shRNA Chd6


title: 90509

description:
Sentrix_ID : 6331441002
Sentrix_Position : D


title: control, Chd6 [9341927038_C]

description: SAMPLE 4


title: sh Chd6 [9341927038_E]

description: SAMPLE 2


title: 60443

description:
Sentrix_ID :6033111129
Sentrix_Position : D

value: D


title: 50177

description:
Sentrix_ID : 6331441002
Sentrix_Position : B

value: M


title: 55291

description:
Sentrix_ID : 6331441002
Sentrix_Position : A

value: N


title: 60477

description:
Sentrix_ID :6033111129
Sentrix_Position : H

value: P

value: F


title: 60464

description:
Sentrix_ID :6033111129
Sentrix_Position : E


title: sh Chd4 [9341927040_E]

description: SAMPLE 5

value: shRNA Chd4


title: endometrium, negative control

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

description:
C 20130523_(hGlue_3_0_v1)
lncRNA  and mRNA expression data from negative healthy endometrium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: hGlue_3_0_v1.pgf
meta-probeset file: hGlue_3_0_v1.TC.mps

source_name: endometrium form healthy female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: subject status

value: healthy

value: endometrium


title: 60474

description:
Sentrix_ID :6033111129
Sentrix_Position : G

tag: batch


title: control, Chd4 [9341927038_B]

description: SAMPLE 2


title: sh Chd4 [9341927040_F]

description: SAMPLE 6

value: Sh-B 30


title: 60404

description:
Sentrix_ID :6033111129
Sentrix_Position : A

tag: bw(body weight in g)


title: control, Chd4 [9341927038_A]

description: SAMPLE 3


title: serum, negative control

description:
serum 1_(hGlue_3_0_v1)
lncRNA and mRNA expression data from negative control serum

source_name: serum from healthy female

value: serum


title: sh Chd4 [9341927040_D]

description: SAMPLE 4


title: eutopic endometrium tissue

description:
EU 20130523_(hGlue_3_0_v1)
lncRNA  and mRNA expression data from eutopic endometrium tissue

source_name: eutopic endometrium tissue from endometriosis patient

value: endometriosis patient

value: ectopic endometrium


title: 60472

description:
Sentrix_ID :6033111129
Sentrix_Position : F

tag: kw1(kidney 1 weight in g)


title: 60416

description:
Sentrix_ID :6033111129
Sentrix_Position : B

tag: kw2 (kidney 2 weight in g)


title: control, Chd4 [9341927038_C]

description: SAMPLE 1

value: control


title: control, Chd8 [5452647037_F]

description: SAMPLE 1


title: sh Chd1 [5452647020_B]

description: SAMPLE 5

value: shRNA Chd1


title: sh Chd6 [9341927038_F]

description: SAMPLE 1


title: 60478

description:
Sentrix_ID :6033111114
Sentrix_Position : G

value: C

tag: lw (liver weight in g)


title: sh Chd1 [5452647020_A]

description: SAMPLE 6


title: control, Chd1 [5452647020_D]

description: SAMPLE 3


title: serum, endometriosis patient

description:
serum 2_(hGlue_3_0_v1)
lncRNA  and mRNA expression data from endometriosis patient serum

source_name: serum from serum from endometriosis patient


title: ectopic endometrium tissue

description:
EC 20130523_(hGlue_3_0_v1)
lncRNA  and mRNA expression data from ectopic endometrium tissue

source_name: ectopic endometrium tissue from endometriosis patient


title: 60417

description:
Sentrix_ID :6033111129
Sentrix_Position : C

tag: kbw (kidney/body weight)


title: sh Chd1 [5452647020_C]

description: SAMPLE 4


title: 66924

description:
Sentrix_ID :6033111114
Sentrix_Position : H

tag: lbw (liver/body weight)


title: 60418

description:
Sentrix_ID :6033111114
Sentrix_Position : C


title: Psl mutant, biological replicate2

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression data from Psl mutant grown till exponential phase

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix Pseudomonas aeruginosa Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Pseudomonas aeruginosa PAO1

source_name: Exponential phase bacterial culture of Psl mutant

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bacterial cells were grown for 6 hrs to reach exponential phase at 37C.

treatment_protocol: Bacterial cells were collected and kept on ice to extract RNA.

tag: strain

tag: genotype/variation

value: Psl mutant

tag: growth protocol

value: liquid LB medium

tag: growth stage

value: Exponential phase


title: Wild type PAO1, biological replicate1

description: Gene expression data from wild type PAO1 grown till exponential phase

source_name: Exponential phase bacterial culture of wild type PAO1

value: Wild type


title: 60468

description:
Sentrix_ID :6033111114
Sentrix_Position : F

value: N

tag: gender

tag: age


title: Colorectal liver metastasis endothelial sample 5

city: Birmingham

first: Joseph

middle: William

last: Wragg

state: West Midlands

address: Edgbaston

department: Institute of Biomedical Research

country: United Kingdom

institute: University of Birmingham

description: Met 5.txt

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851B) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x80k array slides (Scan Area 61x21.6 mm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were processed with Feature Extraction Software 9.1 (Agilent) using default parameters and analysed in R to obtain background subtracted and normalised signal intensities (included in the sample data table).  The data was further analysed to generate gene expression comparison matrices between matched cancer and healthy arrays (provided in the 'custom_data_matrix.txt'). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. An explaination of the R analysis program used is detailed in the 'R analysis command line.txt.

label_protocol: Cy3 labeled cRNA was prepared from 50ng RNA, using the Agilient low input, quick amp, one colour labelling kit according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from the endothelial isolates using the Qiagen miRNA easy kit according to the manufacturer's protocol.

treatment_protocol: Fresh Tumour and matched healthy tissue was taken from resections of renal cell carcinoma, colorectal cancer and colorectal metastasis to the liver. The endothelum was isolated from these tissues using collagenase V digestion, and dynabead magnetic bead isolation conjugated to lectin from Ulex Europaeus (Ulex Europaeus Agglutinin I (UEA I)), which binds human endothelial cells.

tag: age (yrs)

value: female

tag: tumour grade

value: Moderate

tag: tissue

value: Colorectal liver metastasis endothelial


title: 60479

description:
Sentrix_ID :6007473009
Sentrix_Position : G

value: B

tag: genotype

value: M


title: Wild type PAO1, biological replicate2


title: 60463

description:
Sentrix_ID :6033111114
Sentrix_Position : E

tag: batch

value: P

value: F


title: Psl mutant, biological replicate1


title: 60469

description:
Sentrix_ID :6007473009
Sentrix_Position : E

tag: bw(body weight in g)


title: 60415

description:
Sentrix_ID :6033111114
Sentrix_Position : B

tag: kw1(kidney 1 weight in g)


title: 60414

description:
Sentrix_ID :6033111114
Sentrix_Position : A

tag: kw2 (kidney 2 weight in g)


title: Healthy liver endothelial sample 7

description: Liver 7.txt

source_name: Healthy liver endothelial sample

value: male

value: Healthy liver endothelial


title: Healthy liver endothelial sample 4

description: Liver 4.txt


title: Healthy liver endothelial sample 2

description: Liver 2.txt


title: 60461

description:
Sentrix_ID :6033111114
Sentrix_Position : D

tag: lw (liver weight in g)


title: control, Chd1 [5452647020_E]

description: SAMPLE 2

tag: transfection

value: control

tag: sample id


title: 60470

description:
Sentrix_ID :6007473009
Sentrix_Position : F

tag: kbw (kidney/body weight)

tag: lbw (liver/body weight)


title: 66926

description:
Sentrix_ID :6007473009
Sentrix_Position : H


title: Colorectal liver metastasis endothelial sample 4

description: Met 4.txt

tag: tumour location

value: Caecum


title: Colorectal liver metastasis endothelial sample 7

description: Met 7.txt

value: Rectum


title: control, Chd1 [5452647020_F]

