title: uninfected vs. flu infected

description: Quantification of RNA and quality control was done using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA) and a Nan drop photometer (Kisker, Steinfurt, Germany). Dual color hybridizations with 0.25-0.75 µg RNA per Cy-dye were performed for 16-60 h at 42°C with SlideHyb Glass Array Hybridization Buffer #3 (Ambion) and LifterSlips (Erie Scientific, Portsmouth, USA).

hyb_protocol: Arrays encoding the Ambion probe set were hybridized and washed according the supplier's recommendations.

scan_protocol: Scanning of all microarrays was performed with 5µm resolution using a DNA microarray laser scanner (DNA Microarray Scanner BA, Agilent Technologies) according the manufacturers’ instructions.

label_protocol: In the first step of the mirVana miRNA Labeling Kit procedure (Ambion), E. coli Poly(A) Polymerase and a mixture of unmodified and amine-modified nucleotides were used to add a 20–50 nucleotide tail to the 3' end of each RNA in the miRNA enriched sample. The amine-modified miRNAs were then spin-column purified and coupled to amine-reactive labeled moieties as NHS-ester with the CyDye Post-Labelling Reactive Dye Pack (Amersham Biosciences Europe GmbH, Freiburg, Germany) using Cy3 and Cy5 amine-reactive dyes to produce fluorescently-labeled samples for microarray hybridization.

extract_protocol: For miRNA profiling total RNA from influenza A infected (A/WSN/33, MOI 1) or non-infected A549 cells was extracted 24 h p.i. and purified using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen, Hilden, Germany), followed by the enrichment of small miRNAs with the RNeasy MinElute Cleanup Kit using the user-developed protocol ‘Purifying miRNA from cells and soft tissues (RY20 Jan-05)’ formerly published by Qiagen in the internet. Quality control and quantification of samples was done using an Agilent 2100 bioanalyzer (Agilent Technologies) and a Nan drop photometer (Kisker, Steinfurt, Germany).

treatment_protocol: Cell line was grown in DMEM media (Invitrogen, Karlsruhe, Germany) with 4 mM L-glutamine, 4 mM sodium pyruvate, 100 U/ml penicillin/streptomycin and 10% fetal calf serum (FCS) at 37 °C and 5% CO2. Phoenix-ECO packaging cells (G.P. Nolan, Stanford University, USA), 293T (CRL-11268, ATCC-LGC) and MDCK (CCL-34, ATCC-LGC) cells were grown in DMEM supplemented with 4 mM L-glutamine, 100 U/ml penicillin/streptomycin and 10% FCS. Cells were regularly checked for mycoplasma contamination.


title: P01249 Non-failing Left Ventricle

status: Public on Jan 01 2015

type: RNA

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

description:
P01249
PolyA mRNA

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.1 ST Array GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: heart left ventricle, non-failing

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

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

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

tag: tissue

value: heart left ventricle

tag: heart failure

value: no

tag: disease status

value: non-failing

tag: gender

value: male

tag: age


title: P01277 Non-failing Left Ventricle

description:
P01277
PolyA mRNA

value: female


title: P01025 Non-failing Left Ventricle

description:
P01025
PolyA mRNA


title: flu infected vs. uninfected

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

data_processing: Raw microarray images were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.7.5, Agilent Technologies) using almost default settings for miRNA microarrays loaded with a grid file or standard setting. Non-uniformity outlier flagging was done with a 5x default value of the constant coefficient of variation for features ((CV)2 Term (A) = 0.55 ) and background ((CV)2 Term (A) = 0.45 ). Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

source_name: flu infected

treatment_protocol:
Cells were washed with PBS and then infected at the indicated MOIs in PBS (PBS supplemented with 0.2% bovine serum albumin) for 45 min at room temperature (RT). Cells were washed again (in PBS) and incubated for the indicated time periods at 37°C in DMEM containing 0.2% bovine serum albumin, 4 mM L-glutamine and antibiotics, unless otherwise stated.
Numbers of infected versus noninfected cells were determined using automated microscopy (Olympus, Hamburg, Germany).

tag: influenza strains

source_name: uninfected

treatment_protocol: Cell line was grown in DMEM media (Invitrogen, Karlsruhe, Germany) with 4 mM L-glutamine, 4 mM sodium pyruvate, 100 U/ml penicillin/streptomycin and 10% fetal calf serum (FCS) at 37°C and 5% CO2. Phoenix-ECO packaging cells (G.P. Nolan, Stanford University, USA), 293T (CRL-11268, ATCC-LGC) and MDCK (CCL-34, ATCC-LGC) cells were grown in DMEM supplemented with 4 mM L-glutamine, 100 U/ml penicillin/streptomycin and 10% FCS. Cells were regularly checked for mycoplasma contamination.

tag: cell line

value: The A549 human lung epithelial cell line (CCL-185, ATCC-LGC, Wesel, Germany)


title: IDC Breast Cancer [20130110_205611690814_08-4209-A1_11.RCC]

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: The data were normalized using 5 HK genes.  Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: Tumor

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO´s Translational Genomics Group

extract_protocol: Total RNA was isolated from macrodissected FFPE tissue using ROCHE High Pure FFPE Kit

tag: age (years)

tag: tumor size (mm)

tag: relapse-free survival event (0=no recurrence; 1=recurrence)

tag: relapse-free survival time (months)

value: LumB

tag: ror-s score

tag: ror-s groups

value: high


title: P01248 Non-failing Left Ventricle

description:
P01248
PolyA mRNA


title: P01238 Non-failing Left Ventricle

description:
P01238
PolyA mRNA


title: P01251 Non-failing Left Ventricle

description:
P01251
PolyA mRNA


title: wild-type E14,5 DRG replicate3 - technical replicate 2

city: Marseille

first: Aziz

last: Moqrich

address: case 907, campus de luminy

country: France

institute: CNRS

description: Biological replicate 3 of 3. Technical replicate 2. E14,5 DRG extract from wild type embryos.

hyb_protocol: The two labelled aRNA were mixed, fragmented and hybridized on one array of a Nimblegen 12-plex microarray according the manufacturer's instructions.

scan_protocol: Scanned on an Innopsys Innoscan900 scanner

data_processing: Images were quantified using Nimblescan V2.5. The rawdata were normalized by Loess (Limma Package).

organism: Mus musculus

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer’s instructions.

extract_protocol: Spinal columns from E14 embryos from multiple litters were quickly dissected in Hank's Buffered Salt Solution (HBSS) and placed in RNAlater (Ambion) overnight at 4°C awaiting genotyping. DRGs were then dissected out and homogenized using glass beads in Precellys 24 (Bertin Technologies, France), followed by RNA extraction using RNeasy mini kit (Qiagen). RNA was then concentrated by precipitation with lithium chloride (2.5M final concentration). The amount and quality of RNA was assessed using NanoDrop (NanoDrop Technologies) and Experion system (BIO-RAD). Three independent replicates, each containing DRGs from 6-8 embryos from multiple litters, were prepared for each genotype.

value: embryonic day 14,5 (E14,5)

value: dorsal root ganglion (DRG)

tag: genotype/variation

value: wild type

source_name: Total RNA from pooled mouse E14,5 and adult DRGs


title: DW292_Tg_M

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

label: Biotin

label_protocol: Biotin

growth_protocol: Mice harboring a Cyfip1 spanning BAC clone (RP24-333C15) were generated in the UCLA transgenic core (http://tmc.ctrl.ucla.edu/tg-core/) by injection into C57BL/6J pronuclei. Transgenic mice were identified by PCR screening of tail derived DNA.

extract_protocol: Total RNA was isolated from embryonic day 15 frontal cortex from transgenic animals (n=3) and littermates controls (n=3) using the Qiagen RNeasy Kit. RNA quantity and quality was assessed using a Nanodrop (Nanodrop Technologies) and the Agilent Bioanalyzer (Agilent Technologies), respectively. Total RNA (200ng) was amplified, biotinylated and hybridized on Illumina Mouse ref-8 v2.0 BeadChip arrays, querying the expression of ~25,600 well-annotated Refseq transcripts, as per manufacturer's protocol.

treatment_protocol: Mouse frontal cortex was sampled from embryonic day 15 transgenic animals and littermates control using disecction kits.

tag: strain

value: Transgenic

value: Male

value: embryonic day 15

value: frontal cortex


title: DW298_Tg_M


title: wild-type E14,5 DRG replicate2 - technical replicate 2

description: Biological replicate 2 of 3. Technical replicate 2. E14,5 DRG extract from wild type embryos.


title: DW91.2_Tg_M


title: wild-type E14,5 DRG replicate1 - technical replicate 2

description: Biological replicate 1 of 3. Technical replicate 2. E14,5 DRG extract from wild type embryos.


title: DW83_WT_M

value: WT


title: TrkAC-KI E14,5 DRG replicate1 - technical replicate 2

description: Biological replicate 1 of 3. Technical replicate 2. E14,5 DRG extract from TrkAC-KI embryos.

