title: Carotid-Near-Pool-VLI-v2 vs. 114-096_Peripheral_L_SFA(entire)_denovo_RL_25Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 102-201_Peripheral_L_SFA(entire)_denovo_RL_17Jan06

status: Public on Oct 01 2011

type: RNA

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

country: USA

institute: Merck Research Laboratories

description: Gene expression profiling of peripheral plaque. 101 subjects from FoxHollow study, plus 8 carotid plaques used as a reference poolProfiled in the Merck/Agilent 44k v1.1

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral plaque

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: sample name

tag: tissue

value: carotid plaque, pool of 7 plaques

value: peripheral plaque


title: Am251/IDFP3

city: OAKLAND

first: Max

last: Ruby

state: CA

address: 5700 Martin Luther King Jr. Way

institute: Children's Hospital Oakland Reserach Institue

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with background substraction in Beadstudio 3.2

label: biotin

organism: Mus musculus

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit including DNase I treatment in accordance with the prescribed protocol provided with the kit.

tag: strain

value: Swiss-Webster

tag: age

value: 7 weeks

tag: gender

value: Male

value: Liver

tag: pretreatment

value: cannabinoid receptor 1 antagonist (AM251) (10 mg/kg, i.p.)

tag: treatment

value: isopropoyl dodecyl fluorophosphonate (IDFP) (10 mg/kg, i.p.)


title: Am251/IDFP2

description: replicate 2


title: BreastTumorTissue-HEL_065

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The data were log base 2 transformed and normalised using quantile normalisation with R.
Data table below does not report controls.  For complete tables of normalized and non-normalized data, see supplementary files on Series record.

source_name: BreastTumorTissue

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

growth_protocol: Fresh frozen human mammary tumor samples stored in liquid nitrogen

extract_protocol: RNA was isolated using miRvana miRNA isolation kit (Applied Biosystems) according to manufacturers protocol.

treatment_protocol: samples were homogenized with Precellys MK28-R Kit (6800Rpm, 3 x 25 s)

tag: 10years followup time (months)

tag: 10years vital status

value: 2 (breast cancer death)

tag: bddm followup time (months)

tag: bddm status

value: 1 (breast cancer death or distant metastasis)


title: macrophage_m27_C57BL/6-Ldlr-/-

description: Common genetic variants in a 58-kilobase (kb) region of chromosome 9p21, near the CDKN2A/B cell proliferation inhibitor genes, are strongly associated with coronary artery disease (CAD). We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus in a region of homology with the human 9p21 locus. We now report markedly decreased Cdkn2a (cyclin-dependent kinase inhibitor 2a) mRNA expression in macrophages and increased circulating levels of Ly6Chigh inflammatory monocytes in congenic mice compared to controls. A bone marrow (BM) transplantation study revealed that BM-derived cells from Cdkn2a+/- mice are capable of conferring accelerated atherosclerosis, increased inflammatory monocyte subsets and monocyte proliferation in the Ldlr-/- mouse model. These findings provide a mechanistic link between decreased expression of Cdkn2a transcripts, increased monocyte proliferation, and accelerated atherosclerosis.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: macrophages

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cDNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: cell type

value: macrophage

tag: genetic background

tag: genotype


title: Am251/IDFP1

description: replicate 1


title: IDFP8

description: replicate 8


title: Carotid-Near-Pool-VLI-v2 vs. 114-086_Peripheral_R_SFA(entire)_denovo_FF_15Dec05


title: BreastTumorTissue-HEL_069

value: 0 (alive or censored)

value: 0 (no event or censored)


title: BreastTumorTissue-HEL_064


title: BreastTumorTissue-HEL_067


title: macrophage_m22_C57BL/6-Ldlr-/-


title: macrophage_m25_C57BL/6-Ldlr-/-


title: macrophage_m21_C57BL/6-Ldlr-/-


title: macrophage_m23_C57BL/6-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 102-201_Peripheral_R_SFA(mid)_denovo_RL_17Jan06


title: BreastTumorTissue-HEL_066


title: Carotid-Near-Pool-VLI-v2 vs. 114-090_Peripheral_L_SFA(entire)_denovo_FF_28Dec05


title: IDFP7

description: replicate 7


title: BreastTumorTissue-HEL_063


title: Carotid-Near-Pool-VLI-v2 vs. 114-086_Peripheral_L_SFA(entire)_denovo_FF_15Dec05


title: aorta_m20_C57BL/6.MOLFc4(51Mb)-Ldlr-/-

source_name: aorta

value: aorta


title: IDFP6

description: replicate 6


title: BreastTumorTissue-HEL_062


title: IDFP4

description: replicate 4


title: aorta_m18_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 114-094_Peripheral_R_POP(prox)_denovo_RL_25Jan06


title: aorta_m19_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 114-095_Peripheral_L_SFA(mid)_denovo_RL_25Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 114-094_Peripheral_R_SFA(distal)_denovo_RL_25Jan06


title: BreastTumorTissue-HEL_061


title: Carotid-Near-Pool-VLI-v2 vs. 114-095_Peripheral_L_AT(entire)_denovo_RL_25Jan06


title: IDFP3

description: replicate 3


title: aorta_m17_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: IDFP5

description: replicate 5


title: IDFP1

description: replicate 1


title: aorta_m16_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: IDFP2

description: replicate 2


title: BreastTumorTissue-HEL_058


title: BreastTumorTissue-HEL_060


title: aorta_m14_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 820-016_Peripheral_R_POP(prox)_denovo_RL_19Jan06


title: aorta_m15_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: BreastTumorTissue-HEL_057


title: BreastTumorTissue-HEL_059


title: Carotid-Near-Pool-VLI-v2 vs. 820-016_Peripheral_R_SFA(prox-mid)_denovo_RL_19Jan06


title: BreastTumorTissue-HEL_056


title: aorta_m13_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 820-017_Peripheral_R_POP(prox)_denovo_RL_19Jan06


title: Sham-48

city: Aarhus C

first: Anders

middle: Riegels

last: Knudsen

address: Nørrebrogade 44, building 1c, LVN-research

department: Department of Surgery, Section for upper GI surgery

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: The target was loaded onto the GeneChip and hybridised for 16 h. The arrays were washed and stained in the Affymetrix Fluidics Station.

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

data_processing: Raw image files from the quantitative scannings were analysed by Affymetrix Gene Expression Analysis Software and data were normalized using the RMA in Affymetrix Expression Console.

label: Biotin

organism: Rattus norvegicus

source_name: Liver tissue

label_protocol: 150 ng of total RNA was used as target preparation in the starting material for the cDNA Syntesis Kit and WT Terminal Labeling Kit (affymetrix).

growth_protocol: Male Wistar rats, weighing 300–350 g, (M&B Taconic, Eiby, Denmark) were housed in standard animal laboratories with the temperature maintained at 23°C and artificial 12-hour light-dark cycles, and with free access to food and water.

extract_protocol: Biopsies were homogenized in RLT plus buffer on Qiagen Tissuelyser. Total RNA was extracted on the QIAsymphony SP using the QIAsymphony RNA extraction kit.

treatment_protocol: Animals were anaesthetized using 0.75 ml/kg Hypnorm s.c. (fentanyl/fluanisone; Jansen Pharma, Birkeroed, Denmark) and 4 mg/kg Midazolam s.c. (dormicum; La Roche, Basel, Switzerland) and placed on a heated pad.  A midline laparotomy was performed and the hepatoduodenal ligament was mobilised. Liver biopsies were sampled from the right lobe and immediately snap frozen in liquid nitrogen, and stored at -80°C until analysis.

value: Wistar

value: male

tag: ischemia protocol

value: only laparotomy


title: aorta_m12_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Sham-47


title: BreastTumorTissue-HEL_055


title: Sham-46


title: Carotid-Near-Pool-VLI-v2 vs. 820-017_Peripheral_R_SFA(prox)_denovo_RL_19Jan06

value: carotid plaque, pool of 7 plaques


title: BreastTumorTissue-HEL_054


title: Sham-44


title: Carotid-Near-Pool-VLI-v2 vs. 920-002_Peripheral_L_POP(prox)_UNK_RL_24Jan06

value: peripheral plaque


title: aorta_m10_C57BL/6-Ldlr-/-


title: aorta_m8_C57BL/6-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 920-001_Peripheral_R_PT(entire)_UNK_RL_24Jan06-sub1


title: BreastTumorTissue-HEL_051


title: aorta_m7_C57BL/6-Ldlr-/-


title: aorta_m11_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Sham-42


title: Sham-45


title: Sham-43


title: Sham-41


title: BreastTumorTissue-HEL_050


title: aorta_m9_C57BL/6-Ldlr-/-


title: BreastTumorTissue-HEL_052


title: Carotid-Near-Pool-VLI-v2 vs. 920-002_Peripheral_L_SFA(entire)_UNK_RL_24jan06


title: aorta_m6_C57BL/6-Ldlr-/-


title: BreastTumorTissue-HEL_049


title: Carotid-Near-Pool-VLI-v2 vs. 102-202_Peripheral_L_SFA(distal)_UNK_RL_20Jan06


title: BreastTumorTissue-HEL_048


title: BreastTumorTissue-HEL_053


title: Carotid-Near-Pool-VLI-v2 vs. 102-202_Peripheral_L_AT(prox)_UNK_RL_20Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 800-005_Peripheral_R_POP(mid)_denovo_RL_17Jan06


title: IPC+IPO-38

value: IPC + 30 min of total liver ischemia + IPO


title: BreastTumorTissue-HEL_047


title: IPC+IPO-40


title: Carotid-Near-Pool-VLI-v2 vs. 920-001_Peripheral_R_SFA(mid)_UNK_RL_24Jan06


title: aorta_m4_C57BL/6-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 800-005_Peripheral_R_SFA(entire)_denovo_RL_17Jan06


title: IPC+IPO-39


title: aorta_m5_C57BL/6-Ldlr-/-


title: BreastTumorTissue-HEL_045


title: BreastTumorTissue-HEL_043

value: 1 (death from any cause but breast cancer)


title: platelet_control_L

city: Amsterdam

first: Brigitte

last: Sondermeijer

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center

hyb_protocol: A single miRNA-specific oligo (MSO) is used to assay each miRNA on the panel. All MSOs are hybridized to the sample in parallel, followed by a solid-phase primer extension step.

