title: T11DRG_PACS_7Day_rep1

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_1

value: AJS

value: T9, T10, T12, and T13 dermatomes were denervated, but T11 dermatome remained intact

value: PACS was induced by the surgery


title: stool_LNS73

status: Public on Mar 01 2016

type: RNA

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

country: USA

institute: Washington University School of Medicine

description: Gene expression data of stool RNAs from sick child

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA2.0) chips. The chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HTA2.0 arrays were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with Expression Console 1.4.1 software using Affymetrix default analysis settings. The Robust Mutlti-array Averaging (RMA) background correction, median polish probe summarization, and quantile normalization were applied as standard method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: fecal total RNA from study subject

label_protocol: Biotinylated cDNA were prepared according to the vendor's standard protocol from a minimal 100 ng of total RNA using Life Technologies (Ambion) WT-plus RNA Amplification system.

extract_protocol: Stools were enriched by centrifugation for human content prior to RNA extraction. Fecal total RNA was extracted from human-enriched pellets and bacterial-enriched supernatants separately using “Specific A” protocol on the NucliSENS EasyMAG system (bioMérieux, Durham, NC).

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

tag: percent lactulose in urine

tag: gender

value: M

tag: age (month)


title: stool_LNS87


title: m_34_g_72R_UV_high_t_5

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description: Sample name: 254711110026_4

hyb_protocol: Labeled test samples and common reference samples were combined and hybridized to the Agilent custom microarrays (Agilent Technologies).

scan_protocol: After washing, the arrays were scanned with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies) and data was extracted with Feature Extraction software v10.7.3.1 (Agilent Technologies).

data_processing:
The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's) the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.
RMA values summarized on the GeneIDs

organism: Mus musculus

label_protocol: All procedures were performed per manufacturer’s instructions. Briefly, for each test sample, 100 ng total RNA was combined with Spike A and subsequently amplified and labeled using the Quick Amp Labeling Kit (Agilent Technologies). For use as common reference, an equimolar pool of all test samples was made and amplified as described above with the exception that Spike B was included and Cy5 was used for labeling. Amplified cyanine-dye labeled antisense RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen) and yield and dye incorporation were evaluated using a NanoDrop ND-1000.

growth_protocol: All mice were supposed males of 7-10 weeks of age and at least 10 times backcrossed in SKH hairless strain. Wild-type (WT; p53+/+), p5372R/72R, and p5372P/72P mice received normal feed and water ad libitum.

extract_protocol: Total RNA was isolated as previously described in [13]. In short, frozen skin punch biopsies were pulverized in liquid nitrogen and immediately transferred to 0.3 ml Qiazol reagent (Qiagen). RNA was extracted per the manufacturer’s instructions with the addition of Phase-Lock Gel Heavy (5 Prime) to obtain a better phase separation. Further clean-up of the RNA fractions was performed using the RNeasy Minelute Cleanup Kit (Qiagen). RNA yield was measured on a Nanodrop ND-1000 (Thermo Fisher Scientific) and RNA integrity was evaluated using High Sensitivity R6K ScreenTapes on a 2200 TapeStation instrument (Agilent Technologies). RINe values were at least 6, with the exception of two samples (RINe 4.4 and 5.8) .

treatment_protocol: Mice were UV-B exposed at 2 different doses (90, 540 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated. At various time points after treatment (0, 7.5, 9, 10.5, 12, 13.5 hr. for the 90 J/m2 dose and 0, 1, 2, 3, 4, 5 hr. for the 540 J/m2 dose) both treated and untreated mice were anaesthetized by isoflurane and 1.5 mm biopsies were sampled from the back by punching a half moon shape on folded skin. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C until further processing.

tag: strain

value: male

tag: mouse

tag: genotype

tag: uv

value: high

tag: time (hours)

tag: tissue

value: skin biopsy

source_name: Common Reference pool of samples

tag: reference composition

value: an equimolar pool of all test samples


title: T11DRG_naive_rep5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description:
Gene expression data of T11 naive dorsal root ganglion (DRG).
CTRL_N_5

hyb_protocol: Biotinylated aRNA was fragmented and hybridized to Rat 230 2.0 microarrays (Affymetrix) according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: All data analysis was performed in R using bioconductor packages. CEL files were preprocessed and normalized using robust multichip averaging (RMA). Differential expression was performed using Limma.

organism: Rattus norvegicus

source_name: T11 dorsal root ganglion, naïve

label_protocol: 100 ng total RNA per DRG was amplified to produce sufficient biotin labeled antisense RNA for GeneChip analysis. Two round linear amplification was performed using MessageAmp®Ⅱ (Ambion) according to manufacturer’s instructions. Total RNA was converted into first-strand cDNA by using a T7-Oligo (dT) Primer. After the first round in vitro transcription, 2 μg aRNA was used as input for the second round of amplification using biotin labelled nucleotides during in vitro transcription (ENZO BioArray® HighYield® RNA Transcript Labeling Kit (T7), Enzo Life Sciences, Farmingdale, NY, USA). The purity and molecular weight range of aRNA products were confirmed by using agarose gel electrophoresis. Amplified RNA was shipped to the Salk Institute (Gage lab) and confirmed to be intact (not degraded) by formamide-gel electrophoresis.

extract_protocol: Total RNA was extracted from single T11 DRGs using RNeasy Kit (Qiagen Inc., Valencia, CA). RNA concentration was determined by using spectrophotometry (Nanodrop, Ambion) and quality was assessed by capillary gel electrophoresis (Bioanalyzer, Agilent). RNA yields were in excess of 200 ng and A260/A280 ratio in nuclease-free water ranged between 2.0 and 2.1.

treatment_protocol: All surgical procedures were performed in accordance with US. Institutional Animal Care and Use Committee’s (IACUC) approval was secured. Adult female Sprague-Dawley rats (260-310 g) were anesthetized with pentobarbital (65 mg/kg, i.p.). Sprouting of T11 DRG neurons was induced with surgical isolation of cutaneous sensory fields by unilateral transection of T9, T10, T12, and T13 of dorsal and lateral cutaneous nerves. Denervation of dermatomes, and subsequent confirmation of PACS, was confirmed by mapping the innervated/denervated skin border using the cutaneous trunci muscle (CTM) reflex in response to pinch. Noxious stimulation of dorsal skin reflexively activates the CTM reflex which is a localized contraction of the skin of the back (Petruska-JC et al., 2014 J Comp Neurol). When a cutaneous nerve field expanded by collateral sprouting, so did the area of skin from which a CTM reflex could be evoked by pinch. Animals were killed after anesthesia overdose with pentobarbital. Six rats were used for Naïve group and seven rats were used for 7 and 14 days group.