source_name: E14,5 DRG extract from TrkAC-KI embryos

value: TrkAC-KI


title: IDC Breast Cancer [20130110_205611670814_11-9429 A5 S_07.RCC]

value: LumA

value: low


title: IDC Breast Cancer [20130110_205611670814_11-16514 B2 S_11.RCC]

value: Basal


title: IDC Breast Cancer [20130110_205611670814_11-3276 A3 S_03.RCC]


title: DW301_WT_M


title: TrkAC-KI E14,5 DRG replicate2 - technical replicate 2

description: Biological replicate 2 of 3. Technical replicate 2. E14,5 DRG extract from TrkAC-KI embryos.


title: DW307_WT_M


title: P01225 Non-failing Left Ventricle

description:
P01225
PolyA mRNA

value: heart left ventricle

value: no

value: non-failing

value: male


title: TrkAC-KI E14,5 DRG replicate3 - technical replicate 2

description: Biological replicate 3 of 3. Technical replicate 2. E14,5 DRG extract from TrkAC-KI embryos.


title: IDC Breast Cancer [20130110_205611670814_11-14384 A4 S_09.RCC]

value: high


title: IDC Breast Cancer [20130109_205611930814_11-9777 A1 S_09.RCC]


title: P01207 Non-failing Left Ventricle

description:
P01207
PolyA mRNA

value: female


title: IDC Breast Cancer [20130109_205611930814_10-18930 A2 S_05.RCC]


title: P01215 Non-failing Left Ventricle

description:
P01215
PolyA mRNA


title: IDC Breast Cancer [20130109_205611930814_10-23195 A6 S_07.RCC]

value: LumB


title: wild-type E14,5 DRG replicate3 - technical replicate 1

description: Biological replicate 3 of 3. Technical replicate 1. E14,5 DRG extract from wild type embryos.

value: embryonic day 14,5 (E14,5)

value: dorsal root ganglion (DRG)

value: wild type


title: P01199 Non-failing Left Ventricle

description:
P01199
PolyA mRNA


title: wild-type E14,5 DRG replicate2 - technical replicate 1

description: Biological replicate 2 of 3. Technical replicate 1. E14,5 DRG extract from wild type embryos.


title: IDC Breast Cancer [20130109_205611660814_12-7817 A9 S_03.RCC]


title: wild-type E14,5 DRG replicate1 - technical replicate 1

description: Biological replicate 1 of 3. Technical replicate 1. E14,5 DRG extract from wild type embryos.


title: P01185 Non-failing Left Ventricle

description:
P01185
PolyA mRNA


title: P01160 Non-failing Left Ventricle

description:
P01160
PolyA mRNA


title: IDC Breast Cancer [20130109_205611660814_12-3467 A1 S_01.RCC]


title: P01151 Non-failing Left Ventricle

description:
P01151
PolyA mRNA


title: P01119 Non-failing Left Ventricle

description:
P01119
PolyA mRNA


title: TNO Avicel vs ∆MHD Avicel_1

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

description: Biological rep 1 of 3

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: TNO Avicel 24h

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: All A. nidulans strains were grown in CM for 24h, washed twice with dH2O and then transferred to MM plus avicel as a sole carbon source for 24 h.

extract_protocol: Total RNA was extracted with RNeasy® Plant Mini Kit  (Qiagen) following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

source_name: ∆MHD Avicel 24h

value: ∆MHD


title: TNO Avicel vs ∆MHD Avicel_2

description: Biological rep 2 of 3


title: IDC Breast Cancer [20130109_205611660814_12-19599 A2 S_11.RCC]

value: med


title: IDC Breast Cancer [20130109_205611660814_12-12470 A2 S_09.RCC]


title: IDC Breast Cancer [20130109_205611660814_12-11896 A6 S_07.RCC]


title: IDC Breast Cancer [20130109_205611660814_12-11199 A3 S_05.RCC]


title: TrkAC-KI E14,5 DRG replicate3 - technical replicate 1

description: Biological replicate 3 of 3. Technical replicate 1. E14,5 DRG extract from TrkAC-KI embryos.


title: TNO YUU vs ∆MHD YUU_3

description: Biological rep 3 of 3

source_name: TNO YUU 24h

source_name: ∆MHD YUU 24h


title: TrkAC-KI E14,5 DRG replicate2 - technical replicate 1

description: Biological replicate 2 of 3. Technical replicate 1. E14,5 DRG extract from TrkAC-KI embryos.


title: C02034 Ischemic Left Ventricle

description:
C02034
PolyA mRNA

source_name: heart left ventricle, ischemic

value: yes

value: ischemic


title: TNO Avicel vs ∆MHD Avicel_3

description: Biological rep 3 of 3


title: C02141 Ischemic Left Ventricle

description:
C02141
PolyA mRNA


title: C02042 Ischemic Left Ventricle

description:
C02042
PolyA mRNA


title: TNO YUU vs ∆MHD YUU_2

description: Biological rep 2 of 3


title: C02053 Ischemic Left Ventricle

description:
C02053
PolyA mRNA


title: C02136 Ischemic Left Ventricle

description:
C02136
PolyA mRNA


title: TrkAC-KI E14,5 DRG replicate1 - technical replicate 1

description: Biological replicate 1 of 3. Technical replicate 1. E14,5 DRG extract from TrkAC-KI embryos.

value: TrkAC-KI


title: JUVENIL FIBROADENOMA [20130315_205635390814_12-11703-A3_11.RCC]

value: Normal

value: low


title: JUVENIL FIBROADENOMA [20130305_205635410814_11-14889-A2_12.RCC]


title: JUVENIL FIBROADENOMA [20130305_205635410814_11-2272-A3_11.RCC]


title: C01984 Idiopathic Dilated CMP Left Ventricle

description:
C01984
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: heart left ventricle

value: idiopathic dilated CMP


title: C02187 Ischemic Left Ventricle

description:
C02187
PolyA mRNA


title: TNO Avicel vs ∆msbA Avicel_2

description: Biological rep 2 of 3

source_name: ∆msbA Avicel 24h

value: ∆msbA


title: TNO Avicel vs ∆msbA Avicel_3

description: Biological rep 3 of 3


title: TNO YUU vs ∆MHD YUU_1

description: Biological rep 1 of 3


title: TNO YUU vs ∆msbA YUU_3

description: Biological rep 3 of 3

source_name: ∆msbA YUU 24h


title: TNO Avicel vs ∆msbA Avicel_1

description: Biological rep 1 of 3


title: C02142 Ischemic Left Ventricle

description:
C02142
PolyA mRNA

value: male


title: JUVENIL FIBROADENOMA [20130305_205635410814_10-11137-A2_09.RCC]


title: C02082 Ischemic Left Ventricle

description:
C02082
PolyA mRNA


title: TNO YUU vs ∆msbA YUU_2

description: Biological rep 2 of 3


title: JUVENIL FIBROADENOMA [20130227_205635330814_13-1308-A1_04.RCC]

value: Basal


title: TNO YUU vs ∆msbA YUU_1

description: Biological rep 1 of 3


title: FIBROADENOMA  [20130514_205635530814_01-13120-R_08.RCC]


title: FIBROADENOMA  [20130514_205635530814_01-28551_06.RCC]


title: C02146 Ischemic Left Ventricle

description:
C02146
PolyA mRNA

value: female


title: C02182 Idiopathic Dilated CMP Left Ventricle

description:
C02182
PolyA mRNA


title: FIBROADENOMA  [20130319_205635510814_13-2632-A1_12.RCC]


title: C02155 Idiopathic Dilated CMP Left Ventricle

description:
C02155
PolyA mRNA


title: FIBROADENOMA  [20130319_205635510814_13-2657-B4_11.RCC]


title: C02085 Idiopathic Dilated CMP Left Ventricle

description:
C02085
PolyA mRNA


title: C02086 Idiopathic Dilated CMP Left Ventricle

description:
C02086
PolyA mRNA


title: C02071 Ischemic Left Ventricle

description:
C02071
PolyA mRNA


title: C02070 Ischemic Left Ventricle

description:
C02070
PolyA mRNA


title: FIBROADENOMA  [20130319_205635510814_12-25521-A1_09.RCC]


title: FIBROADENOMA  [20130319_205635510814_13-2605-A2_10.RCC]


title: FIBROADENOMA  [20130319_205635510814_07-1288-A3_07.RCC]

value: LumA


title: healthy donor C

type: genomic

city: Tianjin

first: Tian

last: Yuan

address: No.288 Nanjing Road

department: Institute of Hematology and Blood Disease Hospital

country: China

institute: Peking Union Medical College

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Array data were analyzed using Affymetrix Genotyping Console and Chromosome Analysis Suit.

molecule: genomic DNA

source_name: bone marrow from healthy donor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell obtained from bone marrow of ALL patients and healthy donor using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: diagnosis

value: Healthy donor

tag: status

value: untreated


title: C02066 Ischemic Left Ventricle

description:
C02066
PolyA mRNA

tag: tissue


title: healthy donor D


title: FIBROADENOMA  [20130315_205635390814_13-2680-A2_12.RCC]


title: C02065 Idiopathic Dilated CMP Left Ventricle

description:
C02065
PolyA mRNA

tag: heart failure


title: healthy donor B


title: healthy donor A


title: patient 30

source_name: bone marrow from acute lymphoblastic leukemia patient

value: T-ALL

value: newly diagnosed


title: FIBROADENOMA  [20130315_205635390814_07-12137-A1_07.RCC]


title: FIBROADENOMA  [20130315_205635390814_06-26092-A1_06.RCC]

value: med


title: patient 15


title: healthy donor E


title: FIBROADENOMA  [20130315_205635390814_06-23834-A1_05.RCC]


title: M3 tumor dnTbRII, biological rep6

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: RNA extracted by Rneasy

hyb_protocol: Three replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C,  60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.