scan_protocol: Universal amplification of extended products (universal PCR step) creates fluorescently labeled products identifiable by a unique address sequence. Single-stranded PCR products (750ng) were hybridized to the BeadChip, where the labeled strand binds to the bead on the array containing the complementary address sequence. BeadChips were scanned using the Illumina BeadArray Reader, which measures the fluorescence intensity at each addressed bead location. The Human v2 miRNA panel targets 1146 miRNAs (> 97% coverage of miRBase release 12). Each miRNA is targeted by multiple (~300 on average) identical beads.

data_processing: The raw scan data were read using the beadarray package (version 1.12.1), available through Bioconductor. Illumina’s default pre-processing steps were performed using beadarray. In short, estimated background was subtracted from the foreground for each bead. For replicate beads, outliers greater than 3 median absolute deviations (MADs) from the median were removed and the average signal was calculated for the remaining intensities.  Summarized data was log-transformed to ensure that the gene-wise variances are comparable and then quantile normalized. MiRNAs were excluded from the analysis when their log2 expression was less than median expression level on all 24 arrays. Differential expression analysis was performed by fitting a linear model to the 24 arrays and comparing CAD patients and controls using empirical Bayes moderated t-statistics from the Bioconductor software package limma [4]. MiRNAs were considered significantly differentially expressed if the P-values, adjusted for multiple testing by using Benjamini and Hochberg's method, were <0.05. The false discovery rate was thereby controlled to be <5%. Differentially expressed miRNAs (p<0.05) were visualized by hierarchical clustering of the samples (Euclidean distance, complete linkage).

source_name: peripheral blood

label_protocol: Biotinylated cDNA was prepared by standard methods for Illumina arrays

extract_protocol: Platelet RNA was isolated using the mirVana PARIS kit (Ambion, Inc.), according to the manufacturer’s protocol for liquid samples. The protocol was modified such that samples were extracted twice with an equal volume of acid-phenol chloroform and the column was dried for 3 minutes after the last washing step and before elution. Samples were concentrated from 50μl to 12μl, of which 5μl was used for Illumina arrays. Quality control was performed with Agilent Bioanalyser.

value: platelets

tag: disease state

value: healthy control


title: BreastTumorTissue-HEL_044


title: aorta_m2_C57BL/6-Ldlr-/-


title: platelet_control_K


title: IPC+IPO-36


title: Carotid-Near-Pool-VLI-v2 vs. 800-004_Peripheral_R_SFA(mid)_denovo_RL_17Jan06


title: aorta_m3_C57BL/6-Ldlr-/-


title: aorta_m1_C57BL/6-Ldlr-/-


title: BreastTumorTissue-HEL_046


title: IPC+IPO-37


title: Carotid-Near-Pool-VLI-v2 vs. 800-002_Peripheral_R_SFA(prox-mid)_denovo_RL_13Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 800-002_Peripheral_R_CFA(UNK)_denovo_RL_13Jan06


title: IPC+IPO-34


title: IPC+IPO-35


title: platelet_control_G


title: Carotid-Near-Pool-VLI-v2 vs. 760-006_Peripheral_L_POP(entire)_denovo_RL_25Jan06


title: platelet_control_I


title: BreastTumorTissue-HEL_042


title: platelet_control_H


title: IPC+IPO-33


title: BreastTumorTissue-HEL_041


title: BreastTumorTissue-HEL_039


title: Carotid-Near-Pool-VLI-v2 vs. 760-006_Peripheral_L_SFA(entire)_denovo_RL_25Jan06


title: platelet_control_F


title: IPC+IPO-32


title: BreastTumorTissue-HEL_040


title: Carotid-Near-Pool-VLI-v2 vs. 126-137_Peripheral_L_SFA(mid)_denovo_RL_10Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 800-004_Peripheral_R_POP(mid)_denovo_RL_17Jan06


title: platelet_control_J


title: Carotid-Near-Pool-VLI-v2 vs. 126-138_Peripheral_L_SFA(mid)_denovo_RL_16Jan06


title: platelet_control_E


title: platelet_control_D


title: Carotid-Near-Pool-VLI-v2 vs. 126-137_Peripheral_L_AT(prox-mid)_denovo_RL_10Jan06


title: IPC+IPO-31


title: IPO-30

value: 30 min of total liver ischemia + IPO


title: platelet_control_B


title: BreastTumorTissue-HEL_038


title: IPO-27


title: IPO-28


title: IPO-25


title: BreastTumorTissue-HEL_035


title: BreastTumorTissue-HEL_037


title: platelet_control_A


title: platelet_patient_L

value: premature CAD patient


title: Carotid-Near-Pool-VLI-v2 vs. 126-130_Peripheral_L_TPT(entire)_denovo_RL_29Nov05


title: IPO-29


title: IPO-26


title: platelet_control_C


title: Carotid-Near-Pool-VLI-v2 vs. 126-116_Peripheral_L_AT(prox)_denovo_RL_25Oct05


title: Carotid-Near-Pool-VLI-v2 vs. 126-130_Peripheral_L_SFA(distal)_denovo_RL_29Nov05


title: BreastTumorTissue-HEL_034


title: BreastTumorTissue-HEL_036

value: 2 (breast cancer death)


title: BreastTumorTissue-HEL_030


title: IPO-22


title: BreastTumorTissue-HEL_031

value: 1 (breast cancer death or distant metastasis)


title: platelet_patient_I


title: platelet_patient_K


title: IPO-24


title: platelet_patient_H


title: BreastTumorTissue-HEL_033


title: platelet_patient_J


title: BreastTumorTissue-HEL_032


title: Carotid-Near-Pool-VLI-v2 vs. 126-116_Peripheral_L_POP(prox)_denovo_RL_25Oct05


title: Carotid-Near-Pool-VLI-v2 vs. 119-096_Peripheral_L_SFA(distal)_denovo_RL_27Sep05-pool1


title: Carotid-Near-Pool-VLI-v2 vs. 126-116_Peripheral_L_SFA(distal)_denovo_RL_25Oct05


title: IPC-20

value: IPC + 30 min of total liver ischemia


title: BreastTumorTissue-HEL_027


title: Carotid-Near-Pool-VLI-v2 vs. 119-096_Peripheral_L_POP(prox)_denovo_RL_27Sep05-pool1


title: platelet_patient_G


title: BreastTumorTissue-HEL_029


title: platelet_patient_F


title: Carotid-Near-Pool-VLI-v2 vs. 101-105_Peripheral_L_AT(prox)_denovo_RL_12Aug05-pool1


title: IPO-23


title: Carotid-Near-Pool-VLI-v2 vs. 109-070_PeripheralR_SFA(prox)_denovo_RL_1Nov05-pool1


title: BreastTumorTissue-HEL_028

value: 0 (alive or censored)


title: BreastTumorTissue-HEL_026


title: IPO-21


title: IPC-19


title: Carotid-Near-Pool-VLI-v2 vs. 101-105_Peripheral_L_SFA(mid-dist)_denovo_RL_12Aug05-pool2


title: platelet_patient_E


title: IPC-18


title: IPC-17


title: BreastTumorTissue-HEL_025

value: 0 (no event or censored)


title: platelet_patient_D


title: Carotid-Near-Pool-VLI-v2 vs. 101-097_Peripheral_UNK_POP(prox)_denovo_RL_29Jul05-pool1


title: Carotid-Near-Pool-VLI-v2 vs. 101-097_Peripheral_UNK_TPT(entire)_denovo_RL_29Jul05-pool2


title: IPC-16


title: platelet_patient_B


title: platelet_patient_A


title: BreastTumorTissue-HEL_023


title: platelet_patient_C


title: IPC-14


title: IPC-13


title: Carotid-Near-Pool-VLI-v2 vs. 109-064_Peripheral_R_POP(mid)_denovo_RL_24Aug05-pool1


title: BreastTumorTissue-HEL_024


title: IPC-12


title: BreastTumorTissue-HEL_022


title: Carotid-Near-Pool-VLI-v2 vs. 126-084_Peripheral_R_SFA(entire)_denovo_RL_13Sep05-pool3


title: WT_Rep1 5D_Cy3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Biological replicate 1 of 3 of WT. Harvested after kept standing for 5 days.

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Gene Expression 8x15k Mycobacterium tuberculosis Array (AMADID_020181). 300 ng each of cy3 labeled and cy5 labeled Reference samples were combined, fragmented and hybridized to Custom 8x15k Mycobacterium tuberculosis Array (AMADID_020181) and data from these channels were used for comparison to test hybridizations of respective channels. 300 ng of Cy3 and Cy5 labeled test samples were combined, fragmented and hybridized on to Custom 8x15k Mycobacterium tuberculosis Array (AMADID_020181). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327). The hybrdization was carried out for both one two color and one color experiments.

scan_protocol: Scanned using the Agilent Technologies Scanner G2505C at 5 micron resolution. Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1 and 10.5.1.1)

data_processing: Data was analyzed in GeneSpring GX software from Agilent using  Quantile Normalization. Probe intensities generated from feature extraction raw data were split based on channel type. Gene based analysis was performed. Genomic DNA Sample labeled with cy3 and Genomic DNA Sample labeled with cy5 were used as control for normalization against test samples labeled with cy3 and cy5. Fold expression values were obtained after normalization of treated cy3 against control cy3 samples and treated cy5 against control cy5 samples were compared across samples to identify significant gene expression patterns. Normalization of the data was done in GeneSpring GX using Quantile Normalization and Normalize to Specific Samples.. All the cy3-labeled test samples were  compared to control cy3 sample data and all cy5-labeled test samples were compared control cy5 sample data to generate ratios. Genes showing >One fold change in the test sample compared to the reference pool were compiled as differentially regulated genes.( Note; samples of one color expreiments were also included in the analysis)

organism: Mycobacterium tuberculosis H37Rv

source_name: WT-Rep1 hypoxic

label_protocol: The bacterial samples for Gene expression were labeled using MessageAmp II- Bacteria kit (Ambion, Cat No: 1790) as per manufacturer’s instructions. (The labeling was performed for both two color and one color hybrdizations)

growth_protocol: Cultured in Middlebrook Dubos liquid medium containing 0.05% Tween-80 plus 0.5 % Albumin, 0.75 % Dextrose, 0.085 % NaCl under shaking upto an O.D. 595 nm of 0.2-0.3. Cycloheximide used for all cultures at 100 µg/ml. Comp1 was cultured with hygromycin at 50 µg/ml.