value: Sprague-Dawley

tag: developmental stage

value: adult

value: female

tag: rat

value: AKI

tag: surgery

value: naïve control

value: T11 dorsal root ganglion


title: m_20_g_WT_UV_low_t_12

description: Sample name: 254711110022_4

value: at least 10 times backcrossed in SKH hairless strain

value: WT

value: low


title: stool_141A


title: T11DRG_naive_rep4

description:
Gene expression data of T11 naive dorsal root ganglion (DRG).
CTRL_N_4

value: AKH


title: m_18_g_72P_UV_low_t_9

description: Sample name: 254711110022_3


title: stool_LNS142

value: stool

value: F


title: T11DRG_naive_rep2

description:
Gene expression data of T11 naive dorsal root ganglion (DRG).
CTRL_N_2

value: AKG


title: m_19_g_WT_UV_0_t_0

description: Sample name: 254711110022_2

value: male


title: T11DRG_naive_rep1

description:
Gene expression data of T11 naive dorsal root ganglion (DRG).
CTRL_N_1

value: AJP


title: m_18_g_72P_UV_low_t_12

description: Sample name: 254711110021_3

value: skin biopsy


title: stool_276A

value: environmental enteric dysfunction


title: stool_LNS226

value: M


title: m_20_g_WT_UV_low_t_0

description: Sample name: 254711110021_4

value: an equimolar pool of all test samples


title: stool_LNS232


title: m_19_g_WT_UV_0_t_10.5

description: Sample name: 254711110021_2


title: m_17_g_72P_UV_0_t_7.5

description: Sample name: 254711110021_1


title: B925_NOTCH1_MUT

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

country: Italy

institute: CRO Aviano

description: Constitutive Gene expression of CLL cells.

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Dynamic Range of Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CLL Peripheral Blood (PB). Leukemic cells >90%.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from CLL cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: not applicable

value: whole blood


title: B835_NOTCH1_MUT


title: stool_270A


title: stool_LNS98


title: m_16_g_72R_UV_low_t_10.5

description: Sample name: 254711110020_4


title: T11DRG_naive_rep3

description:
Gene expression data of T11 naive dorsal root ganglion (DRG).
CTRL_N_3

value: Sprague-Dawley

value: adult

value: female

value: AJQ


title: m_18_g_72P_UV_low_t_0

description: Sample name: 254711110020_3

value: at least 10 times backcrossed in SKH hairless strain


title: B553_NOTCH1_MUT


title: B539B_NOTCH1_MUT


title: stool_321A


title: stool_LNS161


title: B1153_NOTCH1_MUT


title: m_19_g_WT_UV_0_t_12

description: Sample name: 254711110020_2

value: WT


title: stool_LNS39


title: B-lineage acute lymphoblastic leukemia_14B

type: genomic

city: Rome

first: Monica

last: Messina

address: Via Benevento 26

department: Department of Cellular Biotechnologies and Hematology

institute: Sapienza University

description: Hybridized to Affymetrix SNP 6.0 Array

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

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

data_processing:
CEL files, CHP files and TXT files (generated by Affymetrix Genotyping Console using the Birdseed v2 algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm (see Matrix sheet and attached .cnmz file)
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: genomic DNA extracted from bone marrow of patient 14 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from bone marrow cells (>70% leukemic blasts) at diagnosis or at complete remission using the Promega Wizard® Genomic DNA Purification Kit. Genomic DNA from saliva was extracted using the NucleoSpin Tissue – (MACHEREY-NAGEL). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Not applicable

value: bone marrow sampled at complete remission


title: m_21_g_72R_UV_0_t_10.5

description: Sample name: 254711110019_2


title: stool_LNS8

value: stool


title: m_16_g_72R_UV_low_t_9

description: Sample name: 254711110019_4

value: low


title: B790_NOTCH1_WT


title: stool_089B

value: F


title: B662_NOTCH1_WT


title: stool_144B


title: m_20_g_WT_UV_low_t_10.5

description: Sample name: 254711110018_4

value: male


title: B1122_NOTCH1_WT


title: B816_NOTCH1_WT


title: stool_LNS114


title: B-lineage acute lymphoblastic leukemia_13B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 13 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: stool_LNS48


title: m_19_g_WT_UV_0_t_9

description: Sample name: 254711110018_2


title: B-lineage acute lymphoblastic leukemia_8B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 8 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: m_17_g_72P_UV_0_t_12

description: Sample name: 254711110019_1


title: B1079_NOTCH1_WT


title: m_21_g_72R_UV_0_t_7.5

description: Sample name: 254711110018_1


title: AGS_infected_by Hp_24h_experiement_3

city: Porto

first: Ceu

last: Figueiredo

address: Rua Dr. Roberto Frias S/N

country: Portugal

institute: IPATIMUP

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. To stop fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing using the Agilent G2565AA microarray scanner and the fluorescence intensities were obtained with QuantArray v3.0 software (PerkinElmer)

data_processing: he scanned images were analyzed with Feature Extraction Software 10.5.11 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AGS cell line infected with H. pylori, 24hr,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color RNA Sipke-In Kit (Agilent) according to the manufacturer's instructions (protocol publication 5188-5977), followed by RNeasy Mini Kits column purification (QIAGEN, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from three independent experiments using TriPure Isolation Reagent (Roche, Switzerland) and the procedure was performed following the manufacturer’s instructions. RNA concentration was determined using the Nanodrop Spectrophotometer ND-1000 (Invitrogen, USA). The integrity and quality of RNA samples was checked in a Bioanalyzer Chip (Agilent, USA).

tag: cell line

value: Human gastric carcinoma-derived cell line AGS

tag: infection

value: H. pylori strain 60190


title: B-lineage acute lymphoblastic leukemia_9B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 9 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: stool_LNS20

tag: sample type

value: environmental enteric dysfunction


title: B-lineage acute lymphoblastic leukemia_11B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 11 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: AGS_uninfected_24h_experiment_3

source_name: AGS cell line, 24hr,replicate 3

value: uninfected


title: m_16_g_72R_UV_low_t_0

description: Sample name: 254711110017_4

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_165

tag: disease state


title: B-lineage acute lymphoblastic leukemia_2B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 2 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: B-lineage acute lymphoblastic leukemia_13A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 13 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi

value: bone marrow sampled at diagnosis


title: B-lineage acute lymphoblastic leukemia_3B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from saliva of patient 3

value: Saliva


title: B-lineage acute lymphoblastic leukemia_7B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 7 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: B-lineage acute lymphoblastic leukemia_5B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from saliva of patient 5


title: B-lineage acute lymphoblastic leukemia_9A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 9 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: B-lineage acute lymphoblastic leukemia_6B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 6 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: B-lineage acute lymphoblastic leukemia_4B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 4 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission


title: AGS_infected_by Hp_24h_experiement_1

source_name: AGS cell line infected with H. pylori, 24hr,replicate 1


title: stool_170

source_name: fecal total RNA from study subject

tag: percent lactulose in urine


title: B-lineage acute lymphoblastic leukemia_8A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 8 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: m_17_g_72P_UV_0_t_10.5

description: Sample name: 254711110017_1

tag: gender

source_name: Common Reference pool of samples


title: m_40_g_72R_UV_high_t_5

description: Sample name: 254711110016_4

value: high


title: BACHD_old_4

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: BACHD old replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: BACHD old