data_processing:
Data were analyzed with Partek Genomics Suite (version 6.5) software using the RMA normalization algorithm with default format.  More details needed here?
Original,  Summarized,  Difference,  Filename,  Chip Type,  tumor,  Scan Date,  gene expression

source_name: MCF10CA1h (M3) tumor,  TGF-beta pathway blockade with dnTbRII

label_protocol: 100 ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: MCF10CA1h (M3) cells were infected ex vivo with pLPCX retrovirus with no insert (M3-CON) or pLPCX expressing dominant negative type II TGF-b receptor (M3-dnTbRII) . Cells were selected in DMEM/F12 medium supplemented with 5% Horse serum and 4ug/ml puromycin for 5 days.  5x10e5 cells were implanted orthotopically into female athymic NCr nu/nu mice.

extract_protocol: Total RNA was extracted and purified by RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: refer to the summary for each study.

value: Breast cancer xenograft tumor

tag: treatment

value: TGF-beta pathway blockade with dnTbRII


title: patient 19


title: patient 18


title: FIBROADENOMA  [20130315_205635390814_06-25837-A1_04.RCC]


title: patient 20


title: FIBROADENOMA  [20130315_205635390814_07-20526-A1_08.RCC]


title: M3 tumor dnTbRII, biological rep5

description: RNA extracted by Rneasy


title: patient 17


title: patient 23


title: FIBROADENOMA  [20130315_205635390814_06-23835-A1_02.RCC]


title: patient 16

value: pro-B ALL


title: patient 25

value: pre-B ALL


title: 12h FCS

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: The labeled Input and enriched DNA was precipitated with 11.5 µl 5M NaCl and 1 volume isopropanol, and hybridized in 14.4 µl HybridizationMix containing 2x Hybridization buffer, Hybridization Component A and alignment oligos together with 5.6 µl sample tracking control. Arrays were hybridized in Maui hybridization stations for 40-48h h at 42C, and then washed in wash-buffer I, II, III containing 0,1 % 1M DTT.Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf)

scan_protocol: Arrays were scanned on an nimblegen MS2000 scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 ChIP data extraction.

source_name: 12h differentiated SFME cells in the presence of 10% FCS

label_protocol: 1 µg enriched and Input DNA was directly labeled by Klenow (nimblegen) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: genomic DNA was isolated using NaCl/chloroform extraction

tag: cell type

value: serum free mouse embryo (SFME)

source_name: mouse genomic DNA control


title: 24h TGFB

source_name: 24h differentiated SFME cells in the presence of TGFß


title: FIBROADENOMA  [20130315_205635390814_01-13873-R_01.RCC]

source_name: Tumor

value: Normal

value: low


title: patient 22


title: patient 29


title: M3 tumor dnTbRII, biological rep4

description: RNA extracted by Rneasy


title: M3 tumor dnTbRII, biological rep3

description: RNA extracted by Rneasy


title: patient 33


title: FIBROADENOMA  [20130227_205635330814_98-27575-R_05.RCC]


title: patient 11-3

value: P210+ ALL


title: patient 13


title: M3 tumor dnTbRII, biological rep2

description: RNA extracted by Rneasy


title: patient 12


title: SFME sphere

source_name: SFME sphere cells


title: FIBROADENOMA  [20130227_205635330814_02-10573-R_02.RCC]


title: FIBROADENOMA [20131010_205635340814_03-6066-R_10.RCC]


title: patient 11-1


title: M3 tumor dnTbRII, biological rep1

description: RNA extracted by Rneasy


title: FIBROADENOMA [20130116_205611720814_12-25535-B1_04.RCC]


title: M3 tumor control, biological rep6

description: RNA extracted by Rneasy

source_name: MCF10CA1h (M3) tumor,  control

value: control


title: FIBROADENOMA [20130116_205611720814_12-25535-A2_01.RCC]


title: M3 tumor control, biological rep5

description: RNA extracted by Rneasy


title: FIBROADENOMA [20130116_205611720814_12-25535-C2_02.RCC]


title: patient 21

value: relapse (3)


title: FIBROADENOMA  [20130315_205635390814_06-21508-A1_03.RCC]


title: patient 11-2

value: CR


title: FIBROADENOMA [20130116_205611720814_12-25535-D1_03.RCC]


title: FIBROADENOMA [20130319_205635510814_12-25556-A2_08.RCC]


title: FIBROADENOMA [20130315_205635390814_12-25579-A1_09.RCC]


title: M3 tumor control, biological rep4

description: RNA extracted by Rneasy


title: FIBROADENOMA [20130115_205611640814_12-25556-A2_12.RCC]


title: patient 10-1

value: P190+ ALL


title: Pancreatic cell line transfected with IGFBP2

city: Houston

first: Song

last: Gao

state: TX

address: 1515 Holcombe Blvd

department: Pathology

institute: UT MD Anderson Cancer Center

description: single pair

hyb_protocol: as specificied by Agilent Low Input Labeling v 6.5

scan_protocol: Agilent Technologies Scanner G2505C US23502373

data_processing: Agilent Feature Extraction protocol GE2_1100_Jul11 (Read Only)

source_name: Pancreatic cells

label_protocol: Agilent Low Input Labeling v 6.5

growth_protocol: AsPc-1 cells were cultured in RPMI1640 medium. The media were supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Ambion 1560 miRvana RNA extraction kit

treatment_protocol: For transfection, cells were plated at a density of 5×10^5 cells/well in 6-well plates in medium containing 10% FBS. When the cells were 80% confluent, they were transfected with 4 µg plasmids in Lipofectamine 2000 (Invitrogen) for 48 hours. Stably transfected cells were selected by G418 treatment.

tag: transfection status

value: stable transfection with IGFBP2 gene in pcDNA3.1

value: stable transfection with Empty vector pcDNA3.1


title: M3 tumor control, biological rep2

description: RNA extracted by Rneasy


title: patient 9-1


title: patient 27


title: M3 tumor control, biological rep3

description: RNA extracted by Rneasy


title: patient 14


title: patient 9


title: FIBROADENOMA [20130115_205611640814_12-25579-A2_11.RCC]


title: FIBROADENOMA [20130514_205635530814_02-5040_11.RCC]


title: FIBROADENOMA [20130514_205635530814_10-11094-A6_12.RCC]


title: patient 8-2


title: pSUPER-Scramble vs pSUPER-miR-210

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: microRNA expression data from HUVEC over-expressing miR-210

hyb_protocol: 2-color hybridization was performed using miRCURY LNA microRNA Arrays (v.10.0, EXIQON). 2.5ug of each labeled RNA were co-hybridized at 53°C for 16 hours. Hybridization and washing steps were performed on the HS 400 PRO hybridization station (Tecan).

scan_protocol: MicroRNA arrays were scanned using the GenePix 4100A microarray scanner and the GenePix Pro 6.0.1.25 software (Molecular Devices).

data_processing: The obtained signal intensities were analyzed by using the limma package (Bioconductor 2.5 on R 2.10 ). Background correction (normexp) and within-array normalization (global LOESS) was performed. Differential expression and statistical significance were assessed for each miRNA species across all 4 arrays using linear model fit and empirical Bayes method (lmFit, eBayes), taking into account the dye-swap. Intensities lower than 1.5 times the median signal intensity of the respective slide were considered as bad quality spot. The calling of a miRNA failed if two or more of the four replicates present per miRNA species were bad quality spots and if this occurred on more than two arrays.

label: Hy3, Hy5

source_name: HUVEC infected by retroviral vectors bearing control scramble sequence

label_protocol: 2.5 ug total RNA was labeled with Hy3, Hy5 resepctively according to the manufacturer's protocol (miRCURY LNA microRNA Array Power labeling kit, EXIQON). Three Samples were labelled with Hy3 as control and Hy5 as mir-210 over-expressing, the reverse is true for the dye-swapped slide (CV44_ds.gpr).

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS.