extract_protocol: Total RNA was isolated from M. tuberculosis H37Rv cultures grown in Dubos-ADC medium under aerobic (shaking) and hypoxic (standing) conditions using TRI reagent (Molecular Research Center, USA) according to the manufacturer’s protocol.

treatment_protocol: Cultures of 100 ml grown under shaking upto O.D at 595 nm 0.2-0.3 were taken as aerobic cultures. 10 ml aliquots of aerobic cultures in 50 ml Falcon tubes kept standing for 5 days were taken as hypoxic cultures.

tag: genotype/variation

value: WT

tag: culture condition

value: hypoxic, 5 D


title: IPC-15

value: Wistar

value: male


title: WT_Rep2 0D_Cy3

description: Biological replicate 1 of 3 of WT. Harvested after growing under shaking upto an O.D. of 0.2-0.3

source_name: WT-Rep2 aerobic

value: aerobic, 0 D


title: Mut1_Rep2_5D_Cy3

description: Biological replicate 1 of 5 of Mut1. Harvested after kept standing for 5 days.

source_name: Mut1-Rep2 hypoxic


title: Carotid-Near-Pool-VLI-v2 vs. 126-084_Peripheral_R_CFA(entire)_denovo_RL_13Sep05-pool1

tag: sample name

tag: tissue

value: carotid plaque, pool of 7 plaques

value: peripheral plaque


title: Carotid-Near-Pool-VLI-v2 vs. 109-064_Peripheral_R_SFA(prox)_denovo_RL_24Aug05-pool2


title: BreastTumorTissue-HEL_021


title: IPC-11

tag: strain


title: WT_Rep1 5D (Cy5) vs. WT_Rep1 0D (Cy3)

description: Biological replicate 1 of 3 of WT aerobic compared with biological replicate 1 of 3 of WT hypoxic.

source_name: WT-Rep1 aerobic


title: IRI-10

tag: gender

value: 30 min of total liver ischemia


title: BreastTumorTissue-HEL_020


title: Carotid-Near-Pool-VLI-v2 vs. 126-048_Peripheral_L_PT(prox-mid)_denovo_RL_1Sep05-pool1


title: Carotid-Near-Pool-VLI-v2 vs. 126-048_Peripheral_L_SFA(mid)_restenotic_RL_1Sep05-pool2


title: WT_Rep2 0D (Cy5) vs. WT_Rep2 5D (Cy3)

description: Biological replicate 2 of 3 of WT hypoxic compared with biological replicate 2 of 3 of WT aerobic.

source_name: WT-Rep2 hypoxic


title: IRI-08


title: Carotid-Near-Pool-VLI-v2 vs. 106-061_Peripheral_ L_PER-PRO(prox)_denovo_RL_24Aug05-pool2


title: Mut1_Rep5_0D (Cy5) vs. Mut1_Rep4_0D (Cy3)

description: Biological replicate 4 of 5 of Mut1 aerobic compared with biological replicate 5 of 5 of Mut1 aerobic.

source_name: Mut1-Rep4 aerobic

source_name: Mut1-Rep5 aerobic


title: IRI-09


title: BreastTumorTissue-HEL_019


title: BreastTumorTissue-HEL_018

value: 1 (death from any cause but breast cancer)


title: IRI-07


title: Mut1_Rep3 0D_Cy5 vs. Mut1_Rep3 5D(Cy3)

description: Biological replicate 3 of 5 of Mut1 hypoxic compared with biological replicate 3 of 5 of Mut1 hypoxic.

source_name: Mut1-Rep3 hypoxic

source_name: Mut1-Rep3 aerobic


title: IRI-06


title: IRI-05


title: BreastTumorTissue-HEL_015


title: Carotid Near Pool n=7-VLI vs. CE1-008-WRIWA_carotid_L_Int.(UNK)_FF_29Nov05-LowPCP

value: Carotid Near Pool n=7-VLI


title: Mut1_Rep2_5D (Cy5) vs.Mut1_Rep2 0D (Cy3)

description: Biological replicate 2 of 5 of Mut1 aerobic compared with biological replicate 2 of 5 of Mut1 hypoxic.

source_name: Mut1-Rep2 aerobic


title: Carotid Near Pool n=7-VLI vs. CE1-007_Carotid_R_CC-IC(N/A)_FF_21NOV2005_sub1

source_name: Peripheral plaque


title: Carotid-Near-Pool-VLI-v2 vs. 106-061_Peripheral_L_SFA(mid)_denovo_RL_24Aug05-pool2


title: BreastTumorTissue-HEL_016


title: BreastTumorTissue-HEL_014


title: H37RV (Cy5) vs H37RV (Cy3)

type: genomic

description: Comparison of Cy3/Cy5 labeled genomic DNA of H37Rv (WT)

molecule: genomic DNA

source_name: H37Rv (WT)

value: H37Rv (WT)


title: IRI-04


title: Carotid Near Pool n=7-VLI vs. CE1-005_Carotid_R_CC-IC(N/A)_FF_11NOV2005


title: Comp1_Rep3 0D (Cy5) vs. Comp1_Rep3_5D (Cy3)

description: Biological replicate 3 of 5 of Comp1 hypoxic compared with biological replicate 3 of 5 of Comp1 aerobic.

source_name: Comp1-Rep3 hypoxic

source_name: Comp1-Rep3 aerobic


title: Comp1_Rep5_5D (Cy5) vs. Comp1_ Rep4_5D (Cy3)

description: Biological replicate 4 of 5 of Comp1 hypoxic compared with biological replicate 5 of 5 of Comp1 hypoxic.

source_name: Comp1-Rep4 hypoxic

source_name: Comp1-Rep5 hypoxic


title: Comp1_Rep2_5D (Cy5) vs. Comp1 Rep2 0D (Cy3)

description: Biological replicate 2 of 5 of Comp1 aerobic compared with biological replicate 2 of 5 of Comp1 hypoxic.

source_name: Comp1-Rep2 aerobic

source_name: Comp1-Rep2 hypoxic


title: BreastTumorTissue-HEL_012

source_name: BreastTumorTissue


title: Carotid Near Pool n=7-VLI vs. CE-006_Carotid_L_CC-IC(ost)_FF_18NOV2005_sub2


title: BreastTumorTissue-HEL_013


title: IRI-03

source_name: Liver tissue


title: IRI-02


title: IRI-01


title: BreastTumorTissue-HEL_011


title: BreastTumorTissue-HEL_010


title: Carotid Near Pool n=7-VLI vs. CE1-004_Carotid_R_CC-IC(ost)_FF_04NOV2005


title: Carotid Near Pool n=7-VLI vs. CE1-003_Carotid_L_IC(ost)_FF


title: BreastTumorTissue-HEL_006


title: Carotid Near Pool n=7-VLI vs. CE1-001_Carotid_R_CC-IC(prox)_FF_26SEP2005


title: Carotid Near Pool n=7-VLI vs. CE1-002_Carotid_L_CC-IC(prox)_FF


title: BreastTumorTissue-HEL_009


title: DF508 2

city: Baltimore

first: Jerry

middle: M.

last: Wright

state: MD

address: 725 N. Wolfe St

department: Physiology

institute: Johns Hopkins Medical Institutions

description: Gene expression data IB3 cells transfected with DF508 mutant of CFTR.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on GeneChip the U133 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the AffyMetrix GeneChip Scanner

data_processing: Microarray scans were processed in GCOS 1.2 to determine expression levels using Affymetrix default analysis settings and global scaling as normalization method.The trimmed mean target intensity of each array was set to 100.

source_name: IB3 transfected with DF508

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

growth_protocol: IB3-1 cells (CF genotype _F508/W1282X, bronchial epithelial derivation), were grown in LHC-8 Basal  Medium, 95%; fetal bovine serum, 5%.

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

treatment_protocol: CFTR and mutated forms were subcloned into the mammalian expression vector, pCDNA 3.1 and transfected into cells using Lipofectamine 2000 (Invitrogen)

tag: cell line

value: Bronchial epithelial cell line

tag: transfection

value: CFTR DF508 mutant


title: BreastTumorTissue-HEL_008

tag: 10years followup time (months)


title: Comp1_Rep1_5D (Cy5) vs. WT_Rep3 0D (Cy3)

description: Biological replicate 3 of 3 of WT aerobic compared with biological replicate 1 of 5 of Comp1 hypoxic.

source_name: WT-Rep3 aerobic

source_name: Comp1-Rep1 hypoxic


title: Comp1_Rep2 0D_(Cy5) vs WT_Rep2 0D(Cy3)

description: Biological replicate 2 of 3 of WT aerobic compared with biological replicate 2 of 5 of Comp1 aerobic.

source_name: WT-Rep2 aerobic


title: Control 12

description: Gene expression data untreated IB3 cells.

source_name: IB3 cells untransfected

value: Control


title: Comp1_Rep1 0D (Cy5) vs.  Mut1_Rep1 0D (Cy3)

description: Biological replicate 1 of 5 of Mut1 aerobic compared with biological replicate 1 of 5 of Comp1 aerobic.