description: SAMPLE 1


title: Healthy liver endothelial sample 5

description: Liver 5.txt


title: Colorectal liver metastasis endothelial sample 2

description: Met 2.txt


title: 60466

description:
Sentrix_ID :6007473009
Sentrix_Position : D


title: 60413

description:
Sentrix_ID :6007473009
Sentrix_Position : B


title: 60465

description:
Sentrix_ID :6007473009
Sentrix_Position : C


title: Renal cancer endothelial sample 2

description: RCC 2.txt

source_name: Renal cancer endothelial sample

value: Papillary

tag: tumor stage

value: pT3c N0

value: Renal cancer endothelial


title: Renal cancer endothelial sample 4

description: RCC 4.txt

tag: gender

value: Clear cell

value: 2 to 3

value: pT3a Nx


title: Renal cancer endothelial sample 3

description: RCC 3.txt

value: Clear cell (cystic)

value: pT2a Nx


title: 60467

description:
Sentrix_ID :6007473008
Sentrix_Position : D

value: A

tag: age


title: 66923

description:
Sentrix_ID :6007473008
Sentrix_Position : G


title: Colorectal cancer endothelial sample 4

description: CRC 4.txt

source_name: Colorectal cancer endothelial sample

tag: age (yrs)

value: Moderate

value: pT3 N0

value: Colorectal cancer endothelial


title: 66927

description:
Sentrix_ID :6007473008
Sentrix_Position : H

value: P

value: M


title: Healthy kidney endothelial sample 6

description: Kidney 6.txt

source_name: Healthy kidney endothelial sample

value: female

value: Healthy kidney endothelial


title: Renal cancer endothelial sample 6

description: RCC 6.txt

tag: tumour grade

value: PT3a/b N0


title: 60471

description:
Sentrix_ID :6007473008
Sentrix_Position : E

source_name: Kidney

value: N

value: F


title: 60444

description:
Sentrix_ID :6007473008
Sentrix_Position : C


title: Healthy colon endothelial sample 4

description: Colon 4.txt

source_name: Healthy colon endothelial sample

value: male

tag: tissue

value: Healthy colon endothelial


title: 60403

description:
Sentrix_ID :6007473008
Sentrix_Position : B

tag: genotype


title: 60402

description:
Sentrix_ID :6007473009
Sentrix_Position : A

tag: batch

value: B


title: Healthy colon endothelial sample 3

description: Colon 3.txt


title: Colorectal cancer endothelial sample 1

description: CRC 1.txt

value: Sigmoid

value: pT4b N1


title: Healthy kidney endothelial sample 4

description: Kidney 4.txt


title: 60401

description:
Sentrix_ID :6007473008
Sentrix_Position : A

tag: bw(body weight in g)


title: Colorectal cancer endothelial sample 3

description: CRC 3.txt

value: Rectum

value: Poor

value: pT3 N1


title: KU812 CD25 shRNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Human Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT PLUS Reagent Kit User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

source_name: CML cell line

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Cat.Nr. 902281)

growth_protocol: KU812 cells transduced with a shRNA against CD25 or a control random shRNA were cultured in RPMI medium supplemented with 10% FCS and antibiotics at 37°C

extract_protocol: Total RNA was extracted from CML cells using RNeasy Micro-Kit (Qiagen) and used (5 µg total RNA) for Gene Chip analyses

treatment_protocol: KU812 cells were transduced in the presence of polybrene (7 µg/mL) and selected with puromycin (2 µg/mL). Cells were not further treated before performing gene array analysis

tag: cell line

tag: cell type

value: chronic myeloid leukemia (CML)

value: CD25 negative


title: Colorectal cancer endothelial sample 2

description: CRC 2.txt

value: Moderate

value: pT3 N0

value: Colorectal cancer endothelial


title: Healthy kidney endothelial sample 2

description: Kidney 2.txt

value: female

value: Healthy kidney endothelial


title: Healthy colon endothelial sample 1

description: Colon 1.txt


title: Healthy kidney endothelial sample 3

description: Kidney 3.txt


title: KU812 control shRNA

value: CD25 positive


title: Healthy colon endothelial sample 2

description: Colon 2.txt


title: 1846_aorta

status: Public on Jan 25 2016

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: aortic tissue

hyb_protocol: The HT_MG-430 PM Array plate consists of 96 single MG-430 arrays (retaining only the perfect-match probes) arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: aortas of F1 offspring of inbred strains crossed with C57BL/6J carrying ApoE-Leiden and CETP transgenes fed chow diet for 8 weeks followed by Western diet for 16 weeks

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 24-week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by Western diet for 16 weeks

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

value: 24 weeks

tag: strain

value: aorta


title: 1844_aorta

description: aortic tissue


title: 1860_aorta

description: aortic tissue


title: 1845_aorta

description: aortic tissue


title: 1833_aorta

description: aortic tissue

value: NZB/BlNJ


title: 1843_aorta

description: aortic tissue


title: 1679_aorta

description: aortic tissue


title: 1705_aorta

description: aortic tissue


title: 1658_aorta

description: aortic tissue

value: PL/J


title: 1647_aorta

description: aortic tissue

value: NZW/LacJ


title: 1707_aorta

description: aortic tissue


title: 1773_aorta

description: aortic tissue


title: 1834_aorta

description: aortic tissue


title: 1659_aorta

description: aortic tissue


title: 1831_aorta

description: aortic tissue


title: 1645_aorta

description: aortic tissue


title: 1791_aorta

description: aortic tissue

value: BALB/cByJ


title: 1711_aorta

description: aortic tissue


title: 1706_aorta

description: aortic tissue


title: 1728_aorta

description: aortic tissue


title: 1727_aorta

description: aortic tissue


title: 1750_aorta

description: aortic tissue


title: 1832_aorta

description: aortic tissue


title: 1712_aorta

description: aortic tissue


title: 1630_aorta

description: aortic tissue


title: 1814_aorta

description: aortic tissue


title: 1632_aorta

description: aortic tissue


title: 1644_aorta

description: aortic tissue


title: 1631_aorta

description: aortic tissue


title: 1708_aorta

description: aortic tissue


title: 1604_aorta

description: aortic tissue


title: 1646_aorta

description: aortic tissue


title: 1506_aorta

description: aortic tissue


title: 1525_aorta

description: aortic tissue


title: 1602_aorta

description: aortic tissue


title: 1571_aorta

description: aortic tissue


title: 1570_aorta

description: aortic tissue


title: 1465_aorta

description: aortic tissue


title: 1479_aorta

description: aortic tissue


title: 1461_aorta

description: aortic tissue


title: 1485_aorta

description: aortic tissue


title: 1477_aorta

description: aortic tissue


title: 1505_aorta

description: aortic tissue


title: 1526_aorta

description: aortic tissue


title: 1478_aorta

description: aortic tissue


title: 1484_aorta

description: aortic tissue


title: 1439_aorta

description: aortic tissue


title: 1366_aorta

description: aortic tissue

value: SWR/J


title: 1395_aorta

description: aortic tissue


title: 60475

description:
Sentrix_ID :6007473008
Sentrix_Position : F

value: A

value: P

value: M

tag: kw1(kidney 1 weight in g)

tag: kw2 (kidney 2 weight in g)

tag: lw (liver weight in g)