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

treatment_protocol: To obtain stable miR-210 over-expressing cells, HUVEC were infected by retroviral vectors bearing pre-miR-210 sequence (pSUPER-miR-210) or a control scramble sequence (pSUPER-scramble). Infected cells were then selected in puromycin-containing medium (0.5 μg/ml, Sigma).

value: HUVEC

label: Hy5, Hy3

source_name: HUVEC infected by retroviral vectors bearing pre-miR-210 sequence


title: patient 7-2


title: FIBROADENOMA [20130514_205635530814_01-29326_04.RCC]


title: FIBROADENOMA [20130305_205635410814_07-1185-A3_07.RCC]


title: 3_141996_pléomorph cells DDLPS

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

source_name: Liposarcoma DNA

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

tag: tissue type

source_name: Female DNA control provided in SureTag Labeling Kit

tag: sample type

value: commercial DNA from cell lines


title: 4_141996-3_DDLPS


title: 1_99T1491_WDLPS


title: 5_141996-4_DDLPS


title: FIBROADENOMA [20130305_205635410814_08-12002-A2_08.RCC]

tag: age (years)


title: P350_CRPC

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: 4 x 180

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on Agilent SurePrint G3 Human Catalog CGH 4x180K (Design ID 022060).

scan_protocol: Scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C.

data_processing:
Quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1.
FE files loaded into Nexus Copy Number Software v.7 (Biodiscovery Inc.) for analysis.
CGH data was processed using BioDiscovery's FASST2 Segmentation Algorithm to estimate copy number state. These state values are then used to make calls based on a log-ratio threshold. The significance threshold for segmentation was set at 5.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.2 and -0.23, respectively. The log ratio thresholds for two or more copy gain and homozygous loss were set at 1.14 and -1.1, respectively. Upon loading of raw data files, signal intensities are normalized via division by mean. All samples are corrected for GC wave content using a systematic correction algorithm.

source_name: castrate-resistant prostate cancer cell line xenograft, control

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User's Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cyanine-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit.

tag: sample origin

value: prostate cancer cell line sub-cutaneous xenograft

tag: cell line

value: LNCaP

tag: castrate sensitivity

value: resistant

tag: enzalutamide (enz) sensitivity

value: naïve

tag: psa at diagnosis

source_name: male reference DNA (Promega Corp. cat# G1471)

value: reference

tag: gender

value: male


title: FIBROADENOMA [20130305_205635410814_06-20423-A1_06.RCC]

tag: tumor size (mm)

tag: relapse-free survival event (0=no recurrence; 1=recurrence)

tag: relapse-free survival time (months)

value: Normal

tag: ror-s score

tag: ror-s groups


title: M3 tumor control, biological rep1

description: RNA extracted by Rneasy

tag: tissue

value: Breast cancer xenograft tumor

tag: treatment


title: P252_ENZ-R

description: 4 x 180

source_name: castrate-resistant prostate cancer cell line xenograft, ENZ resistant


title: patient 10-2

tag: diagnosis

tag: status


title: FIBROADENOMA [20130315_205635390814_12-25535-A3_10.RCC]

value: low


title: patient 32

value: Common B ALL

value: newly diagnosed


title: RNA_thp1_B

status: Public on Dec 31 2014

city: Basel

first: Primo

last: Schar

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Samples were prepared and hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to manufacturer's instruction.

data_processing:
oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R
log2 fold change (relative expression thp1Δ/WT was calculated by normalizing the mean of thp1_A, thp1_B and thp1_C to the mean of WT_A, WT_B and WT_C); standard deviation was calculated among WT replicates A-C and thp1Δ replicates A-C

organism: Schizosaccharomyces pombe

source_name: S. pombe thp1Δ

growth_protocol: Strains were isolated from crosses and grown on YEL, no freezing of the cells prior to RNA extraction

extract_protocol: RNA was extracted by using the hot phenol method: 20 ml of exponentially-growing cells were harvested and resuspended in 50 mM sodium acetate (pH 5.2) and 10 mM EDTA. 125 µl of 20% SDS and 1.5 ml of acidic phenol (pH 4.3) was added and the mixture was incubated for 10 min at 65°C,  vigourously mixing  every minute. After 5 min on ice, the supernatant was transfered to 15 ml Phase Lock Gel tubes (Lab force) to which 1.65 ml chloroform was added befor mixing by inverting the tube. The tubes were spun for 10 min at 1864 g and the supernatant was transfered to a fresh tube. The RNA was precipitated using isopropanol and resuspended in RNAse-free water.

treatment_protocol: no treatment

tag: mating type

value: mating type h+

tag: genotype


title: RNA_thp1_C

label_protocol: Samples were prepared and hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Array according to Affymetrix specifications.


title: patient 8-1

source_name: bone marrow from acute lymphoblastic leukemia patient

value: P190+ ALL


title: RNA_thp1_A


title: patient 28


title: P334_CRPC

description: 4 x 180

tag: sample origin

tag: sample type


title: RNA_WT_B

description: WTB

source_name: S. pombe, WT

value: wildtype


title: P163_ENZ-R

description: 4 x 180

tag: cell line

tag: castrate sensitivity


title: RNA_WT_A

description: WTA


title: 2_11T1030_DDLPS

hyb_protocol: DNA was hybridized with the CGX Nimblegen protocol

scan_protocol: We used ScanRI software to control a ScanRI scanner

data_processing:
the image data was processed by DEVA software provided by Perkin Elmer to obtain a .txt file. This file is transform by a soft tool ngpackager supplied by Nimblegen to obtain a .ggx file compiling log Ratio Cy3/Cy5 average for every probe
The .ggx file is performed on Genoglyphix, an online software supplied by Perkin Elmer, to obtain a genome view and to compare it with global data bases. The normalization was performed according default method

label_protocol: DNA was labeled with the CGX Nimblegen protocol

extract_protocol: DNA was extracted from fresh or frozen fragments using Qiamp DNA mini kit.

tag: tissue type

source_name: Promega Human Genomic DNA (G1521)


title: AE104(delta zupT) with 10 µM ZnCl2, replicate 1

status: Public on Dec 16 2014

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: First, dark and light control spots, and foreign DNA control spots were deleted. Secondly, if genes were represented by more than one spot, the mean value coming from these two, three or more spots was used and assigned to the gene number. The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans CH34

source_name: cells of C. metallidurans

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans strains were grown in Mineral salts medium + 0.2 % Na-gluconate with or without ZnCl2 or EDTA to a cell turbidity of 100 Klett, then  cells were harvest by centrifugation for 1' at 4°C in 2.0 ml Tubes.

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: genotype/variation

value: AE104(delta zupT)

value: 10 µM ZnCl2


title: CH34 without treatment, replicate 3

value: wild type CH34


title: AE104(delta zupT) with 50 µM EDTA, replicate 1

value: 50 µM EDTA


title: P111_ENZ-R

description: 4 x 180

value: prostate cancer cell line sub-cutaneous xenograft

value: LNCaP

tag: enzalutamide (enz) sensitivity

tag: psa at diagnosis

tag: gender


title: P145_ENZ-R

description: 4 x 180

value: resistant


title: AE104(delta zupT) with 50 µM EDTA, replicate 2


title: CH34 without treatment, replicate 1


title: CH34 without treatment, replicate 2


title: AE104(delta zupT) with 10 µM ZnCl2, replicate 2


title: patient 31


title: patient 5-2

value: CR


title: AE104 with 50 µM EDTA, replicate 3


title: AE104 with 50 µM EDTA, replicate 2


title: AE104 with 10 µM ZnCl2, replicate 3


title: AE104 with 10 µM ZnCl2, replicate 2


title: AE104 with 50 µM EDTA, replicate 1


title: RNA_WT_C

description: WTC


title: patient 5-1


title: mES EGFP Rep1

status: Public on Dec 01 2014

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Gene expression following EGFP transfection

hyb_protocol: 600ngs of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 il of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Mouse GE 8x60K microarray (Agilent; G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 2x1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 2x1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned on a Nimblegen scanner at 2um resolution to generate single channel TIFF images.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain non-background subtracted and spatially detrended Processed Signal intensities.

molecule: polyA RNA

source_name: mES, EGFP transfected, Replicate 1

label_protocol: 1mg of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent – 5188-5282) and the mixture labelled with cyanine 3 (Cy3) using the Amino Allyl MessageAmp™ II with Cy™3 kit (Ambion; AM1795) according to manufacturer’s instructions.

growth_protocol: E14 ES cells were grown in GMEM supplemented with 15% fetal bovine serum (FBS), 1,000 units/ml LIF, nonessential amino acids, sodium pyruvate, 2-β-mercaptoethanol, L-glutamine, and Penicillin/Streptomycin.

extract_protocol: RNA was prepared using RNeasy mini kit (Qiagen) according to manufacturer’s protocol, including a DNaseI (Qiagen) treatment for 15mn at room temperature

treatment_protocol: ESCs were transfected with plasmids using Lipofectamine® 2000 Reagent (Invitrogen cat. N°11668) following the manufacturer recommendations. Briefly, 1x106 ESCs were transfected in a 6-well plate with 3µg of plasmid and 7µl of lipofectamin. Medium was changed 5h after transfection. Transfected cells were sorted based on eGFP expression by FACS 24h after transfection, re-seeded for another 24h before harvesting for experiment

tag: cell type

value: mouse ES cells

value: EGFP transfection


title: patient 26


title: patient 6-2


title: AE104 without treatment, replicate 1


title: AE104 with 10 µM ZnCl2, replicate 1


title: AE104 without treatment, replicate 2


title: stable synthetic hexaploid_rep3

status: Public on Nov 30 2014

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

country: Japan

institute: Kihara Institute for Biological Research

description: Gene expression of stable synthetic hexaploid

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: After washing, signal intensities were immediately detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).