source_name: Mut1-Rep1 aerobic

source_name: Comp1-Rep1 aerobic


title: Carotid Near Pool n=7-VLI vs. 121-052_Peripheral_R_SFA(prox)_04AUG2005_denovo_FF

description: Gene expression profiling of peripheral plaque. 101 subjects from FoxHollow study, plus 8 carotid plaques used as a reference poolProfiled in the Merck/Agilent 44k v1.1

source_name: Peripheral plaque


title: Carotid Near Pool n=7-VLI vs. 121-060-_Peripheral_R_SFA(mid-dist)_denovo_FF


title: Comp1_ Rep5 0D (Cy5) vs. Comp1_ Rep4 0D (Cy3)

description: Biological replicate 4 of 5 of Comp1 aerobic compared with biological replicate 5 of 5 of Comp1 hypoxic.

source_name: Comp1-Rep4 aerobic

source_name: Comp1-Rep5 aerobic


title: Carotid Near Pool n=7-VLI vs. 119-099_Peripheral_L_SFA(mid)_denovo_FF_Pool2


title: BreastTumorTissue-HEL_007

tag: 10years vital status

value: 2 (breast cancer death)

value: 1 (breast cancer death or distant metastasis)


title: G551D 2

description: Gene expression data IB3 cells transfected with G551D mutant of CFTR.

source_name: IB3 transfected with G551D

value: CFTR G551D mutant


title: CFTR 2

description: Gene expression data IB3 cells transfected with CFTR.

source_name: IB3 transfected with CFTR

value: CFTR


title: Carotid-Near-Pool-VLI-v2 vs. 109-070_Peripheral_R_POP(mid)_denovo_RL_1Nov05-pool1


title: BreastTumorTissue-HEL_003

tag: bddm followup time (months)


title: Carotid Near Pool n=7-VLI vs. 126-058_Peripheral_L_SFA(entire)_28JUL2005_denovo_FF_Pool3-1


title: Carotid Near Pool n=7-VLI vs. 114-072_Peripheral_L_AT(ostial)_denovo_FF_Pool3


title: BreastTumorTissue-HEL_005

value: 0 (alive or censored)

tag: bddm status

value: 0 (no event or censored)


title: BreastTumorTissue-HEL_004


title: Control 10

tag: cell type


title: Carotid Near Pool n=7-VLI vs. 121-044_Peripheral_L_CFA(distal)_denovo_FF_Sub1_PCP-


title: BreastTumorTissue-HEL_001


title: Carotid Near Pool n=7-VLI vs. 119-094_Peripheral_R_AT(entire)_denovo_FF_Pool3_PCP-


title: BreastTumorTissue-HEL_002


title: Control 6


title: Control 7


title: PlatVPostPlat

city: Gainesville

first: Greg

last: Ragland

state: FL

department: Entomology and Nematology

institute: University of Florida

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710002_S01_GE2-v5_10_Apr08_1_3.txt: PlatG2, PostPlatR2
US83800208_252338710002_S01_GE2-v5_10_Apr08_1_4.txt: PostPlatG4, PlatR4
US83800208_252338710005_S01_GE2-v5_10_Apr08_1_3.txt: PlatG1, PostPlatR1
US83800208_252338710005_S01_GE2-v5_10_Apr08_1_4.txt: PostPlatG3, PlatR3

hyb_protocol: A total of 825 ng of labeled aRNA per sample was used for the hybridization, and hybridization and washing were performed according to the manufacturer's protocol using the Gene Expression Hybridization Kit and Gene Expression Wash Buffers (Agilent Technologies, Inc.).  We used a two-color hybridization design with dye swapping, using four hybridizations for each of six direct comparisons of our 6 time points: 24Fridge vs. LateDia, LateDia vs. Break24, LateDia vs. Break48, Break24 vs. Break48, Break48 vs. Plat, and Plat vs. PostPlat.

scan_protocol: The arrays were washed according to the manufacturer's protocol and then scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Data were background corrected and loess normalized using limma (Bioconductor). All reverse probes and non-Rhagoletis pomonella probes were filtered prior to analysis.

label: Cy3, Cy5

organism: Rhagoletis pomonella

source_name: Plat

label_protocol: Labeled aRNA from four individuals from each time point was generated using the Amino Allyl MessageAmp II Amplification kit (Ambion Inc). We used 325ng of total RNA for reverse transcription to synthesize 1st strand cDNA, and then generated labeled aRNA according to the manufacturer’s protocol.

growth_protocol: Infested hawthorn fruit were collected from a field site near Fennville, MI and staged in the lab at 21C, 14:10 LD. Wandering larvae and pupae were collected daily, allowed to sit at 21C for 10 days, and then transferred to 4C for 20 weeks of simulated winter. Following 20 weeks at 4C, diapausing pupae were moved to 24C. After return to warmer conditions, diapausing pupae display a characteristic, biphasic trajectory or metabolic rate increase (Ragland et al., 2009, J. Insect Phys.). We sampled a minimum of six individuals at each of six landmark time points representing early (24Fridge ) and late (LateDia) diapause, twenty-four (Break24) and forty-eight (Break48) hours after the initial metabolic spike, the respiration rate plateau (Plat) and the final, exponential phase of metabolic increase (PostPlat). We used the following sampling criteria: 24 hours after transfer from 4C (24Fridge), two weeks after transfer from 4C (LateDia; only pupa with stable baselines and no metabolic increases over this period), pupa whose metabolic rate increased 40% or more from a stable baseline in a 24 h period (Break24), the day following the  previous observation (Break48), five to seven days after respiration rates stabilized following the initial increase (Plat), and two to three days after pupa had clearly entered the final, exponential phase of increase (PostPlat; ~100% or more increase in respiration rate compared to the plateau).

extract_protocol: Four individuals from each sampling time point were homogenized in Tri-Reagent, and total RNA was extracted from each individual using the Ambion RiboPure Kit.

value: whole pupae

tag: time point

value: in the metabolic rate plateau

label: Cy5, Cy3

source_name: PostPlat

value: in the final, exponential phase of metabolic rate increase


title: Control 2


title: Break48VPlat

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710002_S01_GE2-v5_10_Apr08_1_1.txt: PlatG2, Break48R2
US83800208_252338710002_S01_GE2-v5_10_Apr08_1_2.txt: Break48G4, PlatR4
US83800208_252338710005_S01_GE2-v5_10_Apr08_1_1.txt: PlatG1, Break48R1
US83800208_252338710005_S01_GE2-v5_10_Apr08_1_2.txt: Break48G3, PlatR3

value: 48 hours after initial metabolic rate increase


title: Break24VBreak48

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710001_S01_GE2-v5_10_Apr08_1_3.txt: Break48G4, Break24R2
US83800208_252338710001_S01_GE2-v5_10_Apr08_1_4.txt: Break24G6, Break48R2
US83800208_252338710004_S01_GE2-v5_10_Apr08_1_3.txt: Break48G3, Break24R1
US83800208_252338710004_S01_GE2-v5_10_Apr08_1_4.txt: Break24G5, Break48R1

value: 24 hours after initial metabolic rate increase


title: Carotid Near Pool n=7-VLI vs. 119-074_Peripheral_L_CFA(ostial)_denovo_FF_Pool2_PCP+

value: carotid plaque, pool of 7 plaques

value: peripheral plaque


title: Carotid Near Pool n=7-VLI vs. 121-044_Peripheral_L_SFA(ostial)_denovo_FF_Pool3_PCP+

value: Carotid Near Pool n=7-VLI


title: BreastTumorTissue-HEL_017


title: Mut1_Rep5_5D(Cy5) vs. Mut1_ Rep4_5D (Cy3)

description: Biological replicate 4 of 5 of Mut1 hypoxic compared with biological replicate 5 of 5 of Mut1 hypoxic.

source_name: Mut1-Rep4 hypoxic

value: hypoxic, 5 D

source_name: Mut1-Rep5 hypoxic


title: Control_4

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3,  imported into R  and normalized using the quantile method in the Lumi package

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was isolated from freshly isolated cells using TRIZOL solution (Invitrogen, Carlsbad, Ca). RNA concentration was determined spectrophotometrically at A260nm by NanoDrop and quality was checked on Agilent 2100 bioanalyser.

value: leucocytes


title: Carotid Near Pool n=7-VLI vs. 121-044_Peripheral_L_Prof(prox)_denovo_FF_Sub1_PCP-


title: Control_3


title: Control 8

value: Bronchial epithelial cell line

value: Control


title: LateDiaVBreak48

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710001_S01_GE2-v5_10_Apr08_1_1.txt: LateDiaG2, Break48R2
US83800208_252338710001_S01_GE2-v5_10_Apr08_1_2.txt: Break48G4, LateDiaR4
US83800208_252338710004_S01_GE2-v5_10_Apr08_1_1.txt: LateDiaG1, Break48R1
US83800208_252338710004_S01_GE2-v5_10_Apr08_1_2.txt: Break48G3, LateDiaR3

source_name: LateDia

value: late diapause (2 weeks after transfer from fridge to 24C)


title: Carotid Near Pool n=7-VLI vs. 119-068_Peripheral_L_SFA(dist)_02AUG2005_Pool3_PCP+


title: LateDiaVBreak24

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710000_S01_GE2-v5_10_Apr08_1_3.txt: LateDiaG2, Break24R2
US83800208_252338710000_S01_GE2-v5_10_Apr08_1_4.txt: Break24G6, LateDiaR4
US83800208_252338710003_S01_GE2-v5_10_Apr08_1_3.txt: LateDiaG1, Break24R1
US83800208_252338710003_S01_GE2-v5_10_Apr08_1_4.txt: Break24G5, LateDiaR3


title: Control_2


title: Control_1


title: 24HourFridgeVLateDia

description:
Biological replicates 1-4.