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

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

value: BACHD

tag: age

value: old

value: heart


title: B-lineage acute lymphoblastic leukemia_1B

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from peripheral blood of patient 1 affected by B-lineage acute lymphoblastic leukemia sampled at complete remission

value: bone marrow sampled at complete remission


title: m_18_g_72P_UV_low_t_7.5

description: Sample name: 254711110017_3

tag: strain

value: at least 10 times backcrossed in SKH hairless strain


title: AGS_uninfected_24h_experiment_1

source_name: AGS cell line, 24hr,replicate 1


title: m_21_g_72R_UV_0_t_9

description: Sample name: 254711110017_2

tag: mouse


title: BACHD_young_4

description: BACHD young replicate 4

source_name: BACHD young

value: young


title: stool_172

value: stool

value: M

tag: age (month)


title: WT_old_4

description: WT old replicate 4

source_name: WT old

value: control (WT)


title: stool_98

value: F


title: AGS_infected_by Hp_24h_experiement_2

source_name: AGS cell line infected with H. pylori, 24hr,replicate 2

value: Human gastric carcinoma-derived cell line AGS

value: H. pylori strain 60190


title: AGS_uninfected_24h_experiment_2

source_name: AGS cell line, 24hr,replicate 2

value: uninfected


title: WT_young_4

description: WT young replicate 4

source_name: WT young


title: stool_199

value: environmental enteric dysfunction


title: m_37_g_WT_UV_0_t_3

description: Sample name: 254711110016_2

value: male

tag: genotype

value: WT

tag: uv

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_81


title: B-lineage acute lymphoblastic leukemia_7A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 7 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi

tag: tissue

value: bone marrow sampled at diagnosis


title: stool_80


title: B-lineage acute lymphoblastic leukemia_10A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 10 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: B-lineage acute lymphoblastic leukemia_11A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 11 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: Alveolar Macrophage extracted from 6 wk old wild type mice via Bronchoalveolar lavage, biological replicate 4

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Alveolar Macrophage extracted from wild type mice (age-matched to recipient mice)

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Alveolar macrophage (AMF), extracted from age-matched WT mice via BAL

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Tissues were isolated from the mice at the indicated ages.

extract_protocol: Single cell suspensions were prepared by organ digestion (yolk sac and fetal liver) with 1 mg/ml collagenase A and 10 U/ml DNA (30 and 5 minutes at 37oC), crushing (bones) or flushing of the lungs (broncholaveolar lavage). 2x104 cells were FACS purified into RLT buffer (Qiagen) containing 10 ml/ml 2-mercaptoethanol. RNA was isolated using the RNA isolation kit micro (Qiagen no74034).

value: Bronchoalveolar lavage


title: BACHD_old_3

description: BACHD old replicate 3

value: BACHD

value: old

value: heart


title: Alveolar Macrophage extracted from 6 wk old wild type mice via Bronchoalveolar lavage, biological replicate 3


title: stool_96

value: stool


title: m_38_g_WT_UV_high_t_3

description: Sample name: 254711110015_4

value: at least 10 times backcrossed in SKH hairless strain

value: high

tag: time (hours)

tag: reference composition


title: BACHD_young_3

description: BACHD young replicate 3

value: young


title: B-lineage acute lymphoblastic leukemia_5A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 5 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: m_37_g_WT_UV_0_t_1

description: Sample name: 254711110015_2


title: WT_old_3

description: WT old replicate 3

value: control (WT)


title: stool_5

value: F


title: WT_young_3

description: WT young replicate 3


title: stool_127

value: M


title: B-lineage acute lymphoblastic leukemia_2A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 2 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: m_39_g_72R_UV_0_t_2

description: Sample name: 254711110015_1


title: m_41_g_72P_UV_0_t_4

description: Sample name: 254711110016_1


title: Alveolar Macrophage derived from transferred Alveolar macrophages, 6 wks post-transfer, biological replicate 4

source_name: Alveolar macrophage (AMF), derived from transferred Alveolar macrophages


title: Alveolar Macrophage extracted from 6 wk old wild type mice via Bronchoalveolar lavage, biological replicate 2


title: BACHD_young_2

description: BACHD young replicate 2


title: stool_164

source_name: fecal total RNA from study subject

value: environmental enteric dysfunction


title: m_12_g_72P_UV_low_t_12

description: Sample name: 254711110014_3

value: male

value: low

source_name: Common Reference pool of samples


title: BACHD_old_2

description: BACHD old replicate 2

source_name: BACHD old


title: B-lineage acute lymphoblastic leukemia_14A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 14 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: Alveolar Macrophage extracted from 6 wk old wild type mice via Bronchoalveolar lavage, biological replicate 1


title: B-lineage acute lymphoblastic leukemia_3A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 3 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: WT_old_2

description: WT old replicate 2


title: stool_14


title: Alveolar Macrophage derived from transferred Alveolar macrophages, 6 wks post-transfer, biological replicate 3


title: Alveolar Macrophage derived from transferred Alveolar macrophages, 6 wks post-transfer, biological replicate 2


title: B-lineage acute lymphoblastic leukemia_4A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 4 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: WT_young_2

description: WT young replicate 2


title: m_10_g_72R_UV_low_t_10.5

description: Sample name: 254711110014_4

value: skin biopsy


title: Alveolar Macrophage derived from transferred Alveolar macrophages, 6 wks post-transfer, biological replicate 1


title: B-lineage acute lymphoblastic leukemia_6A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 6 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi


title: m_15_g_72R_UV_0_t_9

description: Sample name: 254711110014_2

value: an equimolar pool of all test samples


title: stool_51


title: m_11_g_72P_UV_0_t_7.5

description: Sample name: 254711110014_1


title: Alveolar Macrophage derived from transferred Yolk Sac Macrophages, 6 wks post-transfer, biological replicate 4

source_name: Alveolar macrophage (AMF), derived from transferred YS macrophages


title: m_14_g_WT_UV_low_t_7.5

description: Sample name: 254711110013_4

value: WT


title: stool_209


title: BACHD_old_1

description: BACHD old replicate 1


title: BACHD_young_1

description: BACHD young replicate 1

source_name: BACHD young


title: Alveolar Macrophage derived from transferred Yolk Sac Macrophages, 6 wks post-transfer, biological replicate 2

value: Bronchoalveolar lavage


title: stool_27


title: stool_50


title: Alveolar Macrophage derived from transferred Yolk Sac Macrophages, 6 wks post-transfer, biological replicate 1


title: m_12_g_72P_UV_low_t_10.5

description: Sample name: 254711110013_3


title: WT_young_1

description: WT young replicate 1

source_name: WT young


title: stool_133


title: stool_4


title: Alveolar Macrophage derived from transferred Yolk Sac Macrophages, 6 wks post-transfer, biological replicate 3