data_processing: Signal intensities were detected from the obtained digital images with Feature Extraction software 9.5 (Agilent Technologies). Fluorescence intensities were analysed with GeneSpring GX v12.6 (Agilent Technologies). Raw data set (raw signal intensity > 1.0 threshold) was transformed to log scale at base 2. Normalization was performed with GeneSpring.

organism: Triticum dicoccon x Aegilops tauschii subsp. strangulata

source_name: KU-221-13, replicate 3

label_protocol: Extracted RNAs (500ng) were labelled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) with cyamine 3-cytidine 5C-triphosphate (CTP).

growth_protocol: All plants were grown in growth chamber controlled by at 22℃, relative humidity 40%, in 16 h length with 6000 lux (64,560 fc) and 8 h dark day cycles.

extract_protocol: Total RNA of each line was extracted using Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s method.

treatment_protocol: Ttriploid embryos were rescued 2 weeks later after pollination. Embryos were placed petridishes with half strength of Murashige & Skoog culture medium (Inagaki et al. 1998) in growth chamber which is maintained at 20℃, 12-h light/12-h dark (5000 lux). Chromosome-doubled hexaploid plants obtained by self-pollination of colchicine treated (0.2% in a 2% DMSO solution) of triploid plants.

value: leaf

tag: age

value: two leaves seedling


title: chromosome-doubled hexaploid_rep2

description: Gene expression of chromosome-doubled hexaploid

source_name: S1_SynH124, replicate 2

tag: tissue


title: newly synthetic triploid_rep3

description: Gene expression of newly synthetic triploid

source_name: S0_SynT124, replicate 3


title: chromosome-doubled hexaploid_rep3

source_name: S1_SynH124, replicate 3


title: stable synthetic hexaploid_rep1

source_name: KU-221-13, replicate 1


title: newly synthetic triploid_rep2

source_name: S0_SynT124, replicate 2


title: patient 24

value: Common B ALL


title: newly synthetic triploid_rep1

source_name: S0_SynT124, replicate 1


title: chromosome-doubled hexaploid_rep1

source_name: S1_SynH124, replicate 1


title: patient 7-1

value: newly diagnosed


title: 35_uRCC

status: Public on Nov 06 2014

data_processing: the image data was processed by DEVA software provided by Perkin Elmer to obtain a .txt file. This file is transform by a soft tool ngpackager supplied by Nimblegen to obtain a .ggx file compiling log Ratio Cy3/Cy5 average for every probe (unknown/default parameters).

value: unclassified renal cell carcinoma (uRCC)

tag: rcc type

value: unclassified

source_name: Promega Human Genomic DNA (G1471/G1521)

value: reference


title: 28_pRCC2

value: Papillary renal cell carcinoma (pRCC)

value: type 2


title: 26_pRCC2


title: 22_pRCC2


title: patient 4-1

tag: diagnosis


title: stable synthetic hexaploid_rep2

source_name: KU-221-13, replicate 2


title: 20_pRCC2


title: 19_pRCC2


title: 34_uRCC


title: 17_pRCC2


title: HeLa cells not  infected time 0.5 rep2

status: Public on Nov 25 2014

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_HeLa cells not  infected time 0.05 rep2

hyb_protocol: samples were hybridized onto Affymetrix human U133 plus 2.0 arrays according to manufacturer's recommendations

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

data_processing:
The data were analyzed with EC 1.1 and scaled to 1250
MAS 5.0

source_name: HeLa cells not  infected time 0.5 rep2

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: HeLa 229 cells were grown at 37oC with 5% CO2 in high-glucose-containing Dulbecco’s modified Eagle medium (DMEM) (Mediatech, Inc.) supplemented with 10% fetal bovine serum.

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: HeLa cells either mock infected or infected with an MOI of 3 of A2497- or A2497 at 30mins, 2 hrs, 4 hrs, 24 hrs, 48 hrs and 72 hrs

value: HeLa 229 cells not infected

value: HeLa 229

tag: infection

tag: time (hours)


title: patient 4-2

tag: status


title: 14_pRCC1

value: type 1


title: 11_pRCC1


title: 10_pRCC1


title: AE104 without treatment, replicate 3

tag: treatment


title: 9_pRCC1

tag: sample type


title: 6_pRCC1


title: HeLa cells not  infected time 0.5 rep3

description: Gene expression data from_HeLa cells not  infected time 0.05 rep3

source_name: HeLa cells not  infected time 0.5 rep3

tag: cell line


title: HeLa cells not  infected time 0.5 rep1

description: Gene expression data from_HeLa cells not  infected time 0.05 rep1

source_name: HeLa cells not  infected time 0.5 rep1


title: 1_pRCC1


title: 4_pRCC1


title: 8_pRCC1


title: patient 3-2

source_name: bone marrow from acute lymphoblastic leukemia patient


title: patient 3-1


title: patient 1-2

value: CR(complete remission) (2)


title: patient 2-2


title: Thyroid-Gland_Acrylamide-treated_female at morning_rep2

status: Public on Oct 06 2014

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

description:
TFM2
Gene expression of thyroid-gland. Acrylamide-treated female at morning rep2.

hyb_protocol: Was also performed according to the Agilent protocol no. G4140-90040, noted above.

scan_protocol: Scanned on an Agilent G2505B microarray scanner

data_processing: Data extraction was performed using Agilent Feature Extraction software.  Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). In JMP Genomics, raw expression data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis.  All probe responses per gene were averaged before using median normalization.  One-way ANOVA was used to find genes that were significantly altered (p < 0.05; fold change greater than ± 1.2). No FDR correction was applied in order to include as many genes as possible for the pathway analyses.

organism: Rattus norvegicus

source_name: TFM

label_protocol: Was used for cDNA synthesis, cRNA labeling, following the manufacturer’s kits and protocols Agilent Low input Quick-amp labelling kit one color (Agilent, Santa Clara, CA, USA).

growth_protocol: Pregnant (F0) female Wistar Han™ rats supplied by Harlan Laboratories GmbH Serumweg (Eystrup, Niedersachsen, Germany) and their offspring (F1) were used in this experiment. Rats were housed 1 per cage in MAKROLON cages, type Ill plus with granulated wood bedding (Brandenburg 49429 Goldensted/Arkeburg). The housing rooms were maintained at a room temperature of 22°C ± 2°C (maximum range) and a relative humidity of 55% ± 15% (maximum range). The cages were cleaned and changed once a week. The rooms were alternately lit (about 150 lux at approx. 1.50 m room height) and darkened in a 12 hours dark/12 hours light cycle. Cage-side observations were conducted twice per day during the week and once per day on weekends.

extract_protocol: Total RNA was extracted from Wistar Han™ rats thyroid samples using RNA STAT-60 (Tel-test, Friendswood, TX) according to manufacturer's protocol.  RNA was reconstituted in RNAsecure (Ambion) and Dnase-1 treated with DNA-free Turbo (Ambion).

treatment_protocol: Sperm positive females Wistar Han™/RccHan™ rats were dosed, via water with 3 mg AA/Kg bw/day, beginning on gestation day 6 and exposures continued in F1 offspring through postnatal (pnd) 35 ±3. The control animals received the same amount of tap water. Drinking water bottles were changed weekly based on the results of a stability test of AA in the drinking water bottles. In order to maintain a constant dose level in relation to the animal's body weight, the concentration in the drinking water was adjusted weekly based on the mean group water consumption per sex. On pnd 35±3 five male and five female pups were euthanized and sacrificed at 10 AM and 10 PM to capture changes in metabolic profiles that may be related to diurnal activity in rats. Thyroid glands were excised and frozen in liquid nitrogen for total RNA extraction and microarrays analysis. Blood was collected for thyroid and pituitary hormone analysis.

tag: strain

value: RccHan Wistar

value: Thyroid glands

value: Female

value: pup

value: exposure to 3 mg/Kg bw/day of AA in water from gestational day 6 to postnatal day 35

tag: collection time

value: morning (10 AM)


title: Thyroid-Gland_Control female at morning_rep4

description:
CTRL-FM4
Gene expression of thyroid-gland. Control female at morning rep4.

source_name: CTRL-FM

value: control


title: Thyroid-Gland_Acrylamide-treated_female at morning_rep1

description:
TFM1
Gene expression of thyroid-gland. Acrylamide-treated female at morning rep1.


title: Thyroid-Gland_Control female at morning_rep1

description:
CTRL-FM1
Gene expression of thyroid-gland. Control female at morning rep1.


title: Thyroid-Gland_Control male at night_rep4

description:
CTRL-MN4
Gene expression of thyroid-gland. Control male at night rep4.

source_name: CTRL-MN

value: Male

value: night (10 PM)


title: Thyroid-Gland_Control female at morning_rep2

description:
CTRL-FM2
Gene expression of thyroid-gland. Control female at morning rep2.


title: Thyroid-Gland_Acrylamide-treated_male at night_rep4

description:
TMN4
Gene expression of thyroid-gland. Acrylamide-treated male at night rep4.

source_name: TMN


title: patient 6-1

value: Common B ALL

value: newly diagnosed


title: Thyroid-Gland_Acrylamide-treated_male at night_rep1

description:
TMN1
Gene expression of thyroid-gland. Acrylamide-treated male at night rep1.