title: 1447_aorta

description: aortic tissue


title: 1437_aorta

description: aortic tissue


title: 1383_aorta

description: aortic tissue


title: 1384_aorta

description: aortic tissue


title: 1438_aorta

description: aortic tissue


title: 1367_aorta

description: aortic tissue


title: 1436_aorta

description: aortic tissue


title: 1483_aorta

description: aortic tissue


title: 1345_aorta

description: aortic tissue


title: 1427_aorta

description: aortic tissue


title: 1337_aorta

description: aortic tissue

value: I/LnJ


title: 1603_aorta

description: aortic tissue


title: 1317_aorta

description: aortic tissue


title: 1310_aorta

description: aortic tissue

value: AKR/J


title: 1322_aorta

description: aortic tissue


title: 1299_aorta

description: aortic tissue


title: 1311_aorta

description: aortic tissue


title: 1297_aorta

description: aortic tissue


title: 1302_aorta

description: aortic tissue


title: 1287_aorta

description: aortic tissue


title: 1316_aorta

description: aortic tissue


title: 1296_aorta

description: aortic tissue


title: 1309_aorta

description: aortic tissue


title: 1286_aorta

description: aortic tissue


title: 1267_aorta

description: aortic tissue

value: RIIIS/J


title: 1298_aorta

description: aortic tissue


title: 1268_aorta

description: aortic tissue


title: 1264_aorta

description: aortic tissue

value: CE/J


title: 1210_aorta

description: aortic tissue

value: female


title: 1321_aorta

description: aortic tissue


title: 1272_aorta

description: aortic tissue


title: 1207_aorta

description: aortic tissue

value: SM/J


title: 1206_aorta

description: aortic tissue


title: 1213_aorta

description: aortic tissue


title: 1199_aorta

description: aortic tissue


title: 1222_aorta

description: aortic tissue


title: 1205_aorta

description: aortic tissue


title: 1265_aorta

description: aortic tissue


title: 1230_aorta

description: aortic tissue


title: 1288_aorta

description: aortic tissue


title: 1179_aorta

description: aortic tissue


title: 1178_aorta

description: aortic tissue


title: 1182_aorta

description: aortic tissue


title: 1105_aorta

description: aortic tissue


title: 1166_aorta

description: aortic tissue


title: 1177_aorta

description: aortic tissue


title: 1195_aorta

description: aortic tissue


title: 1183_aorta

description: aortic tissue


title: 1131_aorta

description: aortic tissue


title: 1148_aorta

description: aortic tissue


title: 1144_aorta

description: aortic tissue


title: 1132_aorta

description: aortic tissue


title: 1130_aorta

description: aortic tissue


title: 1091_aorta

description: aortic tissue

value: LP/J


title: 1082_aorta

description: aortic tissue

value: 24 weeks


title: 1081_aorta

description: aortic tissue

value: aorta


title: 1084_aorta

description: aortic tissue


title: 1149_aorta

description: aortic tissue


title: 1116_aorta

description: aortic tissue


title: 1168_aorta

description: aortic tissue


title: 1111_aorta

description: aortic tissue


title: 1106_aorta

description: aortic tissue


title: 1083_aorta

description: aortic tissue


title: 1167_aorta

description: aortic tissue


title: 1117_aorta

description: aortic tissue


title: 1134_aorta

description: aortic tissue


title: 1174_aorta

description: aortic tissue


title: 1143_aorta

description: aortic tissue


title: 1601_aorta

description: aortic tissue


title: 1080_aorta

description: aortic tissue


title: 1056_aorta

description: aortic tissue


title: 1078_aorta

description: aortic tissue


title: 1064_aorta

description: aortic tissue


title: 1079_aorta

description: aortic tissue


title: 1052_aorta

description: aortic tissue


title: 1053_aorta

description: aortic tissue


title: 1048_aorta

description: aortic tissue

value: CBA/J


title: 1040_aorta

description: aortic tissue


title: 1023_aorta

description: aortic tissue


title: 1041_aorta

description: aortic tissue


title: 1046_aorta

description: aortic tissue


title: 1051_aorta

description: aortic tissue


title: 1025_aorta

description: aortic tissue


title: 1009_aorta

description: aortic tissue


title: 1024_aorta

description: aortic tissue


title: 1047_aorta

description: aortic tissue


title: 1012_aorta

description: aortic tissue


title: 1035_aorta

description: aortic tissue


title: 1022_aorta

description: aortic tissue


title: 1325_aorta

description: aortic tissue


title: 1016_aorta

description: aortic tissue


title: 998_aorta

description: aortic tissue


title: 1010_aorta

description: aortic tissue


title: 1017_aorta

description: aortic tissue


title: 1039_aorta

description: aortic tissue


title: 1015_aorta

description: aortic tissue


title: 997_aorta

description: aortic tissue


title: 999_aorta

description: aortic tissue


title: 1001_aorta

description: aortic tissue


title: 995_aorta

description: aortic tissue


title: 988_aorta

description: aortic tissue


title: 987_aorta

description: aortic tissue


title: 986_aorta

description: aortic tissue


title: 993_aorta

description: aortic tissue


title: 981_aorta

description: aortic tissue


title: 980_aorta

description: aortic tissue


title: 982_aorta

description: aortic tissue


title: 971_aorta

description: aortic tissue


title: 945_aorta

description: aortic tissue

value: MA/MyJ


title: 968_aorta

description: aortic tissue


title: 979_aorta

description: aortic tissue


title: 927_aorta

description: aortic tissue


title: 994_aorta

description: aortic tissue


title: 972_aorta

description: aortic tissue


title: 985_aorta

description: aortic tissue


title: 952_aorta

description: aortic tissue


title: 967_aorta

description: aortic tissue


title: 954_aorta

description: aortic tissue


title: 951_aorta

description: aortic tissue


title: 946_aorta

description: aortic tissue


title: 938_aorta

description: aortic tissue


title: 944_aorta

description: aortic tissue


title: 933_aorta

description: aortic tissue


title: 926_aorta

description: aortic tissue


title: 921_aorta

description: aortic tissue


title: 934_aorta

description: aortic tissue


title: 974_aorta

description: aortic tissue


title: 955_aorta

description: aortic tissue


title: 912_aorta

description: aortic tissue


title: 917_aorta

description: aortic tissue


title: 907_aorta

description: aortic tissue


title: 918_aorta

description: aortic tissue


title: 913_aorta

description: aortic tissue


title: 866_aorta

description: aortic tissue


title: 864_aorta

description: aortic tissue


title: 859_aorta

description: aortic tissue


title: 901_aorta

description: aortic tissue


title: 883_aorta

description: aortic tissue


title: 891_aorta

description: aortic tissue


title: 858_aorta

description: aortic tissue


title: 885_aorta

description: aortic tissue


title: 914_aorta

description: aortic tissue


title: 865_aorta

description: aortic tissue


title: 903_aorta

description: aortic tissue


title: 911_aorta

description: aortic tissue


title: 890_aorta

description: aortic tissue


title: 877_aorta

description: aortic tissue


title: 860_aorta

description: aortic tissue


title: 884_aorta

description: aortic tissue


title: 874_aorta

description: aortic tissue


title: 854_aorta

description: aortic tissue


title: 887_aorta

description: aortic tissue


title: 842_aorta

description: aortic tissue


title: 873_aorta

description: aortic tissue


title: 840_aorta

description: aortic tissue


title: 853_aorta