Raw data file: Individuals hybridized (G=Cy3, R=Cy5)
US83800208_252338710000_S01_GE2-v5_10_Apr08_1_1.txt: LateDiaG2, 24FridgeR1
US83800208_252338710000_S01_GE2-v5_10_Apr08_1_2.txt: 24FridgeG4, LateDiaR4
US83800208_252338710003_S01_GE2-v5_10_Apr08_1_1.txt: LateDiaG1, 24FridgeR1
US83800208_252338710003_S01_GE2-v5_10_Apr08_1_2.txt: 24FridgeG3, LateDiaR3

value: early diapause (24 hours after transfer from fridge to 24C)


title: MM1.S Len res [aCGH]

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: DNA tumor sample

label_protocol: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: pathology

value: Multiple Myeloma

value: MM1.S res, resistant to lenalidomide

source_name: Female reference DNA sample

tag: reference

value: Female reference DNA sample


title: Carotid Near Pool n=7-VLI vs. 126-057_Peripheral_R_CFA-SFA(UNK)_denovo_FF_Pool3_PCP-


title: Patient_2

tag: disease state

value: affected


title: GANT 4

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

country: Germany

institute: UFZ Helmholtz Centre for Environmental Research

description: Gene expression of control embryos treated with GANT-61 for 24 h (0.5hpf - 24hpf)

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit following manufacturer's instructions.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Feature extraction files (processed signals) were used for statistics, quantile normalization of all processed signals before significance testing.

organism: Danio rerio

source_name: zebrafish embryo

label_protocol: Synthesis of cDNA, cRNA and cRNA-labeling was performed with the Agilent One-Color Quick Amp Labeling Kit according to the manufacturer’s instructions. cRNA was labelled with Cy3.

growth_protocol: Zebrafish embryos were collected directly after fertilisation and treated starting 0.5 hpf in exposure medium.

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

treatment_protocol: 100 embryos per treatment, treatments: control, 10 µM Cyclopamine (C), 10 µM SANT-2 (S), 10 µM GANT-61 (G), 24 h (0.5 - 24 hpf), respectively; all in 5 independent replicates

tag: exposure time

tag: treatment


title: Patient_4


title: GANT 3


title: Carotid Near Pool n=7-VLI vs. 126-060_Peripheral_L_SFA(mid)_denovo_FF_Pool2_PCP-

tag: sample name


title: Carotid Near Pool n=7-VLI vs. 119-085_Peripheral_L_SFA(prox-dist)_denovo_FF2)PCP-

tag: tissue


title: Patient_1


title: Patient_3


title: Carotid Near Pool n=7-VLI vs. 119-080_Peripheral_L_SFA(mid)_denovo_FF_Pool2_PCP-


title: Carotid Near Pool n=7-VLI vs. 126-073_Peripheral_L_SFA(entire)_denovo_FF_Pool4_PCP+


title: GANT 5


title: MM.1S [aCGH]

value: MM1.S, sensitive to lenalidomide


title: Carotid Near Pool n=7-VLI vs. 119-067_Peripheral_R_SFA(mid)_denovo_FF_Sub1_PCP+


title: Affymetrix Exon Array Liver, replicate 1

first: Dan

middle: E.

last: Arking

state: Maryland

address: 733 N. Broadway

department: McKusick-Nathans Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description: Affymetrix Exon 1.0 ST Array Sample Dataset

hyb_protocol: Affymetric GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
We analyzed expression data from ~200,000 core probesets that are supported by putative mRNAs from the RefSeq database. Signal processing was performed after quantile normalization and median polish summarization of the PM (Perfect Match) probes by using the Affymetrix power tools and the Robust Multi-Array Analysis (RMA) algorithm [15]. Probes with low p values (p < 0.05) have signals that are distinct from background and are considered to be detected above background (DABG). After, filtering to retain probes flagged as present (DABG < 0.05) in at least one-fourth of the samples, 162,145 probes remained, which mapped to ~15,000 transcripts.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Affymetrix Exon Array Liver

label_protocol: Whole transcript Terminal Labelling Kit

extract_protocol: After rapidly collecting an initial 0 hour time-point to establish a baseline measure of gene expression, the hearts were kept at 37C, and then cooled to room temperature over 12 hours. After reaching ambient temperature, some heart samples were further cooled to 4C (cold-24 hour autolysis) and others were left at room temperature (warm-24 hour autolysis). These two conditions represent two alternate scenarios of tissue harvesting. The first scenario simulates an autopsy where a body may begin cooling to ambient temperature for ~12 hours, before transportation and storage in a refrigerated room in a morgue which accelerates body cooling. The second we consider a 'worst case' scenario where the body is not cooled. At each harvesting time point, tissue was flash frozen in liquid nitrogen or placed in RNAlater from the left and right ventricle free wall. Total RNA was extracted from the tissues using the manufacture’s protocol in the RNeasy Fibrous Tissue Mini kit (Qiagen).

value: reference

tag: sample type


title: Affymetrix Exon Array Liver, replicate 3


title: Carotid Near Pool n=7-VLI vs. 101-081_Peripheral_R_Illiac(entire)_denovo_FF_Pool2_PCP+


title: GANT 1


title: Carotid Near Pool n=7-VLI vs. 126-075_Peripheral_R_SFA(dist)_PT(entire)_denovo_FF_Pool6_PCP-


title: Affymetrix Exon Array Heart, replicate 2

source_name: Affymetrix Exon Array Heart


title: Affymetrix Exon Array Heart, replicate 1


title: Affymetrix Exon Array Liver, replicate 2


title: Affymetrix Exon Array Heart, replicate 3


title: SANT 4

description: Gene expression of control embryos treated with SANT-2 for 24 h (0.5hpf - 24hpf)


title: SANT 5


title: Carotid Near Pool n=7-VLI vs. 126-070_Peripheral_R_SFA(entire)_denovo_FF_Pool5_PCP-


title: SANT 3


title: GANT 2


title: HELA_Control, technical replicate 3

description: reference

value: Hela


title: Carotid Near Pool n=7-VLI vs. 119-076_Peripheral_L_SFA(mid)_denovo_FF_Pool2_PCP+


title: HELA_Control, technical replicate 1

description: reference


title: Carotid Near Pool n=7-VLI vs. 126-059_Peripheral_L_SFA(entire)_denovo_FF_Pool5_PCP-


title: HELA_Control, technical replicate 2

description: reference


title: SANT 1


title: SANT 2


title: Cyclopamine 5

description: Gene expression of control embryos treated with Cyclopamine for 24 h (0.5hpf - 24hpf)


title: Explant heart at 18hr warm simulation (left ventricle)

description: Cardiac transplant operation (explant/failed heart)

value: heart


title: Carotid Near Pool n=7-VLI vs. 126-069_Peripheral_L_SFA(entire)_denovo_FF_Pool7_PCP-

value: carotid plaque, pool of 7 plaques


title: Explant heart at 18hr cold-simulation (left ventricle), biological rep2


title: Carotid Near Pool n=7-VLI vs. 126-066_Peripheral_L_SFA(mid)_denovo_FF_Sub1_PCP-

value: peripheral plaque


title: Carotid Near Pool n=7-VLI vs. 121-055_Peripheral_R_SFA(prox-dist)_denovo_FF_Pool4_PCP-

value: Carotid Near Pool n=7-VLI


title: Gadd45b-/- 12 hr - 4

city: Scarsdale

first: Joseph

last: Locker

state: NY

address: Pathology

institute: Albert Einstein College of Medicine

description:
Biological replicate 4 of 4
G12 - 4
Raw data: G12_Rep4.gpr

hyb_protocol: The labeled cDNAs were hybridized overnight at 50° C

scan_protocol: Microarrays were scanned with a GenePix 4000A scanner (Axon, Burlingame, CA), and data were acquired through GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).

data_processing:
Hybridization data were further normalized without background subtraction, using locally weighted linear regression (LOWESS) analysis via an in-house program. Data were normalized without background subtraction.
Normalization carried out before background subtraction; ratios calculated after background subtraction.

label: Alexa Fluor® 647

source_name: RNA from treated mutant liver

label_protocol: 20 μg RNA was labeled with the Superscript Plus Direct cDNA Labeling System and Alexa Fluor aha-dUTPs (Invitrogen). Labeled product was purified and concentrated with a Microcon YM-50 column.

growth_protocol: The project characterized early liver responses to a mitogenic drug, comparing wild type and  Gadd45b-/- female mice.

extract_protocol: Total RNA was isolated from livers using the guanidium isothiocyanate method (TRIzol; Invitrogen, Carlsbad, CA), followed by precipitation with LiCl

treatment_protocol: Mice were given a single dose of TCPOBOP (1,4-bis[2-(3,5)-dichoropyridyloxy] benzene) by gavage, and then killed at 3, 6, or 12 hr after treatment.

tag: strain

tag: genotype/variation

tag: agent

value: mitogenic drug TCPOBOP

tag: time

value: 12 hr

label: Alexa Fluor® 555

source_name: pooled normal liver RNA


title: Gadd45b-/- 12 hr - 3

description:
Biological replicate 3 of 4
G12 - 3
Raw data: G12_Rep3.gpr


title: Explant heart at 18hr cold-simulation (left ventricle), biological rep1


title: Cyclopamine 1


title: Explant heart at 6hr (left ventricle)

source_name: Explant heart at 6hr (left ventricle)


title: Cyclopamine 3


title: Explant heart at 12hr (left ventricle)

source_name: Explant heart at 12hr (left ventricle)


title: Cyclopamine 2


title: Cyclopamine 4


title: Gadd45b-/- 6 hr - 3

description:
Biological replicate 3 of 3
G6 - 3
Raw data: G6_Rep3.gpr

value: 6 hr


title: EtOH 4

description: Gene expression of control embryos treated with Ethanol for 24 h (0.5hpf - 24hpf)

value: control


title: Carotid Near Pool n=7-VLI vs. 126-072_Peripheral_R_SFA(entire)_denovo_FF_PCP-Pool6

description: Gene expression profiling of peripheral plaque. 101 subjects from FoxHollow study, plus 8 carotid plaques used as a reference poolProfiled in the Merck/Agilent 44k v1.1

source_name: Peripheral plaque


title: Gadd45b-/- 12 hr - 2

description:
Biological replicate 2 of 4
G12 - 2
Raw data: G12_Rep2.gpr


title: Gadd45b-/- 12 hr - 1

description:
Biological replicate 1 of 4
G12 - 1
Raw data: G12_Rep1.gpr


title: LCM_WholeSection_Seg3 vs. (n=9) cRNA reference pool

description: Gene expression profiling of peripheral plaque. Laser Capture Microscopy of smooth muscle cell-rich regions and macrophage-rich regions from  carotid plaque sections. Profiled in the Merck/Agilent 44k v1.1