title: Thyroid-Gland_Acrylamide-treated_female at morning_rep3

description:
TFM3
Gene expression of thyroid-gland. Acrylamide-treated female at morning rep3.


title: mESC_day26_rep2

status: Public on Sep 25 2014

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

hyb_protocol: Labeled samples were hybridized to Mouse Exon 1.0 ST arrays (Affymetrix) and stained on the Fluidics Station 450 (Affymetrix) using program FS450-0001.

scan_protocol: Microarrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Raw data are analyzed with the software package of AltAnalyze using RMA with a raw expression threshold of 122 and DABG p-value of 0.05.
Cel Layout File: MoEx-1_0-st-v1.r2.clf
Probe Group File: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: Mm_gene_extended.mps
Probesets were remapped to Ensembl genes by AltAnalyze internally using file "Mm_Ensembl_probesets.txt" as a part of the "Gene level Analysis" process.

source_name: mESC differentiation day26

label_protocol: Samples from day0, day12, day19 and day26 were processed with a WT Expression kit (Ambion,), fragmented and labelled with a WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: The ESC clone aPIG44 was cultured on mouse embryonic fibroblasts as feeder cells in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with nonessential amino acids (0.1 mM), L-glutamine (2 mM), β-mercaptoethanol (0.1 mM), LIF (ESGRO®) (500 U/ml), neomycin (6 µg/mL), and batch-tested fetal calf serum (FCS) (15% v/v) (all Invitrogen, Karlsruhe, Germany).

extract_protocol: Total RNA from cells at indicated time points were extracted using PeqGold RNApure (Peqlab Biotechnology, Erlangen, Germany) according to the manufacturer's instructions. Quantity of total RNA was measured using a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA). Optical density ratios at 260/280 were consistently above 1.9. The total RNA quality was assayed with a RNA 6000 Nano Kit on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: To start differentiation, ESCs were trypsinized (day0) and cultured in suspension on a horizontal shaker (GFL 3006, GFL, Braunschweig, Germany) to form embryoid bodies (EBs). Medium was exchanged at day5, day7, and day9; Puromyicn (5 µg/mL) was added to select for cardiomyocytes at day9.

tag: differentiation stage

value: cardiomyocyte differentiated

tag: time after differentiation start


title: Thyroid-Gland_Acrylamide-treated_male at night_rep3

description:
TMN3
Gene expression of thyroid-gland. Acrylamide-treated male at night rep3.


title: Thyroid-Gland_Acrylamide-treated_female at night_rep3

description:
TFN3
Gene expression of thyroid-gland. Acrylamide-treated female at night rep3.

source_name: TFN


title: Thyroid-Gland_Acrylamide-treated_female at night_rep2

description:
TFN2
Gene expression of thyroid-gland. Acrylamide-treated female at night rep2.


title: Thyroid-Gland_Acrylamide-treated_male at night_rep2

description:
TMN2
Gene expression of thyroid-gland. Acrylamide-treated male at night rep2.


title: Thyroid-Gland_Control male at night_rep1

description:
CTRL-MN1
Gene expression of thyroid-gland. Control male at night rep1.


title: mESC_day19_rep1

source_name: mESC differentiation day19


title: patient 2-1


title: Thyroid-Gland_Acrylamide-treated_female at night_rep4

description:
TFN4
Gene expression of thyroid-gland. Acrylamide-treated female at night rep4.


title: Thyroid-Gland_Control male at night_rep3

description:
CTRL-MN3
Gene expression of thyroid-gland. Control male at night rep3.


title: patient 1-1

value: newly diagnosed (1)


title: Thyroid-Gland_Acrylamide-treated_female at morning_rep4

description:
TFM4
Gene expression of thyroid-gland. Acrylamide-treated female at morning rep4.


title: mESC_day19_rep2


title: mESC_day0_rep2

source_name: mESC differentiation day0

value: undifferentiated


title: mESC_day12_rep1

source_name: mESC differentiation day12


title: mESC_day0_rep1


title: Genotyping of Stomach Mucosa. UW, Stamlab (NREMC); Gastric tissue; JS-STL001-genotype

status: Public on Aug 05 2014

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19784
sample alias: STL001GA-01
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944

hyb_protocol: 200ng of genomic DNA was first denatured and subsequently neutralized to prepare it for amplification. The denatured DNA was then isothermally amplified in an overnight step at 37°C.  Next, amplified DNA was enzymatically fragmented for 60 minutes at 37°C using an end-point fragmentation process.  The fragmented DNA was then precipitated with isopropanol, allowed to air dry, then resuspended in hybridization buffer.  Eight samples were subsequently applied to each HumanOmni2.5-8v1.1 beadchip, which were kept separate with an IntelliHyb seal.  The prepared beadchip was incubated overnight in a hybridization oven at 48°C for 16-24 hours with rocking.  The amplified and fragmented DNA samples annealed to locus-specific 50mers during hybridization. Following hybridization, unhybridized and non-specifically hybridized DNA was washed away, and the chip was prepared for staining and extension.

scan_protocol: Beadchips were scanned using an Illumina iScan+ with ICS v3.2.28

data_processing: Intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Genotyping Module v1.9.4) with a GenCall cutoff of 0.15.

label: Illumina protocol

source_name: Gastric tissue; JS-STL001-genotype

label_protocol: The chip underwent staining and extension in capillary flow-through chambers.  Allele-specific single-base extension of the oligos on the beadchip, using the captured DNA as template, incorporated detectable labels on the beadchip and determined the genotype call for the sample.

extract_protocol: Qiagen DNeasy Blood and Tissue kit (cat #69506).

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Gastric

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American


title: Genotyping of Ovary. UW, Stamlab (NREMC); Ovary tissue; JS-STL002-genotype

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19790
sample alias: STL002OV-01
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360

source_name: Ovary tissue; JS-STL002-genotype

value: iron deficiency, bipolar

value: Ovary

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian


title: Genotyping of Small Intestine Mucosa. UW, Stamlab (NREMC); Small Intestine tissue; JS-STL003-genotype

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19786
sample alias: STL003SB-01
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844

value: Small Intestine

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male


title: Thyroid-Gland_Control male at night_rep2

description:
CTRL-MN2
Gene expression of thyroid-gland. Control male at night rep2.

value: RccHan Wistar

value: Thyroid glands

tag: gender

value: pup

value: control

value: night (10 PM)


title: Thyroid-Gland_Control female at night_rep4

description:
CTRL-FN4
Gene expression of thyroid-gland. Control female at night rep4.

source_name: CTRL-FN


title: Genotyping of Skin Keratinocytes. UW, Stamlab (NREMC); Penis, Foreskin, Keratinocyte Primary Cells; JS-SK02-genotype

description:
sample_term_id: CL_1001606
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19788
sample alias: Penis, Foreskin, Keratinocyte skin02
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9573

source_name: Penis, Foreskin, Keratinocyte Primary Cells skin02; JS-SK02-genotype

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Keratinocyte

tag: markers

value: Invitrogen 154CF + HKGS + .07mM Ca

value: Neonate

value: Disease Free

tag: karyotype

tag: parity


title: Genotyping of CD4+. UW, Stamlab (NREMC); flow sorted CD4+ Primary Cells, Mobilized, year 37; JS-RO-01701-genotype

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19808
sample alias: CD4.RO_01701
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6988

value: FHCRC HEIMFELD

value: Primary Cell

value: Mobilized CD4 Primary Cells

value: year 37

value: Hispanic


title: Thyroid-Gland_Acrylamide-treated_female at night_rep1

description:
TFN1
Gene expression of thyroid-gland. Acrylamide-treated female at night rep1.

tag: tissue

value: Female

tag: age

value: exposure to 3 mg/Kg bw/day of AA in water from gestational day 6 to postnatal day 35


title: Thyroid-Gland_Control female at night_rep2

description:
CTRL-FN2
Gene expression of thyroid-gland. Control female at night rep2.

value: RccHan Wistar

value: Thyroid glands


title: Genotyping of CD14+. UW, Stamlab (NREMC); flow sorted CD14+ Cells,year 21; JS-RO-01679-genotype

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19810
sample alias: CD14.RO_01721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355

value: CD14 Primary Cells

value: year 21

value: Male

value: Caucasian


title: Genotyping of CD14+. UW, Stamlab (NREMC); flow sorted CD14+ Cells, year 33; JS-RO-01670-genotype

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19812
sample alias: CD14.RO_01670
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.19814

value: year 33


title: Genotyping of vHMEC. UW, Stamlab (NREMC); Breast, vHMEC, RM035; JS-RM035-genotype

description:
sample_term_id: CL_0002327
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19704
sample alias: Breast vHMEC RM035
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.2872

source_name: Breast, vHMEC, RM035; JS-RM035-genotype

value: Tlsty Lab, University of California, San Francisco

value: Primary Cell Culture

value: Variant Human Mammary Epithelial Cells

value: spilt 1:5 in MEGM medium (Lonza Inc.)