description: aortic tissue


title: 892_aorta

description: aortic tissue


title: 836_aorta

description: aortic tissue


title: 838_aorta

description: aortic tissue


title: 837_aorta

description: aortic tissue


title: 849_aorta

description: aortic tissue


title: 835_aorta

description: aortic tissue


title: 774_aorta

description: aortic tissue


title: 823_aorta

description: aortic tissue


title: 821_aorta

description: aortic tissue


title: 775_aorta

description: aortic tissue


title: 827_aorta

description: aortic tissue


title: 817_aorta

description: aortic tissue


title: 735_aorta

description: aortic tissue

value: A/J


title: 818_aorta

description: aortic tissue


title: 766_aorta

description: aortic tissue

value: SEA/GnJ


title: 828_aorta

description: aortic tissue


title: 779_aorta

description: aortic tissue

value: NON/ShiLtJ


title: 745_aorta

description: aortic tissue


title: 820_aorta

description: aortic tissue


title: 801_aorta

description: aortic tissue


title: 752_aorta

description: aortic tissue


title: 750_aorta

description: aortic tissue


title: 738_aorta

description: aortic tissue


title: 808_aorta

description: aortic tissue


title: 772_aorta

description: aortic tissue


title: 759_aorta

description: aortic tissue


title: 744_aorta

description: aortic tissue


title: 793_aorta

description: aortic tissue


title: 765_aorta

description: aortic tissue


title: 732_aorta

description: aortic tissue


title: 773_aorta

description: aortic tissue


title: 809_aorta

description: aortic tissue


title: 824_aorta

description: aortic tissue


title: 736_aorta

description: aortic tissue


title: 725_aorta

description: aortic tissue


title: 707_aorta

description: aortic tissue


title: 720_aorta

description: aortic tissue


title: 726_aorta

description: aortic tissue


title: 701_aorta

description: aortic tissue

value: BALB/cJ


title: 694_aorta

description: aortic tissue


title: 692_aorta

description: aortic tissue


title: 685_aorta

description: aortic tissue


title: 674_aorta

description: aortic tissue


title: 593_aorta

description: aortic tissue


title: 636_aorta

description: aortic tissue


title: 659_aorta

description: aortic tissue


title: 660_aorta

description: aortic tissue


title: 638_aorta

description: aortic tissue


title: 651_aorta

description: aortic tissue


title: 583_aorta

description: aortic tissue


title: 717_aorta

description: aortic tissue


title: 705_aorta

description: aortic tissue


title: 684_aorta

description: aortic tissue


title: 592_aorta

description: aortic tissue


title: 649_aorta

description: aortic tissue


title: 637_aorta

description: aortic tissue


title: 613_aorta

description: aortic tissue


title: 700_aorta

description: aortic tissue


title: 618_aorta

description: aortic tissue


title: 614_aorta

description: aortic tissue


title: 702_aorta

description: aortic tissue


title: 601_aorta

description: aortic tissue


title: 575_aorta

description: aortic tissue

value: KK/HlJ


title: 577_aorta

description: aortic tissue


title: 572_aorta

description: aortic tissue


title: 540_aorta

description: aortic tissue


title: 551_aorta

description: aortic tissue


title: 556_aorta

description: aortic tissue


title: 543_aorta

description: aortic tissue


title: 564_aorta

description: aortic tissue


title: 550_aorta

description: aortic tissue


title: 541_aorta

description: aortic tissue


title: 508_aorta

description: aortic tissue


title: 471_aorta

description: aortic tissue


title: 492_aorta

description: aortic tissue

value: BTBR T<+> tf/J


title: 534_aorta

description: aortic tissue


title: 536_aorta

description: aortic tissue


title: 542_aorta

description: aortic tissue


title: 464_aorta

description: aortic tissue

value: LG/J


title: 478_aorta

description: aortic tissue


title: 474_aorta

description: aortic tissue


title: 557_aorta

description: aortic tissue


title: 505_aorta

description: aortic tissue


title: 473_aorta

description: aortic tissue


title: 509_aorta

description: aortic tissue


title: 462_aorta

description: aortic tissue


title: 461_aorta

description: aortic tissue


title: 465_aorta

description: aortic tissue


title: 440_aorta

description: aortic tissue


title: 457_aorta

description: aortic tissue


title: 456_aorta

description: aortic tissue


title: 432_aorta

description: aortic tissue


title: 434_aorta

description: aortic tissue


title: 463_aorta

description: aortic tissue


title: 394_aorta

description: aortic tissue


title: 409_aorta

description: aortic tissue


title: 421_aorta

description: aortic tissue


title: 407_aorta

description: aortic tissue


title: 406_aorta

description: aortic tissue


title: 388_aorta

description: aortic tissue


title: 385_aorta

description: aortic tissue


title: 389_aorta

description: aortic tissue


title: 335_aorta

description: aortic tissue


title: 349_aorta

description: aortic tissue


title: 348_aorta

description: aortic tissue


title: 488_aorta

description: aortic tissue


title: 386_aorta

description: aortic tissue


title: 433_aorta

description: aortic tissue


title: 320_aorta

description: aortic tissue


title: 351_aorta

description: aortic tissue


title: 384_aorta

description: aortic tissue


title: 334_aorta

description: aortic tissue


title: 322_aorta

description: aortic tissue


title: 332_aorta

description: aortic tissue


title: 321_aorta

description: aortic tissue


title: 405_aorta

description: aortic tissue


title: 275_aorta

description: aortic tissue


title: 316_aorta

description: aortic tissue


title: 296_aorta

description: aortic tissue


title: 208_aorta

description: aortic tissue


title: 268_aorta

description: aortic tissue


title: 265_aorta

description: aortic tissue

value: SJL/J


title: 191_aorta

description: aortic tissue


title: 210_aorta

description: aortic tissue


title: 240_aorta

description: aortic tissue


title: 273_aorta

description: aortic tissue


title: 220_aorta

description: aortic tissue


title: 254_aorta

description: aortic tissue


title: 230_aorta

description: aortic tissue

value: RIIIS/J


title: 232_aorta

description: aortic tissue


title: 239_aorta

description: aortic tissue


title: 221_aorta

description: aortic tissue


title: 135_aorta

description: aortic tissue


title: 109_aorta

description: aortic tissue


title: 77_aorta

description: aortic tissue


title: 226_aorta

description: aortic tissue


title: 71_aorta

description: aortic tissue


title: 72_aorta

description: aortic tissue


title: 79_aorta

description: aortic tissue


title: 113_aorta

description: aortic tissue


title: 114_aorta

description: aortic tissue


title: 66_aorta

description: aortic tissue

value: BUB/BnJ


title: 102_aorta

description: aortic tissue

value: female


title: 37_aorta

description: aortic tissue


title: 55_aorta

description: aortic tissue


title: 25_aorta

description: aortic tissue

value: FVB/NJ


title: 22_aorta

description: aortic tissue


title: 64_aorta

description: aortic tissue


title: 70_aorta

description: aortic tissue


title: 63_aorta

description: aortic tissue


title: 24_aorta

description: aortic tissue


title: 33_aorta

description: aortic tissue


title: 1645_liver

description: liver

source_name: livers of F1 offspring of inbred strains crossed with C57BL/6J carrying ApoE-Leiden and CETP transgenes fed chow diet for 8 weeks followed by Western diet for 16 weeks