title: m_11_g_72P_UV_0_t_9

description: Sample name: 254711110013_1


title: WT_old_1

description: WT old replicate 1

source_name: WT old


title: Alveolar Macrophage derived from transferred Fetal Liver Monocytes, 6 wks post-transfer, biological replicate 4

source_name: Alveolar macrophage (AMF), derived from transferred FL monocytes


title: Alveolar Macrophage derived from transferred Fetal Liver Monocytes, 6 wks post-transfer, biological replicate 3


title: Alveolar Macrophage derived from transferred Fetal Liver Monocytes, 6 wks post-transfer, biological replicate 1


title: Alveolar Macrophage derived from transferred Fetal Liver Monocytes, 6 wks post-transfer, biological replicate 2


title: m_38_g_WT_UV_high_t_0

description: Sample name: 254711110012_4


title: stool_37


title: m_39_g_72R_UV_0_t_0

description: Sample name: 254711110011_2


title: BQ 0.1uM Y rep3

description: replicate 3

data_processing: The data were normalized using quantile normalisation with IlluminaGUI in R. One outlier sample was excluded from subsequent normalization and differential expression analysis

source_name: Cultured neurons

tag: cell type

value: Cultured neurons

tag: treatment

value: Adaptaquin

tag: adaptaquin concentration

tag: hcatreatment

value: Yes


title: stool_59

tag: sample type

value: stool


title: BQ 0.1uM N rep3

description: replicate 3

value: No


title: m_37_g_WT_UV_0_t_5

description: Sample name: 254711110012_2

value: at least 10 times backcrossed in SKH hairless strain


title: m_38_g_WT_UV_high_t_4

description: Sample name: 254711110011_4

value: high


title: m_41_g_72P_UV_0_t_1

description: Sample name: 254711110012_1


title: B-lineage acute lymphoblastic leukemia_1A

description: Hybridized to Affymetrix SNP 6.0 Array

source_name: genomic DNA extracted from bone marrow of patient 1 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi

value: bone marrow sampled at diagnosis


title: HCAonlybq 0uM Y rep3 (outlier)

description: replicate 3

value: HCA only


title: Alveolar Macrophage derived from transferred Bone Marrow Monocytes, 6 wks post-transfer, biological replicate 3

source_name: Alveolar macrophage (AMF), derived from transferred BM monocytes


title: stool_208

tag: disease state

value: F


title: BQ 1uM Y rep3

description: replicate 3


title: Alveolar Macrophage derived from transferred Bone Marrow Monocytes, 6 wks post-transfer, biological replicate 2


title: NoTreatbq 0uM N rep3

description: replicate 3

value: No Treatment


title: Alveolar Macrophage derived from transferred Bone Marrow Monocytes, 6 wks post-transfer, biological replicate 4


title: stool_156

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: M


title: Alveolar Macrophage derived from transferred Bone Marrow Monocytes, 6 wks post-transfer, biological replicate 1


title: BQ 1uM N rep3

description: replicate 3


title: stool_1

tag: gender


title: m_40_g_72R_UV_high_t_4

description: Sample name: 254711110010_4

value: male

value: skin biopsy


title: stool_238


title: HCAonlybq 0uM Y rep2

description: replicate 2


title: m_41_g_72P_UV_0_t_3

description: Sample name: 254711110011_1

value: an equimolar pool of all test samples


title: m_37_g_WT_UV_0_t_0

description: Sample name: 254711110010_2

value: WT


title: BQ 1uM Y rep2

description: replicate 2

value: Cultured neurons


title: m_41_g_72P_UV_0_t_5

description: Sample name: 254711110010_1


title: stool_94


title: stool_16


title: BQ 0.1uM Y rep2

description: replicate 2

value: Adaptaquin


title: stool_168


title: m_40_g_72R_UV_high_t_0

description: Sample name: 254711110009_3


title: BQ 0.1uM N rep2

description: replicate 2


title: NoTreatbq 0uM N rep2

description: replicate 2


title: m_38_g_WT_UV_high_t_5

description: Sample name: 254711110008_4


title: BQ 1uM Y rep1

description: replicate 1

value: Yes


title: m_38_g_WT_UV_high_t_1

description: Sample name: 254711110009_4


title: NoTreatbq 0uM N  rep1

description: replicate 1


title: stool_134

value: stool


title: stool_192


title: m_41_g_72P_UV_0_t_0

description: Sample name: 254711110008_1


title: m_40_g_72R_UV_high_t_2

description: Sample name: 254711110008_3


title: m_39_g_72R_UV_0_t_1

description: Sample name: 254711110008_2


title: MSCs_Transfected_Myc-L63RhoA_Rep4

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description:
RNA was extracted at 48 hours post transfection
L63_RHOA_4

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.

data_processing:
The expression values were log2 transformed and quantile normalized using the LumiR R package.
Matrix non-normalized -Illumina GenomeStudio generated raw intensity values.

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

growth_protocol: MSCs were cultured in αMEM supplied with 10% FCS at 37℃.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini Kit.

treatment_protocol: The transfection of Myc-L63RhoA or empty vector were performed with Lipofectamine® LTX with Plus™ Reagent (Life Technologies).

tag: cell line

value: Mesenchymal stem cells (MSCs)

tag: passage

value: Passage 6

tag: transfected with

tag: time point

value: 48 hrs post transfection


title: stool_115

tag: age (month)


title: m_37_g_WT_UV_0_t_4

description: Sample name: 254711110007_2

tag: strain

value: at least 10 times backcrossed in SKH hairless strain

tag: mouse

tag: genotype

tag: uv


title: BQ 1uM N rep2

description: replicate 2

tag: cell type

value: No


title: m_40_g_72R_UV_high_t_1

description: Sample name: 254711110007_3

value: high

tag: time (hours)

tag: tissue

tag: reference composition


title: m_37_g_WT_UV_0_t_2

description: Sample name: 254711110009_2


title: stool_198

tag: sample type


title: stool_223

tag: disease state


title: m_39_g_72R_UV_0_t_5

description: Sample name: 254711110009_1


title: BQ 0.1uM Y rep1

description: replicate 1

tag: treatment

tag: adaptaquin concentration

tag: hcatreatment


title: HCAonlybq 0uM Y rep1

description: replicate 1

value: HCA only


title: m_38_g_WT_UV_high_t_2

description: Sample name: 254711110007_4

tag: gender


title: MSCs_Transfected_Myc-L63RhoA_Rep2

description:
RNA was extracted at 48 hours post transfection
L63_RHOA_2

tag: cell line

tag: passage

tag: transfected with


title: BQ 0.1uM N rep1

description: replicate 1


title: stool_97

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: F

tag: age (month)