value: (n=9) cRNA reference pool

value: whole carotid plaques from 9 samples

value: carotid plaque from whole section


title: LCM_SmoothMuscle_Seg3 vs. (n=9) cRNA reference pool

value: carotid plaque from smooth muscle cell rich section


title: LCM_Macrophage_Seg3 vs. (n=9) cRNA reference pool

value: carotid plaque from macrophage rich section


title: Autopsy heart at 24hr warm-simulation (left ventricle)

description: Rapid-autopsy program (autopsy/non-failed heart)


title: Carotid Near Pool n=7-VLI vs. 101-086_Peripheral_L_SFA(entire)_denovo_FF_Pool3_PCP-


title: Explant heart at 0hr (left ventricle), biological rep2

source_name: Explant heart at 0hr (left ventricle)


title: Explant heart at 0hr (left ventricle), biological rep1


title: EtOH 5


title: Gadd45b-/- 3 hr - 4

description:
Biological replicate 4 of 4
G3 - 4
Raw data: G3_Rep4.gpr

value: 3 hr


title: Gadd45b-/- 6 hr - 1

description:
Biological replicate 1 of 3
G6 - 1
Raw data: G6_Rep1.gpr


title: LCM_WholeSection_Seg2 vs. (n=9) cRNA reference pool


title: Autopsy heart at 24hr cold-simulation (left ventricle)


title: Gadd45b-/- 3 hr - 3

description:
Biological replicate 3 of 4
G3 - 3
Raw data: G3_Rep3.gpr


title: Gadd45b-/- 6 hr - 2

description:
Biological replicate 2 of 3
G6 - 2
Raw data: G6_Rep2.gpr


title: EtOH 1


title: EtOH 2


title: Autopsy heart at 18hr warm-simulation (right ventricle), biological rep1


title: Autopsy heart at 18hr cold-simulation (right ventricle), biological rep3


title: EtOH 3


title: Autopsy heart at 18hr warm-simulation (left ventricle), biological rep1


title: LCM_SmoothMuscle_Seg2 vs. (n=9) cRNA reference pool


title: LCM_Macrophage_Seg2 vs. (n=9) cRNA reference pool


title: LCM_WholeSection_Seg1 vs. (n=9) cRNA reference pool


title: Gadd45b-/- 3 hr - 1

description:
Biological replicate 1 of 4
G3 - 1
Raw data: G3_Rep1.gpr


title: WT - 12 hr - 2

description:
Biological replicate 2 of 2
W12 - 2
Raw data: W12_Rep2.gpr

source_name: RNA from treated wild-type liver

value: wild type


title: Control 11

description: Gene expression data untreated IB3 cells.

source_name: IB3 cells untransfected

tag: cell line

value: Bronchial epithelial cell line

tag: transfection

value: Control


title: Gadd45b-/- 3 hr - 2

description:
Biological replicate 2 of 4
G3 - 2
Raw data: G3_Rep2.gpr


title: LCM_Macrophage_Seg1 vs. (n=9) cRNA reference pool


title: LCM_SmoothMuscle_Seg1 vs. (n=9) cRNA reference pool


title: Autopsy heart at 18hr cold-simulation (left ventricle), biological rep2

value: heart


title: G551D 1

description: Gene expression data IB3 cells transfected with G551D mutant of CFTR.

source_name: IB3 transfected with G551D

value: CFTR G551D mutant


title: WT - 12 hr - 1

description:
Biological replicate 1 of 2
W12 - 1
Raw data: W12_Rep1.gpr


title: DF508 1

description: Gene expression data IB3 cells transfected with DF508 mutant of CFTR.

source_name: IB3 transfected with DF508

value: CFTR DF508 mutant


title: WT - 6 hr - 2

description:
Biological replicate 2 of 3
W6 - 2
Raw data: W6_Rep2.gpr


title: Autopsy heart at 12hr (right ventricle), biological rep2

source_name: Autopsy heart at 12hr (right ventricle)


title: WT - 6 hr - 3

description:
Biological replicate 3 of 3
W6 - 3
Raw data: W6_Rep3.gpr


title: LuxS_vs._WT_Dilute_medium_rep3

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

description: Wild type

hyb_protocol: The labelled samples were mixed and competitively hybridised using an Agilent Gene Expression Hybridisation Kit (part number: 5188-5242) in an Agilent hybridization oven (G2545A) at 65°C for 24 hours.

scan_protocol: Microarray slides were scanned using a GenePix 400B Scanner (Axon Instruments, USA) and the GenePix Pro 6.0 software. The slides were scanned at 5 μm and a photo-multiplier tube (PMT) setting of 720 for the red channel (635 nm laser measuring the CyTM5 labelled nucleic acid) and 630 for the green channel (532 nm laser measuring the CyTM3 labelled nucleic acid). The GenePix array list (GAL) file was used for extraction of the microarray results.

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5.3.1) which performs a lowess normalization. Microarray data was processed as described by García de la Nava et al 2003 and van Hijum et al 2005. Differential gene expression was determined by Cyber-T test (Long 2001).

organism: Limosilactobacillus reuteri subsp. rodentium

source_name: luxS mutant Lactobacillus reuteri 100-23 grown in dlute MRS

label_protocol: Two micrograms of total RNA was labelled with either Cy5- or Cy3-dCTP during first-strand synthesis with SuperScript II (Invitrogen) reverse transcriptase kit following the manufacturer’s protocol. Labelled cDNA was purified using a MinElute PCR purification kit (Qiagen) and the dye incorporation rate was determined by NanoDrop ND-1000 UV-Vis spectrophotometer.

growth_protocol: Lactobacillus reuteri 100-23 was cultured in Lactobacilli MRS medium (Difco, Becton Dickinson Co., Sparks, MD, USA) incubated anaerobically at 37oC. Lactobacilli MRS medium was either full strength of diluted to one-fifth concentration according to experimental requirements. Liquid media were filter-sterilised, agar media were autoclaved.

extract_protocol: Bacterial cells were harvested by brief centrifugation at 12,000 x g and washed with 750 µl of RNAprotect reagent (Qiagen). The bacterial cells were disrupted by bead beating (5000 rpm, 2 x 40 seconds) in TRIzol™ reagent (Invitrogen) and extracted with chloroform. RNA was precipitated with iso-propanol and dried after removal of iso-propanol. The dried RNA was then dissolved in nuclease-free water. The RNA was further purified using the RNeasy Mini Kit (Qiagen) and DNase treated using a DNA-free kit (Ambion). RNA quality was assessed using a Bioanalyzer 2100 instrument (Agilent Technologies) and quantified by NanoDrop ND-1000 (Nanodrop).

treatment_protocol: Total RNA was extracted from cultures of strain 100-23 grown in Lactobacilli MRS medium for four hours, eight hours or under dilute medium culture on reaching an OD600 of 0.4.

tag: growth stage

value: Exponential

value: LuxS mutant

source_name: Wild type Lactobacillus reuteri 100-23 grown in dlute MRS

value: Wild type


title: LuxS_vs._WT_Dilute_medium_rep2

description: Wild type


title: LuxS_vs._WT_Dilute_medium_rep1

description: Wild type


title: Autopsy heart at 12hr (left ventricle), biological rep1

source_name: Autopsy heart at 12hr (left ventricle)


title: LuxS_vs._WT_Dilute_medium_rep4

description: Wild type


title: LuxS_vs._WT_Stationary_phase_rep2

description: Wild type

source_name: luxS mutant Lactobacillus reuteri 100-23 grown in MRS to stationary phase

value: Stationary

source_name: Wild type Lactobacillus reuteri 100-23 grown in MRS to stationary phase


title: Autopsy heart at 6hr (left ventricle)

source_name: Autopsy heart at 6hr (left ventricle)


title: WT - 3 hr - 2

description:
Biological replicate 2 of 2
W3 - 2
Raw data: W3_Rep2.gpr

value: mitogenic drug TCPOBOP


title: WT - 3 hr - 1

description:
Biological replicate 1 of 2
W3 - 1
Raw data: W3_Rep1.gpr


title: Autopsy heart at 0hr (right ventricle), biological rep3

source_name: Autopsy heart at 0hr (right ventricle)


title: WT - 6 hr - 1

description:
Biological replicate 1 of 3
W6 - 1
Raw data: W6_Rep1.gpr

value: 6 hr

source_name: pooled normal liver RNA


title: LuxS_vs._WT_Stationary_phase_rep1

description: Wild type


title: Autopsy heart at 0hr (left ventricle), biological rep2

description: Rapid-autopsy program (autopsy/non-failed heart)

source_name: Autopsy heart at 0hr (left ventricle)


title: Control 9

tag: cell type


title: LuxS_vs._WT_Log_phase_rep1

description: Wild type

source_name: luxS mutant Lactobacillus reuteri 100-23 grown in MRS to log phase

source_name: Wild type Lactobacillus reuteri 100-23 grown in MRS to log phase


title: Untreated Gadd45b-/- 2

description:
Biological replicate 2 of 2
G0 - 2
Raw data: G0_Rep2.gpr

source_name: RNA from untreated  mutant liver

value: untreated


title: Control 3


title: CFTR 1

description: Gene expression data IB3 cells transfected with CFTR.

source_name: IB3 transfected with CFTR

value: CFTR


title: Untreated Gadd45b-/- 1

description:
Biological replicate 1 of 2
G0 - 1
Raw data: G0_Rep1.gpr


title: Control 4

source_name: IB3 cells untransfected


title: Control 5


title: Autopsy heart at 0hr (left ventricle), biological rep1


title: LuxS_vs._WT_Log_phase_rep2

description: Wild type


title: patient 16, baseline

status: Public on Sep 30 2011

city: Kontiolahti

first: Andreas

last: Scherer

address: Pajutie 3A

institute: Spheromics

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
16_Bsl

hyb_protocol: Following fragmentation, approximately 10 ug of cRNA were hybridized for 17 hr at 45C on Gene Chip HG U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GSC3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: patient 16, baseline