value: NZW/LacJ

value: liver


title: 65_aorta

description: aortic tissue

value: 24 weeks

value: aorta


title: 32_aorta

description: aortic tissue


title: 48_aorta

description: aortic tissue


title: 51_aorta

description: aortic tissue


title: 18_aorta

description: aortic tissue


title: 1644_liver

description: liver


title: 466_aorta

description: aortic tissue


title: 1632_liver

description: liver


title: 1601_liver

description: liver


title: 1479_liver

description: liver


title: 1_aorta

description: aortic tissue

value: NOD/ShiLtJ


title: 1478_liver

description: liver


title: 1427_liver

description: liver

value: PL/J


title: 1459_liver

description: liver


title: 1399_liver

description: liver

value: AKR/J


title: 1384_liver

description: liver


title: 1649_liver

description: liver


title: 1437_liver

description: liver


title: 1380_liver

description: liver


title: 1337_liver

description: liver

value: I/LnJ


title: 1383_liver

description: liver


title: 1359_liver

description: liver


title: 1265_liver

description: liver

value: CE/J


title: 1360_liver

description: liver


title: 1316_liver

description: liver


title: 1253_liver

description: liver

value: SWR/J


title: 1257_liver

description: liver

value: SM/J


title: 1199_liver

description: liver


title: 1264_liver

description: liver


title: 1222_liver

description: liver


title: 1213_liver

description: liver


title: 1236_liver

description: liver


title: 1231_liver

description: liver


title: 1244_liver

description: liver


title: 1178_liver

description: liver


title: 1177_liver

description: liver


title: 1167_liver

description: liver


title: 1166_liver

description: liver


title: 1149_liver

description: liver


title: 1148_liver

description: liver


title: 1107_liver

description: liver


title: 1132_liver

description: liver


title: 1130_liver

description: liver


title: 1056_liver

description: liver


title: 1046_liver

description: liver


title: 177_aorta

description: aortic tissue


title: 1017_liver

description: liver


title: 1039_liver

description: liver


title: 1106_liver

description: liver


title: 995_liver

description: liver


title: 1016_liver

description: liver


title: 994_liver

description: liver


title: 1010_liver

description: liver


title: 1009_liver

description: liver


title: 981_liver

description: liver


title: 987_liver

description: liver


title: 982_liver

description: liver


title: 980_liver

description: liver


title: 985_liver

description: liver


title: 993_liver

description: liver


title: 986_liver

description: liver


title: 1006_liver

description: liver


title: 968_liver

description: liver


title: 1604_liver

description: liver


title: 930_liver

description: liver


title: 952_liver

description: liver


title: 974_liver

description: liver

value: CBA/J


title: 1630_liver

description: liver


title: 940_liver

description: liver


title: 944_liver

description: liver


title: 921_liver

description: liver


title: 926_liver

description: liver


title: 927_liver

description: liver


title: 979_liver

description: liver


title: 912_liver

description: liver


title: 918_liver

description: liver


title: 907_liver

description: liver


title: 938_liver

description: liver


title: 1602_liver

description: liver


title: 1255_liver

description: liver


title: 917_liver

description: liver


title: 914_liver

description: liver

value: LP/J


title: 890_liver

description: liver


title: 885_liver

description: liver

value: MA/MyJ


title: 892_liver

description: liver


title: 891_liver

description: liver


title: 887_liver

description: liver


title: 929_liver

description: liver


title: 883_liver

description: liver


title: 863_liver

description: liver


title: 873_liver

description: liver


title: 859_liver

description: liver


title: 1252_liver

description: liver


title: 865_liver

description: liver


title: 852_liver

description: liver


title: 853_liver

description: liver


title: 954_liver

description: liver


title: 1648_liver

description: liver


title: 2_aorta

description: aortic tissue


title: 860_liver

description: liver


title: 847_liver

description: liver


title: 846_liver

description: liver


title: 837_liver

description: liver


title: 828_liver

description: liver


title: 793_liver

description: liver


title: 819_liver

description: liver


title: 818_liver

description: liver


title: 809_liver

description: liver


title: 779_liver

description: liver

value: NON/ShiLtJ


title: 836_liver

description: liver

value: female


title: 817_liver

description: liver


title: 773_liver

description: liver


title: 772_liver

description: liver


title: 827_liver

description: liver


title: 745_liver

description: liver


title: 738_liver

description: liver


title: 736_liver

description: liver

value: A/J


title: 752_liver

description: liver


title: 808_liver

description: liver


title: 730_liver

description: liver


title: 770_liver

description: liver


title: 735_liver

description: liver


title: 726_liver

description: liver


title: 727_liver

description: liver


title: 732_liver

description: liver


title: 729_liver

description: liver


title: 750_liver

description: liver


title: 659_liver

description: liver


title: 724_liver

description: liver


title: 694_liver

description: liver


title: 637_liver

description: liver


title: 613_liver

description: liver


title: 636_liver

description: liver


title: 660_liver

description: liver


title: 618_liver

description: liver


title: 684_liver

description: liver


title: 717_liver

description: liver


title: 685_liver

description: liver


title: 911_liver

description: liver


title: 638_liver

description: liver


title: 720_liver

description: liver


title: 649_liver

description: liver


title: 592_liver

description: liver


title: 593_liver

description: liver


title: 583_liver

description: liver


title: 572_liver

description: liver


title: 577_liver

description: liver

value: KK/HlJ


title: 557_liver

description: liver

value: liver


title: 541_liver

description: liver

value: 24 weeks


title: 540_liver

description: liver


title: 564_liver

description: liver


title: 551_liver

description: liver


title: 556_liver

description: liver


title: 542_liver

description: liver


title: 550_liver

description: liver


title: 536_liver

description: liver


title: 534_liver

description: liver


title: 505_liver

description: liver

value: BALB/cJ


title: 509_liver

description: liver


title: 504_liver

description: liver


title: 474_liver

description: liver

value: BTBR T<+> tf/J


title: 470_liver

description: liver


title: 508_liver

description: liver


title: 433_liver

description: liver


title: 492_liver

description: liver


title: 488_liver

description: liver


title: 506_liver

description: liver


title: 457_liver

description: liver


title: 471_liver

description: liver


title: 466_liver

description: liver


title: 462_liver

description: liver

value: LG/J


title: 464_liver

description: liver


title: 432_liver

description: liver


title: 854_liver

description: liver


title: 434_liver

description: liver


title: 463_liver

description: liver


title: 413_liver

description: liver


title: 405_liver

description: liver


title: 421_liver

description: liver


title: 877_liver

description: liver


title: 406_liver

description: liver


title: 394_liver

description: liver

value: SEA/GnJ


title: 407_liver

description: liver


title: 384_liver

description: liver


title: 386_liver

description: liver


title: 334_liver

description: liver


title: 348_liver

description: liver


title: 389_liver

description: liver


title: 275_liver

description: liver


title: 385_liver

description: liver


title: 335_liver

description: liver


title: 320_liver

description: liver


title: 351_liver

description: liver


title: 316_liver

description: liver


title: 349_liver

description: liver


title: 322_liver

description: liver


title: Olfactory_Mix pLD_pLD_6

city: Seattle

first: James

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Agilent

scan_protocol: Arrays were scanned using an Agilent DNA microarray scanner through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Expression values were first background-corrected by subtracting the median background intensity, and then normalized using variance stabilization normalization (VSN, Huber et al, doi 10.1093/bioinformatics/18.suppl_1.S96).

label: Cy5 fluorescent label

organism: Oncorhynchus kisutch

source_name: Mix pLD pLD

label_protocol: For microarray hybridization, RNA was processed for hybridization to the Agilent-025055 Koop Lab Salmonid 44K Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: The olfactory rosettes were dissected for subsequent RNA isolation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen Inc, Valencia, CA) according to the vendor's protocol and stored at -80C.

treatment_protocol: Pesticide stock solutions or carrier solutions containing no pesticide were added to 70L hatchery water in 90L glass aquaria containing eight individual fish. The aquaria were contained within a large chilled recirculating water bath (11C) and received aeration. Fish were exposed for 24h.

value: olfactory rosettes

tag: developmental stage

value: juvenile

tag: body weight

value: 1 year


title: Olfactory_Mix pLD_pLD_4


title: 230_liver

description: liver

value: RIIIS/J


title: 221_liver

description: liver


title: Olfactory_Mix pLD_pLD_1


title: Olfactory_Mix pLD_pLD_8


title: 321_liver

description: liver


title: 220_liver

description: liver


title: Olfactory_Mix pLD_pLD_3


title: 240_liver

description: liver


title: 210_liver

description: liver


title: Olfactory_Mix pLD_Control_8

source_name: Mix pLD Control


title: Olfactory_Mix pLD_Control_7


title: 232_liver

description: liver


title: 191_liver

description: liver


title: 208_liver

description: liver


title: 135_liver

description: liver


title: Olfactory_Malathion_High_6

source_name: Malathion High


title: Olfactory_Malathion_High_4


title: 114_liver

description: liver


title: Olfactory_Mix pLD_Control_5


title: Olfactory_Mix pLD_Control_4


title: 165_liver

description: liver


title: 113_liver

description: liver


title: 164_liver

description: liver


title: Olfactory_Malathion_High_2


title: 72_liver

description: liver

value: SJL/J


title: 71_liver

description: liver


title: Olfactory_Malathion_High_5


title: Olfactory_Mix pLD_Control_1


title: Olfactory_Malathion_Medium_7

source_name: Malathion Medium


title: 102_liver

description: liver


title: Olfactory_Malathion_Medium_5


title: 109_liver

description: liver


title: STHdhQ111/Q111, Specific ASOs

city: Boston

first: Guo-Lin

last: Chen

state: Massachusetts

address: 360 Huntington Avenue

institute: Northeastern University

description:
Gene expression data from STHdhQ111/Q111 cells (treated with specific ASOs)
Q111-C (ASOs)

hyb_protocol: Affymetrix Manual Section 2 Chapter 2: Eukaryotic Target Hybridization

scan_protocol: GeneChip® Scanner 3000 7G protocol

data_processing: Partek Genomic Suite Software, Gene Expression protocol

source_name: Striatal cell line derived from transgenic mice expressing humanized Htt exon 1 with 111 polyQ repeats

label_protocol: The Ambion® WT Expression Kit

growth_protocol: Cells were cultured in advanced DMEM (Invitrogen) supplemented with 10% heat-inactivated FBS, 1% penicillin/streptomycin and 200 µg/ml G418 (Invitrogen) at 33°C in a 5% CO2 incubator.