title: stool_123


title: BQ 1uM N rep1

description: replicate 1


title: m_41_g_72P_UV_0_t_2

description: Sample name: 254711110006_1

tag: strain

value: male

tag: mouse

tag: genotype


title: stool_131


title: MSCs_Transfected_Myc-L63RhoA_Rep3

description:
RNA was extracted at 48 hours post transfection
L63_RHOA_3

tag: time point


title: stool_232

value: M


title: stool_250


title: stool_21


title: stool_120


title: m_14_g_WT_UV_low_t_9

description: Sample name: 254711110005_4

tag: uv

value: low

tag: time (hours)

tag: tissue

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_201

tag: sample type

tag: disease state


title: m_39_g_72R_UV_0_t_3

description: Sample name: 254711110007_1

tag: reference composition


title: m_39_g_72R_UV_0_t_4

description: Sample name: 254711110006_2


title: m_10_g_72R_UV_low_t_12

description: Sample name: 254711110005_3


title: MSCs_Transfected_Myc-L63RhoA_Rep1

description:
RNA was extracted at 48 hours post transfection
L63_RHOA_1


title: MSCs_Transfected_Empty Vector_Rep3

description:
RNA was extracted at 48 hours post transfection
EV_CONT_3

source_name: MSCs_Transfected_Empty Vector

value: Empty Vector


title: m_40_g_72R_UV_high_t_3

description: Sample name: 254711110006_4


title: stool_188


title: stool_219


title: stool_294A


title: SCOS#12 Dox ON 72h

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data were processed using Genespring software.

source_name: osteosarcoma cell lines

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: DMEM+10%FBS+PS (SCOS#2 and #12) / Knockout DMEM+15%FBS+PS+L-glutamine+βME+LIF (Sarcoma iPSC)

extract_protocol: RNeasy Plus Mini kit

treatment_protocol: SCOS#2 and #12 Dox ON samples were treated with Dox (2µg/ml) containing medium for 72hours. SCOS#2 and #12 Dox OFF samples were mainteined with Dox-free medium for 72hours. RNA of sarcoma iPSCs was collected after removal of feeder cells (MEF).

tag: cell type

value: osteosarcoma cell lines

tag: treatment

value: Dox (2µg/ml)


title: Sarcoma iPSC#2-A1

source_name: sarcoma-derived iPSCs

value: sarcoma-derived iPSCs


title: MSCs_Transfected_Empty Vector_Rep1

description:
RNA was extracted at 48 hours post transfection
EV_CONT_1

tag: cell line

value: Mesenchymal stem cells (MSCs)

value: Passage 6


title: MSCs_Transfected_Empty Vector_Rep4

description:
RNA was extracted at 48 hours post transfection
EV_CONT_4

tag: passage

value: 48 hrs post transfection


title: K/BxN

city: Seoul

first: Eunkyeong

last: Jang

address: 17, Haengdang 1-dong, Seongdong-gu,

country: South Korea

institute: Hanyang University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using fold-change.

source_name: Mouse spleen plasma cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

value: K/BxN

value: Spleen

tag: age

value: 8 weeks

tag: gender

value: plasma


title: MSCs_Transfected_Empty Vector_Rep2

description:
RNA was extracted at 48 hours post transfection
EV_CONT_2

tag: transfected with


title: stool_278B

source_name: fecal total RNA from study subject

value: stool

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: F

tag: age (month)


title: stool_221B

value: M


title: stool_219A


title: Sarcoma iPSC#2-B5


title: m_12_g_72P_UV_low_t_7.5

description: Sample name: 254711110004_3

tag: strain

value: at least 10 times backcrossed in SKH hairless strain

value: male

tag: mouse

tag: genotype

value: low

value: skin biopsy

source_name: Common Reference pool of samples


title: m_15_g_72R_UV_0_t_0

description: Sample name: 254711110005_2

tag: uv

tag: time (hours)

value: an equimolar pool of all test samples


title: m_13_g_WT_UV_0_t_12

description: Sample name: 254711110004_2

value: WT

tag: tissue


title: m_10_g_72R_UV_low_t_0

description: Sample name: 254711110004_4


title: m_10_g_72R_UV_low_t_7.5

description: Sample name: 254711110003_4


title: SCOS#12 Dox OFF 72h

value: osteosarcoma cell lines


title: Nur77_IL4_8h_rep_3

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

description: raw data file column: 101799-34

scan_protocol: The samples were scanned using the Illumina iScan array scanner

data_processing: Data were retrieved using Illumina's Genomestudio v. 2011.1 software. Analyses were carried out with Bioconductor packages in the statistical software package R (version 2.14.0). Normexp-by-control background correction, quantile normalization, and log2 transformation (Shi et al, NAR, 2010) were performed on the Illumina sample and control probe profiles using the limma package (version 3.10.2), function neqc.

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate biotin-labeled (biotin-16-UTP) amplified cRNA

growth_protocol: Each batch of bone marrow cells was isolated from femurs and tibiae of 3 wild-type (WT) mice and 3 Nur77-KO mice (Hamers et al, Circ Res, 2012). In brief, cells were cultured in RPMI-1640 (GIBCO Invitrogen) with 100 U/ml penicillin/streptomycin (GIBCO Invitrogen), 10% heat-inactivated fetal calf serum (FCS; GIBCO Invitrogen) and 15% L929 conditioned medium (LCM) for 8 days to generate BMM. BMM were seeded at a density of 1.5×105 cells/cm2 24 hrs before stimulation.

extract_protocol: RNA was isolated using the Aurum total RNA isolation kit (Bio-Rad). The Agilent Bioanalyzer was used to analyze the quality and integrity of the RNA samples.

treatment_protocol: BMMs were polarized toward an M1-proinflammatory phenotype using 100 ng/ml LPS (Sigma) or were M2a-activated using 50 ng/mL interleukin (IL)-4 (R&D systems)

value: bone marrow macrophages

tag: stimulus

tag: timepoint

tag: slide

tag: slide position

value: D


title: MuRF1 +/+ CHOW rep2

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

state: NC

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

description: MuRF1 +/+ Mouse biological replicate 19

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

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner. Images were quantified using Genepix Pro (version 6.0).

data_processing: LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal by Genepix Pro V 6.0. Data was subsequently downloaded and filtered for features present in less than 70% of arrays.