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

treatment_protocol: Treated twice daily for 3 weeks on 1 upper limb with 1% pimecrolimus cream and on the other upper limb with 0.1% betamethasone valerate cream in a double blind manner.

tag: atopic dermatitis

value: mild-to-moderate AD

value: skin biopsy

tag: peasi reduction [%]


title: patient 16, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
16_PC

source_name: patient 16, right arm treated with pimecrolimus until day 22


title: patient 15, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
15_PC

source_name: patient 15, right arm treated with pimecrolimus until day 22


title: patient 15, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
15_Bsl

source_name: patient 15, baseline


title: patient 14, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
14_PC

source_name: patient 14, right arm treated with pimecrolimus until day 22


title: patient 14, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
14_Bsl

source_name: patient 14, baseline


title: Control 1

description: Gene expression data untreated IB3 cells.


title: patient 16, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
16_BM

source_name: patient 16, left arm treated with betamethasone until day 22


title: patient 15, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
15_BM

source_name: patient 15, left arm treated with betamethasone until day 22


title: patient 13, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
13_PC

source_name: patient 13, right arm treated with pimecrolimus until day 22


title: patient 13, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
13_Bsl

source_name: patient 13, baseline


title: patient 13, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
13_BM

source_name: patient 13, left arm treated with betamethasone until day 22


title: patient 12, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
12_PC

source_name: patient 12, left arm treated with pimecrolimus until day 22


title: patient 11, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
11_PC

source_name: patient 11, left arm treated with pimecrolimus until day 22


title: patient 12, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
12_Bsl

source_name: patient 12, baseline


title: patient 12, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
12_BM

source_name: patient 12, right arm treated with betamethasone until day 22


title: patient 11, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
11_BM

source_name: patient 11, right arm treated with betamethasone until day 22


title: patient 11, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
11_Bsl

source_name: patient 11, baseline


title: patient 10, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
10_PC

source_name: patient 10, right arm treated with pimecrolimus until day 22


title: patient 14, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
14_BM

source_name: patient 14, left arm treated with betamethasone until day 22


title: patient 8, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
8_BM

source_name: patient 8, right arm treated with betamethasone until day 22

tag: target lesion score (peasi)


title: patient 10, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
10_Bsl

source_name: patient 10, baseline


title: patient 10, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
10_BM

source_name: patient 10, left arm treated with betamethasone until day 22


title: patient 8, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
8_PC

source_name: patient 8, left arm treated with pimecrolimus until day 22


title: patient 8, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
8_Bsl

source_name: patient 8, baseline


title: patient 7, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
7_BM

source_name: patient 7, left arm treated with betamethasone until day 22


title: patient 7, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
7_Bsl

source_name: patient 7, baseline


title: patient 6, arm treated with betamethasone

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
6_BM

source_name: patient 6, right arm treated with betamethasone until day 22


title: patient 7, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
7_PC

source_name: patient 7, right arm treated with pimecrolimus until day 22


title: PNF22_Plexiform_Neurofibroma

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Tumor and constitutional DNAs were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours. The sandwiched slides were hybridized for 24 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).

data_processing: Log ratios were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s CGH Analytics v3.5 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.

source_name: plexiform neurofibroma

label_protocol: 500 ng of genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions. tumor and constitutional DNA were labeled with Cy5-dUTP and Cy3-dUTP, respectively

extract_protocol:
High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from wholeblood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.

value: plexiform neurofibroma

source_name: constitutional DNA

value: whole-blood leukocytes


title: Autopsy heart at 18hr cold-simulation (left ventricle), biological rep1

description: Rapid-autopsy program (autopsy/non-failed heart)


title: PNF21_Plexiform_Neurofibroma


title: PNF15_Plexiform_Neurofibroma


title: PNF20_Plexiform_Neurofibroma


title: PNF3_Plexiform_Neurofibroma


title: PNF6_Plexiform_Neurofibroma


title: PNF13_Plexiform_Neurofibroma


title: hMSC Ctrl, biological rep 2

status: Public on Sep 16 2011

city: Greenville

first: Barbara

last: Muller-Borer

state: NC

address: 115 Heart Drive, East Carolina Heart Institute, Room 2247

department: Cardiovascular Sciences

institute: East Carolina University

description: Gene expression data from native hMSCS  grown for 4 days

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 400 with R- phycoerythrin Streptavidin.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Only the perfect-match (PM) probe intensities were used for the robust multi-array analysis (RMA), which includes preprocesses of background correction, quantile normalization and probe set summarization. The background was estimated by using a kernel density estimation method. The background corrected values then undertook a quantile normalization across all arrays to make all tested samples have the same expression distribution. Finally median polishing, a robust model fitting technique, was applied for probe-set measurement summarization. For better comparison of and viewing the data the preprocessed values above were normalized to 50th percentile each array (per chip normalization) and then normalized to median value across all arrays for each gene (per gene normalization). The principle component analysis and hierarchical clustering over test conditions and M-A plot were conducted for data quality estimation and control to ensure that no outlier array(s) was included in the analyzed data set.  The probe sets with equal to or greater than 1.2 fold changes between the experimental conditions were kept for further analysis. Welch t-test, which does not assume equal variation between conditions, was applied to the gene list above filtered based on the fold change. The differentially expressed gene list was created following multiple testing correction using Benjamini and Hochberg false discovery rate, with the p-value cut-off 0.05, to reduce false positive discoveries.

source_name: Control - Human mesenchymal stem cells grown for 4 days in culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix micro array protocol from 7mg of total RNA. (Bio Array High Yield Transcript Kit).

growth_protocol: hMSCs were expanded in completed alpha MEM medium containing 10% Fetal Bovine Serum, split and seeded for each experimental condition. Prior to co culture, all cells were changed to medium containing 2% Horse serum 24hrs

extract_protocol: Total RNA from FACS dsRed fluorescent cells was isolated using the Qiagen RNeasy Mini Kit standard method

treatment_protocol: HMSCs were trypsinized using TrypLE dissociation reagent and seeded onto primary neonatal cardiomyocytes at a ratio of 1:4. After 4 days of coculture, cells were dissociated using TrypLE and dsRED HMSC were gated using Texas Red filters to isolate dsRed fluorescent cells.

value: Marrow Stromal Cells

value: hMSCs grown alone


title: PNF11_Plexiform_Neurofibroma


title: PNF16_Plexiform_Neurofibroma


title: PNF5_Plexiform_Neurofibroma


title: PNF10_Plexiform_Neurofibroma


title: PNF7_Plexiform_Neurofibroma


title: PNF19_Plexiform_Neurofibroma


title: hMSC Ctrl, biological rep 3


title: hMSC Ctrl, biological rep 1


title: PNF9_Plexiform_Neurofibroma


title: PNF17_Plexiform_Neurofibroma


title: PNF4_Plexiform_Neurofibroma


title: PNF12_Plexiform_Neurofibroma


title: PNF14_Plexiform_Neurofibroma


title: hMSC Co-culture, biological rep 3

description: Gene expression data from hMSCS harvested from cardiomyocyte co-cultures at 4 days

source_name: Human mesenchymal stem cells co-cultured with neonatal rat cardiomyocytes for 4 days

value: hMSCs co-cultured for 4 days with rat neonatal cardiomyocytes


title: hMSC Co-culture, biological rep 2


title: PNF18_Plexiform_Neurofibroma


title: hMSC Co-culture, biological rep 1


title: PNF8_Plexiform_Neurofibroma


title: Small intestine, distal part, high fat group, mouse 14

status: Public on Sep 14 2011

city: Marseille Cedex 5

first: Charles

last: Desmarchelier

address: 27 Boulevard Jean Moulin

department: Nutriments Lipidiques et Prévention des Maladies Métaboliques

institute: UMR INRA 1260 / INSERM 476 - Universités Aix-Marseille I & II

hyb_protocol: Hybridization of 15µg cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701021, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 3 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701021, revision 5).

data_processing: The quality of the data was analyzed by a Bioconductor and R based method in the Nutrigenomics Organisation NuGO Array Pipeline. Expression levels of probe sets were normalized using GCRMA.

source_name: Distal small intestine, scraped off epithelial (mucosal) cells, high fat group

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 15 µg of total RNA. The protocol was conducted using the reagents provided by Affymetrix, following the manufacturer's instructions provided in the eukaryotic section of the Genechip Expression Analysis Technical Manual from Affymetrix (P/N 701021, revision 5).

extract_protocol: Total RNA from the upper and lower small intestine was isolated using Trizol reagent (Invitrogen) until the ethanol precipitation step and further purified using the QIAGEN RNeasy Mini Kit spin columns (QIAGEN GmbH). RNA concentration and purity were measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies).

treatment_protocol:
Conventionally raised eight-week-old male C57BL/6NCrl mice (Charles River Laboratories) were housed individually in a light- and temperature-controlled facility (lights on 7 AM - 7 PM, 22 °C) and had free access to water and food. They were fed a standard laboratory chow (Ssniff GmbH, cat. no. V1534) for two weeks and thereafter divided into two groups with similar mean body weights (n = 12). Mice were then fed group-specific pellet diets (control; high fat) (Ssniff GmbH, cat. no. E15000-04 and E15741-34, respectively). Throughout the feeding trial, body weight, food and water consumption were recorded once per week. Energy intake was corrected for spilled food, collected under metal grids placed below the food containers.
After 12 weeks, mice in a non-fasting state were anesthetized using isoflurane and blood was collected from the retro-orbital sinus. Mice were then killed by cervical dislocation. Tissues were harvested at the same time of the day for both groups to avoid diurnal variability. The small intestine was divided into two equal parts along the longitudinal axis (proximal and distal), mucosa was scraped off, snap-frozen in liquid nitrogen and stored at -80 °C until further processing.