title: Genotyping of IMR90. UW, Stamlab (NREMC); IMR90 Cell Line.; JS-IMR-genotype

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19796
sample alias: IMR90
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632

source_name: IMR90 Cell Line.; JS-IMR-genotype

value: ATCC

value: Cell Line

tag: line

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

tag: batch


title: Thyroid-Gland_Control female at morning_rep3

description:
CTRL-FM3
Gene expression of thyroid-gland. Control female at morning rep3.

tag: strain

value: Female

value: pup

tag: treatment

value: control

value: morning (10 AM)


title: Thyroid-Gland_Control female at night_rep1

description:
CTRL-FN1
Gene expression of thyroid-gland. Control female at night rep1.

value: RccHan Wistar

value: Thyroid glands

tag: collection time

value: night (10 PM)


title: Thyroid-Gland_Control female at night_rep3

description:
CTRL-FN3
Gene expression of thyroid-gland. Control female at night rep3.


title: mESC_day12_rep2

tag: differentiation stage

value: cardiomyocyte differentiated

tag: time after differentiation start


title: Genotyping of fLiver. UW, Stamlab (NREMC); Fetal Liver primary tissue, day 110; JS-H24644-genotype

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19818
sample alias: fLiver.H-24644d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.19820

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Liver

value: UW

value: fetal

value: day 110


title: Genotyping of fKidney R. UW, Stamlab (NREMC); Fetal Kidney, Right primary tissue, day 108; JS-H24595-genotype

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19802
sample alias: fKidney_Right.H-24595d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14335

value: Fetal Kidney, Right

value: day 108

value: Male


title: Genotyping of fKidney. UW, Stamlab (NREMC); Fetal  primary tissue, day 108; JS-H23769-genotype

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19806
sample alias: fKidney_renal_cortex.H-23769d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7070

value: Fetal Renal Cortex


title: Genotyping of fLiver. UW, Stamlab (NREMC); Fetal Liver primary tissue, day 96; JS-H22662-genotype

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19821
sample alias: fLiver.H-22662d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.19823

value: day 96

value: Unknown


title: Genotyping of H9. UW, Stamlab (NREMC); H9 cell line; JS-ESC-genotype

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19798
sample alias: H9-05
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; JS-ESC-genotype

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Female


title: Genotyping of iPS 6 9. UW, Stamlab (NREMC); iPS DF 6.9 Cell Line, Induced pluripotent stem cell; JS-DF-6.9-genotype

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19792
sample alias: iPS_6_9
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5336

source_name: iPS DF 6.9 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; JS-DF-6.9-genotype

value: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison

value: iPS DF 6.9 Cell Line

value: Derived from newborn foreskin fibroblast:Cat# CRL-2097TM, ATCC

value: Induced pluripotent stem cell


title: Genotyping of H1. UW, Stamlab (NREMC). H1 cell line; JS-ESCH1-genotype

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19800
sample alias: H1-13
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; JS-ESCH1-genotype

value: Between 20 and 40


title: Genotyping of iPS 19 11. UW, Stamlab (NREMC); iPS DF 19.11 Cell Line, Induced pluripotent stem cell; JS-DE19.11-genotype

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19794
sample alias: iPS_19_11
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5333

source_name: iPS DF 19.11 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; JS-DE19.11-genotype

value: iPS DF 19.11 Cell Line


title: Genotyping of fAdrenal. UW, Stamlab (NREMC); Fetal Adrenal Gland primary tissue, day 113; JS-H24409-genotype

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19804
sample alias: fAdrenal.H-24409d113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11631

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Adrenal Gland

value: UW

value: fetal

value: day 113


title: Genotyping of fLiver. UW, Stamlab (NREMC); Fetal Liver primary tissue, day 97; JS-H24800-genotype

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001393
nucleic_acid_term_id: SO_0000352
Genotyping
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19815
sample alias: fLiver.H-24800d97
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.19817

value: Fetal Liver

value: day 97

value: Male


title: mESC_day26_rep1

value: cardiomyocyte differentiated


title: cartilage_RAAK_40_Healthy

status: Public on Jul 28 2014

city: Leiden

first: Yolande

middle: F. M.

last: Ramos

address: Einthovenweg 20

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit

scan_protocol: Slides were scanned with the Illumina Beadscanner 500GX

data_processing: Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization or background substraction and with imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst)

source_name: articular cartilage

label_protocol: To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).

value: Female

tag: age (yrs)

value: cartilage

tag: disease state

value: Healthy


title: Control matched sample pair anterior cingulate cortex MD3_ACC #29

status: Public on May 16 2014

city: Pittsburgh

first: Etienne

last: Sibille

address: 450 Technology Drive, Suite 231

department: Psychiatry

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2 cm caudal to the temporal pole

hyb_protocol: The sections were then hybridized with [35S]-labeled riboprobes (10^6 cpm/uL) in hybridization buffer at 56 °C for 16h. The hybridization buffer contained 50% formamide, 0.75 M NaCl, 20 mM 1,4-piperazine diethane sulfonic acid, pH 6.8, 10 mM ethylenediaminetetraacetic acid (EDTA), 10% dextran sulfate, 5X Denhardt’s solution (0.2 mg/mL Ficoll, 0.2 mg/mL polyvinylpyrrolidone, 0.2 mg/mL bovine serum albumin), 50 mM dithiothreitol, 0.2% sodium dodecyl sulfate, and 100 ug/mL yeast transfer RNA.

scan_protocol: DirecHyb Gene Expression. iScan Control Software 1.3.10+

data_processing:
Probeset signals were extracted with the Beadarray software following the default quality control parameters and batch-normalized.
GenomeStudio Gene Expression Module v1.6+

source_name: Control sample, brain anterior cingulate cortex

label_protocol: standard Illumina protocol

growth_protocol: not applicable

extract_protocol: 1µg of total high quality total RNA was reverse transcribed into single stranded cDNA, that was then converted into double stranded cDNA and purified using the Illumina TotalPrep RNA Amplification Kit. An in vitro transcription reaction was carried out overnight in the presence of biotinylated UTP and CTP to obtain biotin-labeled cRNA from the double stranded cDNA. The cRNA was purified using the same Amplification Kit, and quality control was assessed.

treatment_protocol: not applicable

value: brain anterior cingulate cortex

value: Control


title: Control matched sample pair anterior cingulate cortex MD3_ACC #32


title: Control matched sample pair anterior cingulate cortex MD3_ACC #28


title: cartilage_RAAK_1_Healthy


title: Control matched sample pair anterior cingulate cortex MD3_ACC #31


title: Control matched sample pair anterior cingulate cortex MD3_ACC #22


title: Control matched sample pair anterior cingulate cortex MD3_ACC #34


title: cartilage_RAAK_2_Healthy


title: Control matched sample pair anterior cingulate cortex MD3_ACC #23


title: cartilage_RAAK_39_Healthy


title: cartilage_RAAK_37_Healthy


title: Control matched sample pair anterior cingulate cortex MD3_ACC #35


title: Control matched sample pair anterior cingulate cortex MD3_ACC #30


title: cartilage_RAAK_38_Healthy


title: Control matched sample pair anterior cingulate cortex MD3_ACC #25


title: Control matched sample pair anterior cingulate cortex MD3_ACC #3


title: Control matched sample pair anterior cingulate cortex MD3_ACC #21


title: Control matched sample pair anterior cingulate cortex MD3_ACC #24


title: Control matched sample pair anterior cingulate cortex MD3_ACC #13


title: Control matched sample pair anterior cingulate cortex MD3_ACC #11


title: Control matched sample pair anterior cingulate cortex MD3_ACC #15


title: Control matched sample pair anterior cingulate cortex MD3_ACC #16


title: Control matched sample pair anterior cingulate cortex MD3_ACC #17


title: Control matched sample pair anterior cingulate cortex MD3_ACC #27


title: Control matched sample pair anterior cingulate cortex MD3_ACC #26


title: Control matched sample pair anterior cingulate cortex MD3_ACC #33


title: Control matched sample pair anterior cingulate cortex MD3_ACC #19


title: Control matched sample pair anterior cingulate cortex MD3_ACC #20


title: Bisulfite-Seq analysis of RRBS_Lib 363 derived from human Duodenum mucosa cells; RRBS_Lib 363

status: Public on Mar 26 2014

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 363
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19071
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: Primary duodenum mucosal tissue; RRBS_Lib 363

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

tag: sra sample accession

value: Surgery

value: presumed normal

value: Duodenum Mucosa

value: Caucasian

value: Duodenum

value: MGH

value: 59.0 Years

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS_Lib 362 derived from human stomach mucosa cells; RRBS_Lib 362

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 362
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19070
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary stomach mucosal tissue; RRBS_Lib 362

value: Surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: Stomach Mucosa

value: Male

value: Primary Tissue

value: Stomach


title: Bisulfite-Seq analysis of RRBS_Lib 361 derived from human colonic mucosa cells; RRBS_Lib 361

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 361
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19069
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.14740
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; RRBS_Lib 361

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

value: Colonic Mucosa

value: Caucasian

value: Female

value: Colon

value: MGH

value: 56.0 Years


title: Bisulfite-Seq analysis of RRBS_Lib 364 derived from human stomach smooth muscle cells; RRBS_Lib 364