source_name: Total RNA from murine heart labeled with Cyanin-5 (red)

label_protocol: 50 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

extract_protocol: Total RNA extracted using Qiagen All-Prep kit following manufacturer's instructions

value: Cardiac tissue

tag: treatment

value: 8 wk with Chow diet

value: MuRF1 +/+

source_name: Total RNA from pooled whole mouse neonates (day 1), labeled w/ Cy-3 (green)

value: postnatal Day 1

value: whole pup


title: Nur77_LPS_8h_rep_3

description: raw data file column: 101799-36

tag: cell type

value: LPS


title: m_12_g_72P_UV_low_t_0

description: Sample name: 254711110002_3

tag: reference composition


title: stool_127A

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

tag: gender


title: SCOS#2 Dox OFF 72h

tag: cell line


title: stool_118B

tag: percent lactulose in urine

value: F

tag: age (month)


title: MuRF1 +/+ 8WK FENO rep3

description: MuRF1 +/+ Mouse biological replicate 17

value: 8 wk 0.05% Fenofibrate w/w with Chow diet

tag: genotype

tag: strain

tag: age


title: Nur77_LPS_8h_rep_2

description: raw data file column: 101799-30


title: stool_160B

value: M


title: K/BxNsf

value: K/BxNsf

tag: tissue

value: Spleen

value: 5 weeks

value: male

value: plasma


title: m_11_g_72P_UV_0_t_0

description: Sample name: 254711110003_1

value: at least 10 times backcrossed in SKH hairless strain

tag: mouse

tag: uv

tag: time (hours)

value: skin biopsy

value: an equimolar pool of all test samples


title: MuRF1 +/+ CHOW rep1

description: MuRF1 +/+ Mouse biological replicate 18

value: Cardiac tissue

value: 8 wk with Chow diet

value: MuRF1 +/+


title: MuRF1 +/+ CHOW rep3

description: MuRF1 +/+ Mouse biological replicate 20

value: postnatal Day 1

value: whole pup


title: stool_205A

value: stool

value: environmental enteric dysfunction


title: WT_LPS_8h_rep_3

description: raw data file column: 101799-31

value: bone marrow macrophages

value: Wild-type

tag: stimulus

value: LPS

tag: timepoint

tag: slide

tag: slide position

value: A


title: WT_IL4_8h_rep_3

description: raw data file column: 101799-35

tag: cell type

value: E


title: MuRF1 +/+ 8WK FENO rep1

description: MuRF1 +/+ Mouse biological replicate 15

tag: treatment

value: 8 wk 0.05% Fenofibrate w/w with Chow diet


title: m_13_g_WT_UV_0_t_9

description: Sample name: 254711110002_2

tag: gender

value: male

value: WT

tag: reference composition


title: MuRF1 +/+ 8WK FENO rep2

description: MuRF1 +/+ Mouse biological replicate 16


title: Nur77_IL4_8h_rep_2

description: raw data file column: 101799-27

value: C


title: m_11_g_72P_UV_0_t_10.5

description: Sample name: 254711110002_1

value: at least 10 times backcrossed in SKH hairless strain

value: skin biopsy

value: an equimolar pool of all test samples


title: MuRF1 +/+ 3WK FENO rep4

description: MuRF1 +/+ Mouse biological replicate 14

value: Cardiac tissue

value: 3 wk 0.05% Fenofibrate w/w with Chow diet

value: MuRF1 +/+


title: Bur6_3

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

hyb_protocol: We followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), using the GeneChip® Hybridization, Wash and Stain Kit.

data_processing:
Raw .CEL images were processed with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default.
The resulting files were obtained with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. BioGRO samples where normalized against a reference genomic DNA hybridized on the same Affymetrix tiling arrays (ArrayExpress E-TABM-590).

organism: Saccharomyces cerevisiae

source_name: Yeast cells grown in YPD to exponential phase.

growth_protocol: See treatment protocol for details. For each sample we used an aliquot of 100 mL cells.

extract_protocol: RNA extraction was done using the acid Phenol:Chloroform extraction method. Once extracted, genomic DNA was removed digesting with 2 µL of RNase-free DNase I (Roche) for 30 min at 37 °C. The purified RNA was resuspended in 32 µL of water and spectrophotometrically quantified.

treatment_protocol: Yeast cells were cultured at 28ºC in YPGal (Yeast extract 1%, Peptone 2%, Galactose 2%) to OD600 of about 0.5. At that time cells were recovered by centrifugation and resuspended in YPD (same medium but 2% Glucose instead of Galactose) and grown for additional 4h before RNA extraction.

value: Bur6 strain:MATα leu2Δ1 ura3-52 his3Δ200 KanMX6::GAL10::3HA-BUR6


title: m_14_g_WT_UV_low_t_10.5

description: Sample name: 254711110001_4

value: low


title: SCOS#2 Dox ON 72h

tag: cell line

value: osteosarcoma cell lines

value: Dox (2µg/ml)


title: Bur6_2

scan_protocol: We followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), using the GeneChip® Hybridization, Wash and Stain Kit.


title: m_13_g_WT_UV_0_t_10.5

description: Sample name: 254711110003_2


title: stool_079B

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: F

tag: age (month)


title: m_13_g_WT_UV_0_t_0

description: Sample name: 254711110001_2

tag: strain

tag: genotype

tag: tissue


title: stool_098A


title: WT_none_0h_rep_3

description: raw data file column: 101799-22

value: bone marrow macrophages

value: Wild-type

value: D


title: stool_071B

value: M


title: stool_054A


title: stool_060A


title: Nur77_IL4_8h_rep_1

description: raw data file column: 101799-20

value: B


title: MuRF1 +/+ 3WK FENO rep3

description: MuRF1 +/+ Mouse biological replicate 13

tag: age

value: postnatal Day 1

value: whole pup


title: MuRF1 -/- CHOW rep1

description: MuRF1 -/- Mouse biological replicate 8

value: Cardiac tissue

value: 8 wk with Chow diet

value: MuRF1 -/-


title: MuRF1 +/+ 3WK FENO rep1

description: MuRF1 +/+ Mouse biological replicate 11

value: 3 wk 0.05% Fenofibrate w/w with Chow diet

value: MuRF1 +/+


title: MuRF1 +/+ 3WK FENO rep2

description: MuRF1 +/+ Mouse biological replicate 12


title: Bur6_1

label_protocol: We followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880)

value: Bur6 strain:MATα leu2Δ1 ura3-52 his3Δ200 KanMX6::GAL10::3HA-BUR6


title: Ydr1_3

value: Ydr1 strain:MATα leu2Δ1 ura3-52 his3Δ200 KanMX6::GAL10::3HA-YDR1


title: Nur77_none_0h_rep_3

description: raw data file column: 101799-19

tag: stimulus

value: A


title: WT_LPS_8h_rep_2

description: raw data file column: 101799-15

value: LPS

tag: timepoint

value: C


title: m_15_g_72R_UV_0_t_12

description: Sample name: 254711110001_1

value: at least 10 times backcrossed in SKH hairless strain

value: male

tag: mouse

tag: uv

tag: time (hours)