treatment_protocol: Specific morpholino ASOs (I2E3+E3I3, 3 µM of each) targeting the splice sites REST E3, or a non-specific control morpholino oligo, were delivered into cells using 6 µM of Endo-Porter (Gene Tools). Cells were harvested at 48 hr post treatment.

value: STHdhQ111/Q111 cells

tag: treatment

value: specific ASOs (inducing ∆E3)


title: 65_liver

description: liver

tag: gender

value: BUB/BnJ


title: Olfactory_Malathion_High_1

tag: age


title: Olfactory_Malathion_Low_8

source_name: Malathion Low


title: Olfactory_Malathion_Medium_4


title: Olfactory_Malathion_Low_5


title: 66_liver

description: liver

value: female


title: STHdhQ111/Q111, Control oligo

description:
Gene expression data from STHdhQ111/Q111 cells (treated with control oligo)
Q111-D (CTL)

value: control oligo


title: Olfactory_Malathion_Medium_2


title: 48_liver

description: liver


title: STHdhQ7/Q7, Control oligo

description:
Gene expression data from STHdhQ7/Q7 cells (treated with control oligo)
Q7-D (CTL)

source_name: Striatal cell line derived from transgenic mice expressing humanized Htt exon 1 with 7 polyQ repeats

value: STHdhQ7/Q7 cells


title: Olfactory_Malathion_Low_3


title: 70_liver

description: liver

value: liver


title: Olfactory_Malathion_Medium_3


title: 64_liver

description: liver

value: 24 weeks


title: 41_liver

description: liver


title: 42_liver

description: liver


title: Atg7-/- Treg cells rapamycin treated replicate 4

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: Treg cells from rapamycin-treated Atg7fl/flFoxp3-Cre mouse

label_protocol: One to five nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Lymphocytes were isolated from spleen and peripheral lymph nodes, that included inguinal, auxiliary and cervical lymph nodes, and Treg cells (CD4+Foxp3-YFP+) were sorted on a MoFlow (Beckman-Coulter) or Reflection (i-Cyt).

extract_protocol: RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

treatment_protocol: Atg7+/flFoxp3-Cre and Atg7fl/flFoxp3-Cre mice were left untreated or treated with rapamycin. For treatment with rapamycin, mice were injected intraperitoneally with rapamycin (4 mg per kg body weight) daily for five days, and then Treg cells (CD4+Foxp3-YFP+) were sorted. Treg cells from untreated or rapamycin-treated mice were then were stimulated with plate-bound anti-CD3 and anti-CD28 for 4 hours.

value: rapamycin-treated

value: Atg7-/- Treg

tag: genotype/variation


title: Atg7-/- Treg cells rapamycin treated replicate 3


title: Atg7-/- Treg cells rapamycin treated replicate 1


title: Olfactory_Malathion_Low_2


title: Atg7+/- Treg cells rapamycin treated replicate 1

source_name: Treg cells from rapamycin-treated Atg7+/flFoxp3-Cre mouse

value: Atg7+/- Treg


title: 22_liver

description: liver

value: FVB/NJ


title: 32_liver

description: liver


title: Atg7-/- Treg cells rapamycin treated replicate 2


title: 37_liver

description: liver

value: NON/ShiLtJ


title: Atg7+/- Treg cells untreated replicate 1

source_name: Treg cells from untreated  Atg7+/flFoxp3-Cre mouse

value: untreated


title: Olfactory_Malathion_Control_6

source_name: Malathion Control

value: olfactory rosettes

value: juvenile

value: 1 year


title: Olfactory_Malathion_Control_2


title: Atg7-/- Treg cells untreated replicate 1

source_name: Treg cells from untreated Atg7fl/flFoxp3-Cre mouse


title: Atg7+/- Treg cells rapamycin treated replicate 4


title: Atg7-/- Treg cells untreated replicate 2


title: Atg7+/- Treg cells rapamycin treated replicate 3


title: 18_liver

description: liver


title: 2_liver

description: liver

value: NOD/ShiLtJ


title: Olfactory_Malathion_Control_3


title: Olfactory_Chlorpyrifos_High_8

source_name: Chlorpyrifos High


title: Atg7+/- Treg cells untreated replicate 2


title: 1_liver

description: liver


title: Olfactory_Malathion_Control_7


title: Atg7-/- Treg cells untreated replicate 4


title: Olfactory_Malathion_Control_4


title: Atg7+/- Treg cells untreated replicate 3


title: Atg7-/- Treg cells untreated replicate 3


title: Atg7+/- Treg cells untreated replicate 4


title: Atg7+/- Treg cells rapamycin treated replicate 2


title: 21_liver

description: liver


title: Olfactory_Malathion_Low_1


title: pBAD-SdsR 2

type: mixed

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

institute: IMIB Würzburg

hyb_protocol: Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. pBAD-ctr serves as control for pBAD-SdsR.

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica SL1344_pBAD-SdsR_genomic DNA

label_protocol: total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System

growth_protocol: Salmonella carrying pBAD-ctr or pBAD-SdsR were grown in LB-media to OD=1.5.

extract_protocol: SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit

treatment_protocol: At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.

value: carrying pBAD-SdsR

tag: treated with

value: 0.2% (final conc.) L-arabinose

tag: time point

value: 10 min post treatment

source_name: Salmonella enterica SL1344_pBAD-SdsR_total RNA


title: pBAD-SdsR 3


title: pBAD-ctr.3 (control)

source_name: Salmonella enterica SL1344_pBAD-ctr_genomic DNA

value: carrying pBAD-ctr

source_name: Salmonella enterica SL1344_pBAD-ctr_total RNA


title: pBAD-ctr.2 (control)


title: Olfactory_Chlorpyrifos_High_6

tag: tissue


title: pBAD-SdsR 1


title: pBAD-ctr.1 (control)


title: Olfactory_Chlorpyrifos_Medium_8

source_name: Chlorpyrifos Medium


title: Olfactory_Chlorpyrifos_Medium_2


title: Olfactory_Chlorpyrifos_Control_6

source_name: Chlorpyrifos Control


title: Olfactory_Chlorpyrifos_High_5


title: Olfactory_Chlorpyrifos_Low_6

source_name: Chlorpyrifos Low


title: Olfactory_Chlorpyrifos_High_2


title: Olfactory_Chlorpyrifos_Control_4


title: Olfactory_Chlorpyrifos_Medium_6


title: Olfactory_Chlorpyrifos_Low_7


title: Olfactory_Chlorpyrifos_Medium_5


title: Olfactory_Chlorpyrifos_Control_5


title: Olfactory_Chlorpyrifos_High_4


title: Olfactory_Chlorpyrifos_Control_1


title: Olfactory_Chlorpyrifos_Control_3


title: Olfactory_Chlorpyrifos_Medium_7


title: Olfactory_Chlorpyrifos_Low_5


title: Olfactory_Chlorpyrifos_Low_2


title: Olfactory_Chlorpyrifos/Malathion_High_3

source_name: Chlorpyrifos/Malathion High


title: Olfactory_Chlorpyrifos_Low_1


title: Olfactory_Chlorpyrifos/Malathion_High_2


title: Olfactory_Chlorpyrifos/Malathion_High_7


title: Olfactory_Chlorpyrifos/Malathion_High_8


title: Olfactory_Chlorpyrifos/Malathion_Medium_6

source_name: Chlorpyrifos/Malathion Medium


title: Olfactory_Chlorpyrifos/Malathion_Medium_5


title: Olfactory_Chlorpyrifos/Malathion_Medium_4


title: Olfactory_Chlorpyrifos/Malathion_High_5


title: Olfactory_Chlorpyrifos/Malathion_Low_6

source_name: Chlorpyrifos/Malathion Low


title: RA cbc1 t45

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
Time 45 min processed data: Run-on labelling for cbc1Δ strain
gDNA hybridization: gDNA.v10-L1-F13.txt
gDNA hybridization: gDNA.v10-L1-F9.txt
gDNA hybridization: gDNA.v10-L3-F11.txt

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. macroarrays were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 3 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, macroarrays were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the macroarrays were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) until quantification.