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 364
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19067
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary stomach smooth muscle tissue; RRBS_Lib 364

value: NL smooth muscle, stomach rmvd as part of pancr., CA

value: Smooth Muscle

value: 59.0 Years

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232


title: Bisulfite-Seq analysis of RRBS_Lib 360 derived from human colon smooth muscle cells; RRBS_Lib 360

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 360
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19068
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.19072
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary colon smooth muscle tissue; RRBS_Lib 360

tag: sample alias

tag: sample common name

value: Colon Smooth Muscle

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: Primary Tissue

value: 77.0 Years

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS_Lib 358 derived from human kidney cells; RRBS_Lib 358

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 358
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19066
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary kidney tissue; RRBS_Lib 358

value: Surgery

value: NL kidney,right kidney resection for RCC

value: Adult Kidney

value: Caucasian

value: Male

value: Kidney

value: MGH

value: 50.0 Years


title: Bisulfite-Seq analysis of RRBS_Lib 354 derived from human cingulate gyrus cells; RRBS_Lib 354

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 354
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19063
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: human post mortem brain region from a non Alzheimer's donor; RRBS_Lib 354

value: post-mortem

value: Cingulate Gyrus

value: Female

value: brain

value: Rush University Medical Center

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS_Lib 356 derived from human angular gyrus cells; RRBS_Lib 356

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 356
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19065
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8183
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: human post mortem brain region from a non Alzheimer's donor; RRBS_Lib 356

value: Angular Gyrus

value: Primary Tissue

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS_Lib 355 derived from human inferior temporal lobe cells; RRBS_Lib 355

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 355
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19062
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: human post mortem brain region from a non Alzheimer's donor; RRBS_Lib 355

value: post-mortem

value: Inferior Temporal Lobe


title: Bisulfite-Seq analysis of RRBS_Lib 357 derived from human hippocampus middle cells; RRBS_Lib 357

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 357
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19064
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 357

value: Post-Mortem

value: no AD evident at demise

value: Hippocampus Middle

value: Male

value: Brain

value: 81.0 Years


title: Control matched sample pair anterior cingulate cortex MD3_ACC #14

tag: tissue

value: brain anterior cingulate cortex

value: Control


title: genomic DNA from patient mHGA18

status: Public on Mar 09 2014

city: Montrea

first: Simon

last: Papillon-Cavanagh

state: Quebec

address: 740 Dr Penfield

department: Human Genetics

institute: McGill University

description: BIOPSY

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: We removed probes with missing values, binding multiple genomic regions, binding targets with known sequence variants (1000 Genomes Project, SNPs with a minor allele frequency ≥ 2/120), or being located on the X or Y chromosomes. The final set contains 309,015 probes

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: mutation

value: glioblastomas

tag: brain region

value: Infratentorial Midline (DIPG)


title: genomic DNA from patient GLIOMA 52

source_name: GLIOMA 52

value: WT


title: genomic DNA from patient mHGA25

description: BIOPSY


title: genomic DNA from patient mHGA35

description: BIOPSY


title: genomic DNA from patient mHGA14

description: BIOPSY


title: genomic DNA from patient GLIOMA 48

source_name: GLIOMA 48


title: genomic DNA from patient GLIOMA 49

source_name: GLIOMA 49


title: genomic DNA from patient mHGA31

description: BIOPSY


title: Control matched sample pair anterior cingulate cortex MD3_ACC #18


title: genomic DNA from patient mHGA23

description: BIOPSY


title: genomic DNA from patient GLIOMA 47

source_name: GLIOMA 47

value: Supratentorial Midline (GBM)


title: genomic DNA from patient mHGA1

description: BIOPSY


title: genomic DNA from patient GLIOMA 45

source_name: GLIOMA 45


title: genomic DNA from patient GLIOMA 44

source_name: GLIOMA 44


title: genomic DNA from patient GLIOMA 43

source_name: GLIOMA 43


title: genomic DNA from patient GLIOMA 34

source_name: GLIOMA 34


title: genomic DNA from patient mHGA34

description: BIOPSY


title: genomic DNA from patient GLIOMA 41

source_name: GLIOMA 41


title: genomic DNA from patient GLIOMA 37

source_name: GLIOMA 37


title: genomic DNA from patient GLIOMA 50

source_name: GLIOMA 50


title: genomic DNA from patient cHGA-HGG8


title: genomic DNA from patient GLIOMA 42

source_name: GLIOMA 42


title: genomic DNA from patient GLIOMA 46

source_name: GLIOMA 46


title: genomic DNA from patient mHGA19

description: BIOPSY


title: genomic DNA from patient GLIOMA 51

source_name: GLIOMA 51


title: genomic DNA from patient GLIOMA 39

source_name: GLIOMA 39


title: genomic DNA from patient GLIOMA 35

source_name: GLIOMA 35


title: genomic DNA from patient GLIOMA 36

source_name: GLIOMA 36


title: genomic DNA from patient GLIOMA 38

source_name: GLIOMA 38


title: genomic DNA from patient GLIOMA 40

source_name: GLIOMA 40


title: genomic DNA from patient GLIOMA 33

source_name: GLIOMA 33

value: Thalamus


title: genomic DNA from patient GLIOMA 32

source_name: GLIOMA 32


title: genomic DNA from patient GLIOMA 31

source_name: GLIOMA 31


title: genomic DNA from patient GLIOMA 29

source_name: GLIOMA 29


title: genomic DNA from patient GLIOMA 28

source_name: GLIOMA 28


title: genomic DNA from patient GLIOMA 22

source_name: GLIOMA 22


title: genomic DNA from patient GLIOMA 30

source_name: GLIOMA 30


title: genomic DNA from patient GLIOMA 19

source_name: GLIOMA 19


title: genomic DNA from patient mHGA28


title: genomic DNA from patient cHGA-HGG2


title: genomic DNA from patient GLIOMA 11

source_name: GLIOMA 11


title: genomic DNA from patient GLIOMA 15

source_name: GLIOMA 15


title: genomic DNA from patient GLIOMA 18

source_name: GLIOMA 18


title: genomic DNA from patient GLIOMA 12

source_name: GLIOMA 12


title: genomic DNA from patient mHGA11


title: genomic DNA from patient GLIOMA 20

source_name: GLIOMA 20


title: genomic DNA from patient mHGA29


title: genomic DNA from patient GLIOMA 26

source_name: GLIOMA 26


title: genomic DNA from patient GLIOMA 13

source_name: GLIOMA 13


title: genomic DNA from patient GLIOMA 23

source_name: GLIOMA 23


title: genomic DNA from patient GLIOMA 24

source_name: GLIOMA 24


title: genomic DNA from patient GLIOMA 17

source_name: GLIOMA 17


title: genomic DNA from patient GLIOMA 21

source_name: GLIOMA 21


title: genomic DNA from patient GLIOMA 25

source_name: GLIOMA 25


title: genomic DNA from patient GLIOMA 27

source_name: GLIOMA 27


title: genomic DNA from patient GLIOMA 10

source_name: GLIOMA 10


title: genomic DNA from patient GLIOMA 14

source_name: GLIOMA 14


title: genomic DNA from patient mHGA10


title: genomic DNA from patient cHGA-HGG29


title: genomic DNA from patient GLIOMA 9

source_name: GLIOMA 9


title: genomic DNA from patient GLIOMA 16

source_name: GLIOMA 16


title: genomic DNA from patient GLIOMA 8

source_name: GLIOMA 8


title: genomic DNA from patient cHGA-HGG22


title: genomic DNA from patient cHGA-HGG4


title: genomic DNA from patient cHGA-HGG21


title: genomic DNA from patient cHGA-HGG23


title: genomic DNA from patient cHGA-HGG38


title: genomic DNA from patient cHGA-HGG31


title: genomic DNA from patient GLIOMA 2

source_name: GLIOMA 2


title: genomic DNA from patient GLIOMA 5

source_name: GLIOMA 5


title: genomic DNA from patient cHGA-HGG9


title: genomic DNA from patient GLIOMA 7

source_name: GLIOMA 7


title: genomic DNA from patient mHGA24


title: genomic DNA from patient cHGA-HGG3


title: genomic DNA from patient cHGA-HGG13


title: genomic DNA from patient mHGA5


title: genomic DNA from patient cHGA-HGG16


title: genomic DNA from patient GLIOMA 3

source_name: GLIOMA 3


title: genomic DNA from patient mHGA12


title: genomic DNA from patient cHGA-HGG6


title: genomic DNA from patient mHGA36


title: genomic DNA from patient GLIOMA 6

source_name: GLIOMA 6


title: genomic DNA from patient cHGA-HGG32


title: genomic DNA from patient cHGA-HGG35


title: genomic DNA from patient cHGA-HGG12


title: genomic DNA from patient cHGA-HGG1


title: genomic DNA from patient mHGA9


title: genomic DNA from patient cHGA-HGG34


title: genomic DNA from patient cHGA-HGA27


title: genomic DNA from patient cHGA-HGG5


title: genomic DNA from patient cHGA-HGG17