tag: gender

value: male

tag: age

value: 22 weeks

value: distal small intestine

value: mucosal

tag: diet

value: high fat


title: PNF1_Plexiform_Neurofibroma


title: Small intestine, distal part, control group, mouse 16

source_name: Distal small intestine, scraped off epithelial (mucosal) cells, control group

value: control


title: Small intestine, distal part, high fat group, mouse 5


title: Small intestine, distal part, high fat group, mouse 8


title: Small intestine, distal part, control group, mouse 13


title: Small intestine, distal part, high fat group, mouse 2


title: Small intestine, distal part, control group, mouse 4


title: patient 6, arm treated with pimecrolimus

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
6_PC

source_name: patient 6, left arm treated with pimecrolimus until day 22


title: Small intestine, distal part, high fat group, mouse 11


title: Small intestine, distal part, high fat group, mouse 17


title: PNF2_Plexiform_Neurofibroma


title: Small intestine, distal part, control group, mouse 1


title: 23A

status: Public on Aug 28 2011

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HT_HG-U133A microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing: Data was normalized by robust multichip average using GeneSpring GX (Agilent).

label_protocol: RNA was amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from Nugen amplified RNA.

growth_protocol: Standard protocol for primary human tissue

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

tag: sample #

tag: cell source

value: AML

tag: leukemia stem cells (lsc)

tag: sorted fraction


title: 22A


title: Small intestine, distal part, control group, mouse 7

tag: strain

tag: tissue


title: 20A


title: 23C


title: Small intestine, distal part, control group, mouse 10


title: 21A


title: 19A


title: 22C


title: 18C


title: 21C


title: 20C


title: 18A


title: 16E

value: LSC-


title: 17C


title: 16H

value: Unsorted


title: 16C


title: 19C


title: 16G


title: 15C


title: 15A


title: 15E


title: 16A


title: 14G


title: 17A


title: 15H


title: 14C


title: 13C

value: LSC+


title: 13G


title: 13E


title: 14H


title: 15G


title: patient 6, baseline

description:
Gene expression data from human skin biopsy sample from atopic dermatitis patient
6_Bsl

source_name: patient 6, baseline

value: mild-to-moderate AD


title: 12H


title: 12A


title: 12E


title: 12C


title: 12G


title: 14A


title: 14E


title: 13A


title: 11C


title: 10H


title: 11A


title: 11G


title: 10G


title: 11H


title: 11E


title: 10E


title: 10C


title: 9C


title: 9H


title: 7A


title: 8G


title: 9G


title: 10A


title: 9E


title: 9A


title: 8H


title: 8C


title: 6G


title: 7E


title: 8E


title: 6H


title: 5E


title: 6A


title: 7G


title: 5G


title: 5H


title: 6C


title: 8A


title: 6E


title: 4H


title: 7C


title: 4E


title: 4G


title: 5A


title: 5C


title: 2E


title: 2G


title: 2C


title: 4C


title: 4A


title: HSC2c_HG-U133B

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133B microarrays (Affymetrix, Santa Clara, CA)

data_processing: Data was normalized by robust multichip average using either RMA Express version 1.0.4.

source_name: cord blood CD34+/CD38lo/CD36-

label_protocol: RNA was amplified using a linear in vitro transcription technique. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.


title: Prog c_HG-U133B

source_name: cord blood CD34+/CD38+


title: 3C


title: 3G


title: HSC2c_HG-U133A

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133A microarrays (Affymetrix, Santa Clara, CA)

growth_protocol: Primary human tissue

value: cord blood


title: Lin+ c_HG-U133A

source_name: Cord blood Lin+ and Lin- cells

value: Lin+ and Lin- cells


title: 1A


title: Lin+ c_HG-U133B


title: 3H


title: 3A


title: 3E


title: 2H


title: HSC1c_HG-U133A

source_name: cord blood CD34+/CD38-


title: Prog c_HG-U133A


title: 1C


title: Lin+ b_HG-U133A


title: Prog b_HG-U133A


title: Prog a_HG-U133A


title: 1E


title: HSC1b_HG-U133A


title: Lin+ a_HG-U133B


title: HSC1a_HG-U133B


title: 2A


title: Lin+ b_HG-U133B


title: Lin+ a_HG-U133A


title: 1H


title: 1G


title: HSC2a_HG-U133B


title: HSC1a_HG-U133A


title: HSC1c_HG-U133B


title: HSC2a_HG-U133A


title: HSC2b_HG-U133A


title: Prog a_HG-U133B


title: Prog b_HG-U133B


title: HSC1b_HG-U133B


title: trophectoderm TE_7

status: Public on Jul 15 2011

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

institute: PhyMedExp INSERM U1046

description: Human mural trophectoderm was mechanically separated from 5 days blastocyst and lysed for RNA extraction.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Human mural trophectoderm_tropho_7

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

extract_protocol: Total RNA was isolated using RNeasy micro kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

value: mural trophectoderm


title: HSC2b_HG-U133B


title: trophectoderm TE_D2E2

source_name: Human mural trophectoderm_D2E2


title: trophectoderm TE_5

source_name: Human mural trophectoderm_tropho_5


title: trophectoderm TE_D2E5

source_name: Human mural trophectoderm_D2E5


title: trophectoderm TE_D2E6

source_name: Human mural trophectoderm_D2E6


title: E10_otic_vesicle_wt_replicate1

status: Public on Jul 01 2011

city: Chicago

first: Samin

last: Sajan

state: IL

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

description: Otic vesicle at E10, replicate1

hyb_protocol: Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.

source_name: Mouse otic vesicle at E10 wt

label_protocol: To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.

growth_protocol: Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

treatment_protocol: Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

value: inner ear

tag: genotype/variation

value: Wild-type


title: tup1-del-1-d

status: Public on May 23 2011

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only  dye-bias corrections for yeast.
limma, A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.    The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: genotype

source_name: refpool

value: wild type


title: tup1-del-1-c


title: ssn6-del-2-a


title: [E-MTAB-5] run40_s7

status: Public on Feb 05 2011

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

library_source: transcriptomic

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM41_solexa_logscore_Rchrm1.txt
normM41_solexa_logscore_Rchrm2.txt
normM41_solexa_logscore_Rchrm3.txt
normM42_solexa_logscore_Rchrm1.txt
normM42_solexa_logscore_Rchrm2.txt
normM42_solexa_logscore_Rchrm3.txt
normM43_solexa_logscore_Rchrm1.txt
normM43_solexa_logscore_Rchrm2.txt
normM43_solexa_logscore_Rchrm3.txt

organism: Schizosaccharomyces pombe

extract_protocol: nucleic_acid_extraction | All cDNA samples used for Illumina sequencing were prepared by first treating ~1 mg of total RNA for 30 min with amplification grade RNase-free DNase (Invitrogen), according to the manufacturers protocols. PolyA enriched RNA was then prepared using an oligo(dT) selection kit (Oligotex Direct mRNA MiniKit, Qiagen). The resulting poly(A)-enriched RNA was then converted to double-stranded cDNA using a cDNA synthesis kit (Superscript choice system for cDNA synthesis, Invitrogen) , primed by an oligo(dT) primer, according to the manufacturers protocols. Random-primed RNA from rapidly proliferating cells was treated with an enzyme that specifically degrades non-capped RNA molecules (mRNA-only, Eukaryotic mRNA isolation kit, Epicentre Biotechnologies) according to the manufacturers protocols. The resulting cDNA was then converted to double-stranded cDNA as above, except that the reaction was primed with random hexamers. RNA samples from the pooled meiotic timepoints were subjected to IVT amplification after undergoing a poly(A) enrichment step as described above. RNA from the oxidative stress condition and prp2 mutant was treated in the same way as the rapidly proliferating samples with oligo(dT)-primed cDNA synthesis after mRNA enrichment.

tag: material type

tag: Sex

tag: strainorline

tag: growthcondition

value: meiosis

tag: time

tag: temperature

tag: media

value: EMM low nitrogen

tag: culture density


title: [E-MTAB-5] run40_s8


title: Renal_Cell_Carcinoma_A4

status: Public on Feb 28 2011

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

description: Gene expression data from Human RCC sample_A4

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). UNC Microarry Database software was used. Missing data was imputed with KNN (k=10) in SAM.

source_name: Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility.  H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology.
RNA was extracted with Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer.

tag: identifier

value: kidney

tag: histology

value: Clear Cell

tag: disease state

value: Clear Cell Carcinoma

tag: biosourcetype

value: Frozen Sample

source_name: Perou lab reference RNA

value: Cancer cell lines

tag: cell line

value: various cancer cell lines (reference)


title: Renal_Cell_Carcinoma_C1

description: Gene expression data from Human RCC sample_C1


title: Renal_Cell_Carcinoma_A18

description: Gene expression data from Human RCC sample_A18


title: ssn6-del-2-b

tag: strain


title: [E-MTAB-5] run38_s7

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM31_solexa_logscore_Rchrm1.txt
normM31_solexa_logscore_Rchrm2.txt
normM31_solexa_logscore_Rchrm3.txt
normM32_solexa_logscore_Rchrm1.txt
normM32_solexa_logscore_Rchrm2.txt
normM32_solexa_logscore_Rchrm3.txt
normM33_solexa_logscore_Rchrm1.txt
normM33_solexa_logscore_Rchrm2.txt
normM33_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run38_s8


title: Renal_Cell_Carcinoma_C5

description: Gene expression data from Human RCC sample_C5

tag: tissue


title: ccr4-del-2-b


title: Renal_Cell_Carcinoma_A27

description: Gene expression data from Human RCC sample_A27


title: Renal_Cell_Carcinoma_A5

description: Gene expression data from Human RCC sample_A5


title: Renal_Cell_Carcinoma_C13

description: Gene expression data from Human RCC sample_C13


title: ccr4-del-2-a


title: [E-MTAB-5] run38_s5

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM21_solexa_logscore_Rchrm1.txt
normM21_solexa_logscore_Rchrm2.txt
normM21_solexa_logscore_Rchrm3.txt
normM22_solexa_logscore_Rchrm1.txt
normM22_solexa_logscore_Rchrm2.txt
normM22_solexa_logscore_Rchrm3.txt
normM23_solexa_logscore_Rchrm1.txt
normM23_solexa_logscore_Rchrm2.txt
normM23_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run38_s6


title: Renal_Cell_Carcinoma_A16

description: Gene expression data from Human RCC sample_A16