data_processing: Raw data was pre-processed in Excel 2007 and comes from image quantization and local background subtracted. Only data above 10% regard to local background was considered. Each GRO and cDNA replicate were corrected by normalization with gDNA hybridization for corresponding microarray used (gDNA hybridization raw files are available in a tar archive on the series record). Processed data is the average that results from Median Absolute Desviation normalization of each gDNA corrected replicate using ArrayStat software. For RA (mRNA), average processed values were corrected by percentage of guanines and for TR (GRO) the average processed value for each gene was corrected by percentage of uridines present in each probe-coding strand. The mRNA levels was adjusted using the concentration of mRNA/cell for each strain regard the wild type strain determined by a dot blot assay and mRNA extractions as described in García-Martinez 2004.

organism: Saccharomyces cerevisiae

source_name: cbc1Δ mutant in YPD with KCl 0.6M

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, the cells were washed and then were permeabilized with 20 mL of 0.5% sarkosyl. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Osmotic stress conditions were created by addition of KCl at 0.6 M. Experiments were initiated from exponential cultures growing in YPD. t0: before adding KCl and samples were taken at 8, 15, 30 and 45 minutes.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: cbc1Δ mutant


title: RA cbc1 t15

description:
Time 15 min processed data: Run-on labelling for cbc1Δ strain
gDNA hybridization: gDNA.v10-L1-F11.txt
gDNA hybridization: gDNA.v10-L1-F12.txt
gDNA hybridization: gDNA.v10-L3-F9.txt


title: RA cbc1 t30

description:
Time 30 min processed data: Run-on labelling for cbc1Δ strain
gDNA hybridization: gDNA.v10-L1-F12.txt
gDNA hybridization: gDNA.v10-L1-F13.txt
gDNA hybridization: gDNA.v10-L3-F10.txt


title: RA cbc1 t8

description:
Time 8 min processed data: Run-on labelling for cbc1Δ strain
gDNA hybridization: gDNA.v10-L1-F10.txt
gDNA hybridization: gDNA.v10-L1-F11.txt
gDNA hybridization: gDNA.v10-L3-F8.txt


title: Olfactory_Chlorpyrifos/Malathion_Low_4


title: RA cbc1 t0

description:
Time 0 processed data: Run-on labelling for cbc1Δ strain
gDNA hybridization: gDNA.v10-L1-F9.txt
gDNA hybridization: gDNA.v10-L1-F10.txt
gDNA hybridization: gDNA.v10-L3-F7.txt

source_name: cbc1Δ mutant grown in YPD


title: Olfactory_Chlorpyrifos/Malathion_Low_1


title: Olfactory_Chlorpyrifos/Malathion_Medium_3


title: Olfactory_Chlorpyrifos/Malathion_Control_5

source_name: Chlorpyrifos/Malathion Control


title: RA WT t30

description:
Time 30 min processed data: Run-on labelling for WT BY4741
gDNA hybridization: gDNA.v10-L1-F17.txt
gDNA hybridization: gDNA.v10-L1-F18.txt
gDNA hybridization: gDNA.v10-L3-F10.txt

source_name: Wild type cells in YPD with KCl 0.6M

value: BY4741 wild type


title: Olfactory_Chlorpyrifos/Malathion_Medium_2


title: TR cbc1 t8


title: TR cbc1 t15


title: TR cbc1 t30


title: Olfactory_Chlorpyrifos/Malathion_Low_3


title: TR cbc1 t0


title: Olfactory_Chlorpyrifos/Malathion_Low_2


title: TR cbc1 t45


title: Olfactory_Chlorpyrifos/Malathion_Control_3


title: Olfactory_Chlorpyrifos/Malathion_Control_2


title: TR WT t30


title: TR WT t15

description:
Time 15 min processed data: Run-on labelling for WT BY4741
gDNA hybridization: gDNA.v10-L1-F16.txt
gDNA hybridization: gDNA.v10-L1-F17.txt
gDNA hybridization: gDNA.v10-L3-F9.txt


title: TR WT t45

description:
Time 45 min processed data: Run-on labelling for WT BY4741
gDNA hybridization: gDNA.v10-L1-F18.txt
gDNA hybridization: gDNA.v10-L1-F14.txt
gDNA hybridization: gDNA.v10-L3-F11.txt


title: RA WT t8

description:
Time 8 min processed data: Run-on labelling for WT BY4741
gDNA hybridization: gDNA.v10-L1-F15.txt
gDNA hybridization: gDNA.v10-L1-F16.txt
gDNA hybridization: gDNA.v10-L3-F8.txt


title: RA WT t0

description:
Time 0 processed data:Run-on labelling for WT BY4741
gDNA hybridization: gDNA.v10-L1-F14.txt
gDNA hybridization: gDNA.v10-L1-F15.txt
gDNA hybridization: gDNA.v10-L3-F7.txt

source_name: Wild type cells grown in YPD to exponential phase.


title: Olfactory_Chlorpyrifos/Malathion_Control_1


title: RA WT t15


title: TR WT t8


title: RA WT t45


title: Olfactory_Chlorpyrifos/Malathion_Control_4


title: Cg-Cello02(evo)-glu-2

status: Public on Jan 24 2016

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).
Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Global normalization.

source_name: Evolved C. glutamicum strain 2

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: CgXII medium with 2%(w/v) cellobiose or 2% (w/v) glucose

extract_protocol: Total RNA was extracted by using TRIzol (Invitrogen, Carlsbad, CA), according to the manufacturer’s protocol.

tag: growth media with

value: 2%(w/v) Glucose


title: Cg-Cello02(evo)-cello-2

value: 2%(w/v) Cellobiose


title: Cg-Cello02(evo)-glu-1


title: Cg-Cello01(evo)-cello-2

source_name: Evolved C. glutamicum strain 1


title: TR WT t0


title: Cg-Cello01(evo)-glu-2


title: Cg-Cello01(evo)-glu-1


title: Cg-pBbEB1c-glu-2

source_name: C. glutamicum Wt with an empty vector


title: WT_CpG_IL21_rep1

status: Public on Jan 23 2016

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8.

source_name: splenic follicular B cells, WT, IL21

label_protocol: Biotin-labeled complementary RNA (cRNA) was made using the EpiCentre TargetAmp-Nano kit.

growth_protocol: In vitro cultures of CD23+ splenic B cells were enriched by positive selection using MACS bead system (Miltenyi Biotec) and cultured at 37°C and 5.5% CO2 in RPMI supplemented with 10% characterized FBS (HyClone), 1% HEPES (Gibco), 1% glutamine (Invitrogen), 50 μM 2-mercaptoethanol (Gibco), 1% minimal essential amino acids (Gibco), and 1% OPI supplement (Sigma).

extract_protocol: 20 hours post-stimulation with ODN1826 and IFNG or IL21, cells were immediately processed for RNA extraction using the Qiagen RNeasy Plus kit.

treatment_protocol: Cells from each mouse were stimulated with ODN1826 (1 uM) and either IL21 (25 ng/ml) or IFNG (10ng/ml) for 20 hours.

tag: strain/background

value: splenic follicular B cells

value: interleukin-21 (IL21)

tag: Sex

value: female


title: TbetKO_CpG_IL21_rep2

source_name: splenic follicular B cells, Tbet KO, IL21

tag: cell type


title: WT_CpG_IL21_rep2


title: WT_CpG_IFNG_rep1

source_name: splenic follicular B cells, WT, IFNG

value: interferon-gamma (IFNG)


title: TbetKO_CpG_IL21_rep1


title: WT_CpG_IFNG_rep2


title: TbetKO_CpG_IFNG_rep2

source_name: splenic follicular B cells, Tbet KO, IFNG


title: TbetKO_CpG_IFNG_rep1


title: liver_UR_T3_rep2

city: Dummerstorf

first: Constance

last: Nebendahl

address: Wilhelm-Stahl Allee 2

institute: Leibniz Institute for Farm Animal Biology

description: after 5-week refeeding period, d 103

hyb_protocol: The Agilent Gene Expression Hybridization Kit was used to hybridize Cy3-labelled cRNA on oligonucleotide microarrays according to the manufacturer´s instructions and protocol (Agilent One-Color Microarray-Based Gene Expression Analysis)

scan_protocol: Arrays were scanned on an Agilent Microarray scanner with the use of software tools such as Agilent Feature Extraction version 10.5.1.1. and the scan software Agilent Scan control.