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_004A

value: stool

value: environmental enteric dysfunction

value: F


title: WT_LPS_8h_rep_1

description: raw data file column: 101799-14

tag: cell type

value: bone marrow macrophages

value: Wild-type

tag: slide

tag: slide position

value: B


title: MuRF1 -/- CHOW rep2

description: MuRF1 -/- Mouse biological replicate 9

value: Cardiac tissue

tag: treatment

value: 8 wk with Chow diet

value: MuRF1 -/-

value: postnatal Day 1

value: whole pup


title: WT_IL4_8h_rep_2

description: raw data file column: 101799-21


title: MuRF1 -/- CHOW rep3

description: MuRF1 -/- Mouse biological replicate 10


title: stool_010A

tag: sample type

tag: gender


title: stool_025B

tag: disease state

tag: percent lactulose in urine


title: stool_149B

tag: age (month)


title: MuRF1 -/- 8WK FENO rep3

description: MuRF1 -/- Mouse biological replicate 7

value: 8 wk 0.05% Fenofibrate w/w with Chow diet

tag: genotype

tag: strain


title: stool_008A

value: M


title: Ydr1_2

value: Ydr1 strain:MATα leu2Δ1 ura3-52 his3Δ200 KanMX6::GAL10::3HA-YDR1


title: Ydr1_1


title: stool_168A, replicate A


title: MuRF1 -/- 8WK FENO rep1

description: MuRF1 -/- Mouse biological replicate 5

tag: tissue

tag: age


title: WT_2

value: WT strain:FY86 (MATα leu2Δ1 ura3-52 his3Δ200)


title: MuRF1 -/- 8WK FENO rep2

description: MuRF1 -/- Mouse biological replicate 6


title: WT_1


title: WT_3


title: MuRF1 -/- 3WK FENO rep4

description: MuRF1 -/- Mouse biological replicate 4

value: 3 wk 0.05% Fenofibrate w/w with Chow diet


title: WT_none_0h_rep_2

description: raw data file column: 101799-07

tag: stimulus

tag: timepoint

value: A


title: MuRF1 -/- 3WK FENO rep3

description: MuRF1 -/- Mouse biological replicate 3


title: stool_134B

value: stool


title: stool_007A, replicate A

value: environmental enteric dysfunction


title: Nur77_none_0h_rep_1

description: raw data file column: 101799-08


title: Nur77_LPS_8h_rep_1

description: raw data file column: 101799-03

value: LPS

value: C


title: WT_IL4_8h_rep_1

description: raw data file column: 101799-02

value: bone marrow macrophages

value: Wild-type


title: Nur77_none_0h_rep_2

description: raw data file column: 101799-13


title: stool_022A, replicate A


title: MuRF1 -/- 3WK FENO rep2

description: MuRF1 -/- Mouse biological replicate 2

value: Cardiac tissue


title: stool_316B


title: WT_none_0h_rep_1

description: raw data file column: 101799-01


title: HL-60 PMA 24h

status: Public on Feb 28 2016

city: Beijing

first: Yu

last: Zuyin

address: No. 27 Taiping Road

department: Department of Pathophysiology

country: China

institute: Beijing Institute of Radiation Medicine

description: Gene expression data from 10 nM PMA treated, 24 h, HL-60 cells

hyb_protocol: Samples were hybridised using a Nimblegen Hybridisation Kit (05 583 934 001), including Sample Tracking Controls (05 223 512 001)

scan_protocol: Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain

data_processing: Images were spearated, gridded and extracted using Nimblegen DEVA software. Pair files were generated and used for RMA normaliziation using DEVA software  Deva generated RMA normalized intensitites were used for analysis

source_name: 10 nM PMA treated, 24 h, HL-60 cells

label_protocol: Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)

growth_protocol: 1640 with 10% FBS

extract_protocol: RNA isolation was peformed by CapitalBio Corporation (Beijing, China). RNA was purified using the NucleoSpin® RNA clean-up Kit (MACHEREY-NAGEL, Germany) according to the manufacturer's protocol.

treatment_protocol: HL-60 cells were treated with vibsanin A, PMA and ATRA for 6 hours or 24 hours.

tag: agent

value: 10 nM PMA treated

tag: time point

tag: cell line

tag: cell line description

value: acute myeloid leukemia


title: HL-60 ATRA 24h

description: Gene expression data from 1 uM ATRA treated, 24 h, HL-60 cells

source_name: 1 uM ATRA treated, 24 h, HL-60 cells

value: 1 uM ATRA treated


title: stool_109A, replicate A

description: Gene expression data of stool RNAs from sick child


title: HL-60 Control 24h

description: Gene expression data from vehicle treated, 24 h, HL-60 cells

source_name: vehicle treated, 24 h, HL-60 cells

value: vehicle treated


title: MuRF1 -/- 3WK FENO rep1

description: MuRF1 -/- Mouse biological replicate 1

value: MuRF1 -/-

value: postnatal Day 1

value: whole pup


title: HL-60 ATRA 6h

description: Gene expression data from 1 uM ATRA treated, 6 h, HL-60 cells

source_name: 1 uM ATRA treated, 6 h, HL-60 cells

value: 6 h


title: HL-60 PMA 6h

description: Gene expression data from 10 nM PMA treated, 6 h, HL-60 cells

source_name: 10 nM PMA treated, 6 h, HL-60 cells


title: circularRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 1

status: Public on Jan 28 2016

city: shi jia zhuang

first: shaoguang

last: sun

state: Hebei

address: zhong shan dong lu 361

department: biochemistry and molecular biology

institute: Hebei medical university

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar).

scan_protocol: The hybridized arrays were washed, fixed, and scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.  The Sample data table includes the detectable signals.

source_name: Human aortic vascular smooth muscle cells

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Smooth Muscle Cell Medium (ScienCell, consists of 500 ml of basal medium, 2 ml of fetal bovine serum (Cat. No. 0010), and 5 ml of penicillin/streptomycin solution (Cat. No. 0503) , 37℃, 5% CO2.

extract_protocol: Total RNA was isolated from three proliferative HAVSMCs(10ng/ml PDGF-BB-treated for 24h) and quiescent HAVSMCs (untreated for 24h) using Trizol reagent (Invitrogen), according to the manufacturer's protocol.

treatment_protocol: Recombinant human platelet-derived growth factor-BB(PDGF-BB) was obtained from R&D Systems Inc. HAVSMCs were treated with 10ng/ml PDGF-BB for 24h.

tag: cell type

tag: growth state

value: quiescent


title: HL-60 Vibsanine A 24h

description: Gene expression data from 10 uM vibsanin A treated, 24 h, HL-60 cells

value: 10 uM vibsanin A treated


title: circularRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 1

value: Human aortic vascular smooth muscle cells

value: proliferative


title: HL-60 Control 6h

description: Gene expression data from vehicle treated, 6 h, HL-60 cells

source_name: vehicle treated, 6 h, HL-60 cells


title: circularRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 2


title: HL-60 Vibsanine A 6h

description: Gene expression data from 10 uM vibsanin A treated, 6 h, HL-60 cells


title: circularRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 3


title: circularRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 2


title: Normal_Healthy_Fibroblast_RED_light_irradiation_for_10_min

status: Public on Feb 18 2016

city: hatyai

first: pongsathorn

last: chotikasemsri

state: songkhla

address: kajanavanich rd

department: faculty of medicine

country: Thailand

institute: prince of songkhla university

description: Gene expression of Normal Healthy fibroblast cell line with 10 min Red light LED irradiation

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242

scan_protocol: Surescan Microarray

data_processing: GeneSpring GX 12.6.1 Software

source_name: GM03440 with artificial wounds, irradiated with RED light for 10 min.