data_processing: The normalisation method selected for this experiment is quantile normalization. After performing normalization all gene expression values lower than 0% quantile were set to the value of this 0% quantile (2.438216375 for this experiment) to eliminate low level signals beeing too much scattered to be used in a reproducible analysis.

organism: Sus scrofa

source_name: liver, low birth weight, restriction, T3

label_protocol: Cy3-labelled cRNA was prepared according to the manufacturer´s instructions (Agilent Quick Amp Labeling Kit, One Color Agilent, 5190-0442).

growth_protocol: Overall, piglets from one litter were selected for low (0.8-1.1 kg, U) or normal (1.4-1.6 kg, N) birth weight. From birth until weaning at day 28, U and N piglets were suckled by their dams with no creep feed. After weaning, piglets were housed individually and had free access to water and food. Feed intake was determined daily and body weights were monitored at weekly intervals. Different diets were administered during the study period to achieve or to exceed the nutrient intake recommendations for growing pigs (GfE (Gesellschaft für Ernährungsphysiologie, 2006). Thus, after weaning period, piglets were fed a diet containing a mixture of 50% (w/w) commercial pig feed, 30% rolled oats and 20% sucrose with a total energy and crude protein content of 16.3 MJ ME/kg.

extract_protocol: Total RNA was isolated with Triazol reagent (Qiazol, Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: From day 76  until day 97 half of the U and N pigs were subjected to feed restriction (50% of ad libitum consumption) of a conventional pig diet (13.6 MJ ME/kg). Subsequently, both restricted (UR, NR) and control groups (UK, NK) were subjected to ad libitum feeding until day 131 (14.1 MJ ME/kg).

tag: development stage

value: adolescent

tag: group

value: UR

value: after 5-week refeeding period, d 103


title: liver_UR_T3_rep3

description: after 5-week refeeding period, d 103


title: liver_UR_T3_rep1

description: after 5-week refeeding period, d 103


title: liver_UK_T3_rep2

description: after 5-week refeeding period, d 103

source_name: liver, low birth weight, control, T3

value: UK


title: liver_UK_T3_rep3

description: after 5-week refeeding period, d 103


title: liver_NR_T3_rep2

description: after 5-week refeeding period, d 103

source_name: liver, normal birth weight, restriction, T3

value: NR


title: liver_NR_T3_rep3

description: after 5-week refeeding period, d 103


title: liver_NR_T3_rep1

description: after 5-week refeeding period, d 103


title: liver_NK_T3_rep3

description: after 5-week refeeding period, d 103

source_name: liver, normal birth weight, control, T3

value: NK


title: liver_NK_T3_rep2

description: after 5-week refeeding period, d 103


title: liver_UK_T3_rep1

description: after 5-week refeeding period, d 103


title: liver_UR_T2_rep2

description: after 3-week feed restriction period, d 97

source_name: liver, low birth weight, restriction, T2


title: liver_UR_T2_rep3

value: after 3-week feed restriction period, d 97


title: 2429.Dura

type: genomic

city: Baltimore

first: Andrew

last: Jaffe

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

description: Cultured human fibroblast sample on the Illumina 450k

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing: idat files were read in using the minfi Bioconductor package and processed using the preprocessQuantile approach

source_name: Dura mater fibroblast

label_protocol: Following manufacturer's protocol

growth_protocol: Scalp and Dura Tissue Cultures: The dura culture medium was prepared out of 1X DMEM (Ref#11960-044, GIBCO) with 10% by volume fetal bovine serum, 2% by volume 100X GlutaMAX (Cat#: 35050, GIBCO), 1% by volume Penicillin-Streptomycin/Amphotercin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin solution (Cat# 17105-041, Quality Biological). This culture medium was used in all subsequent steps of the dura culturing procedure. The scalp culture medium used for all subsequent steps of the scalp culturing procedure was made the same way except without the 1% Gentamycin. A rinsing solution was prepared out of 1X PBS (pH 7.2) (Ref# 21-040-CV, Corning Life Sciences), 1% by volume Penicillin-Streptomycin/Amphotericin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin (Cat# 17105-041, Quality Biological). The dissected scalp sample was washed with the rinsing solution three times, the fat tissues were cut away, and all hair was plucked out with forceps. The scalp sample was then placed epidermis side down on a dish and floated with Dispase II enzyme solution (2.4 units of the Dispase II enzyme per mL of PBS, Dispase II enzyme: Cat#17105-041, GIBCO). The dish was covered with parafilm and foil, and placed in a 37oC incubator for 24 hours. After the 24-hour period, the epidermis was peeled away from the dermis. The dermis was washed with the rinsing solution, dried, and cut into 2-3 mm2 pieces. The pieces were placed in a Falcon Easy Grip tissue culture 35×10 mm dish and one drop of scalp culture medium was added to each piece of scalp. The dish was placed in the incubator at 37oC and 5% CO2 for culturing. A similar procedure was followed for the dura samples. Dura samples were washed with the rinsing solution three times. Then, a few 2-3 mm2 pieces were cut from the dura mater and placed together in an Easy Grip cell culture 35×10 mm dish. One drop of dura culture medium was added to each dura piece. The culture dish was then placed in an incubator (at 37oC and 5% CO2) for culturing. The medium of each culture was changed to fresh medium 2-3 times per week to promote growth of the fibroblasts. On average, fibroblast cells started to proliferate at 7-14 days, however some samples took longer (up to 3 weeks).   Fibroblast Cell Cultures: The dura and scalp tissue cultures were monitored under a phase-contrast microscope. When the fibroblast growth reached 90-95% confluence, 1 mL of a 0.25% trypsin solution (Cat#T4049, Sigma) was added to each culture dish, and the cells were incubated for 5 to 8 min. Then, 1mL of media was added to each dish stop the enzymatic reaction. Next, the contents of each culture dish were transferred into separate 15 mL Falcon conical tubes and 8mL of media was added to each tube. The conical tubes were centrifuged for 5 min at 1100 rpm. The supernatant was discarded, 5mL of fresh media was added to each conical tube, and the contents of the tubes were transferred onto separate 25 cm3 cell culture Easy Flasks (Thermo Scientific, Cat# 156367), where they were kept in cultures for 3-5 days in an incubator (at 37oC and 5% CO2). When the cells reached 90-95% confluence, the cells from each 25 cm3 flask were transferred onto two 75 cm3 cell culture easy flasks (Thermo Scientific, Cat# 156499) and kept in cultures for continued growth. When the cells reached 90-95% confluence, they were incubated with 3 mL of 0.25% trypsin solution for 5 to 8 min, after which 3mL of fresh culture media was added to stop the enzymatic reaction. Then, the contents of the flasks were transferred into separate 15 mL Falcon conical tube and 4mL of media was added to each tube. The tubes were centrifuged (5 min, 1100 rpm), the supernatant was discarded and the pellets containing the fibroblasts were removed from the centrifuge tubes and transferred to cryoTube vials (Cat#375418, Thermo Scientific). 0.5 mL of recovery cell culture freezing medium (Cat#12648-010, GIBCO) was added to each vial, after which the vials were insulated with Styrofoam and placed into a -80oC freezer. Later, the tubes were transferred to a -152oC liquid nitrogen freezer. These frozen dura and scalp fibroblast cells were then used generate DNA methylation data.

extract_protocol: Genomic DNA was extracted from approximately 3 million cultured human fibroblast cells using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

treatment_protocol: Bisulfite conversion of 600 ng genomic DNA was performed with the EZ DNA methylation kit (Zymo Research)

value: M

tag: race

value: HISP

tag: cell line

value: fibroblast


title: liver_UR_T2_rep1


title: liver_UK_T2_rep3

source_name: liver, low birth weight, control, T2


title: 2468.Scalp

source_name: Scalp fibroblast

value: Cauc


title: 2435.Dura


title: 2328.Scalp


title: 2429.Scalp