label_protocol: Agilent’s Quick-Amp labeling Kit (p/n5190-0442) T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

growth_protocol: Normal healthy fibroblast cell line (GM03440) was taken from Coriell Institute for medical research and cultured on DMEM media with 1% penicillin, 1% streptomycin, and 10% Fetal Bovine Serum in a 10 cm. plate.

extract_protocol: Qiagen’s RNeasy minikit Cat#74106

treatment_protocol: In this study, normal fibroblast cell lines were cultured and created some artificial wounds with pipette tips. Then, the cells were separately treated with RED,GREEN,BLUE LED light for 10 minutes. After that, they all were harvested for RNA extraction.

value: Normal healthy fibroblast Cell lines

value: male


title: lncRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.


title: lncRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 1


title: circularRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 3


title: Normal_Healthy_Fibroblast_BLUE_light_irradiation_for_10_min

description: Gene expression of Normal Healthy fibroblast cell line with 10 min Blue light LED irradiation

source_name: GM03440 with artificial wounds, irradiated with BLUE light for 10 min.


title: lncRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 3


title: lncRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 1


title: Apc+/Δ716 mice vs. Apc+/Δ716Id2-/- mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: APC

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: All mice are raised in SPF condition

extract_protocol: Total RNA extracted using Rneasy micro kit (Qiagen) following manufacturer's instructions

treatment_protocol: Samples are isolate by crypt isolation protocol (Sato et al., Nature  459, 262-265.2009）

value: intestine

value: crypt epithelium


title: Normal_Healthy_Fibroblast_GREEN_light_irradiation_for_10_min

description: Gene expression of Normal Healthy fibroblast cell line with 10 min Green light LED irradiation

source_name: GM03440 with artificial wounds, irradiated with GREEN light for 10 min.


title: fhm_F_ovary_5 ug TCC per L_-5

status: Public on Jul 31 2015

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

hyb_protocol: Ovary RNA samples from twenty four fish (n=5 for all treatments except TRB alone; n=4) were selected for microarray analysis. Each sample was hybridized to a custom 15,000 feature microarray (GEO Platform Accession GPL9248) purchased from Agilent Technologies (Palo Alto, CA). Hybridization was conducted according to the manufacturer’s guidelines for One-Color Microarray-Based Gene Expression Analysis (version 5.7). Hybridizations were conducted with 1 μg of total RNA.

scan_protocol: Scanning was conducted at 5 μm resolution using an Axon GenePix 4000B Microarray Scanner (Molecular Devices Inc., Concord, Ontario, Canada).

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer's protocol and recommendations. The microarrays uniformly exceeded the quality control metric "gNegCtrlAveNetSignal" (metric values exceeded the upper limit of 40), suggesting that higher than normal background may have limited sensitivity to detected low-abundance transcripts. Otherwise, QC metrics were within the recommended ranges. Microarray data were normalized using quantile normalization implemented in GeneSpring GX (Agilent Technologies, Santa Clara, CA, USA).

organism: Pimephales promelas

source_name: ovary from female fish exposed continuously to 5 ug triclocarban per liter via water for 22 d

label_protocol: Complementary DNA synthesis, cRNA labeling, amplification, and hybridization were performed following the manufacturer’s kits and protocols (Quick Amp Labeling kit; One-Color Microarray-Based Gene Expression Analysis version 5.7; Agilent).

growth_protocol: The fish were held at 25+1ºC under a 16:8 L:D photoperiod and were fed frozen adult brine shrimp twice daily (San Francisco Bay Brand, Newark, CA, USA).  Fish used for the experiment were from an on-site culture, and all procedures involving animals conformed to guidelines approved by the local Animal Care and Use Committee. Total number of eggs spawned and the number of fertile eggs produced by each pair were recorded daily. General water quality characteristics (mean ± SD) measured regularly over the course of the experiment were: temperature, 24.8 ± 0.7 oC; pH, 7.87 ± 0.04; dissolved oxygen, 6.8 ± 0.35 mg/L

extract_protocol: Total RNA was extracted from ovary and testis tissue using RNeasy kits (Qiagen, Valencia, CA). RNA quantity was determined spectrophotometrically (Nanodrop ND-1000, Nanodrop Technologies, Wilminton, DE) and quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA samples were diluted to 10 ng/µl and stored at -80 oC until analyzed.

treatment_protocol: Reproductively mature Pimephales promelas were continuously exposed to either 1 or 5 μg TCC/L, 0.5 μg 17β-trenbolone (TRB)/L or a mixture (MIX) of 5 μg TCC and 0.5 μg TRB/L for 22 d. All chemicals were delivered in a continuous flow (45 ml/min) of sand filtered, UV treated Lake Superior water without the use of carrier solvents.

value: ovary

tag: ctid (sample id)

tag: treatment

value: TCC 5

tag: date sampled

tag: rep (tank within treatment)

tag: time of day sampled

tag: FISH wet weight (g)

tag: gonad wet wt (g)

tag: gonadal somatic index (%)

tag: plasma testosterone (ng/ml)

tag: plasma vitellogenin (mg/ml)

tag: tubercle score

tag: ex vivo e2 production (ng/ml/12h)

tag: ex vivo t production (ng/ml/12h)


title: lncRNA_Proliferative human aortic vascular smooth muscle cells (HAVSMCs) 2


title: fhm_F_ovary_5 ug TCC per L_-3

tag: tissue


title: Diabetics_Type_II_Fibroblast_10_min_BLUE_light_LED_irradiation

description: Gene expression of Diabetic fibroblast cell line with 10 min Blue light LED irradiation

source_name: AG06083 with artificial wounds, irradiated with BLUE light for 10 min.

growth_protocol: Both type 2 diabetic fibroblast cell line and healthy normal fibroblast cell line (AG06083 and GM03440) were taken from Coriell Institute for medical research and cultured on DMEM media with 1% penicillin, 1% streptomycin, and 10% Fetal Bovine Serum in a 10 cm. plate.

treatment_protocol: In this study, both diabetic and normal fibroblast cell lines were cultured and created some artificial wounds with pipette tips. Then, the cells were separately treated with RED,GREEN,BLUE LED light for 10 minutes. After that, they all were harvested for RNA extraction.

value: Diabetic fibroblast Cell lines

tag: gender

tag: age

tag: cell line


title: Diabetics_Type_II_Fibroblast_10_min_RED_light_LED_irradiation

description: Gene expression of Diabetic fibroblast cell line with 10 min Red light LED irradiation

source_name: AG06083 with artificial wounds, irradiated with RED light for 10 min.


title: Diabetics_Type_II_Fibroblast_No_light_irradiation

description: Gene expression of Diabetic fibroblast cell line as a control group

source_name: AG06083, No light irradiation


title: fhm_F_ovary_5 ug TCC per L_-4

tag: ctid (sample id)


title: lncRNA_Quiescent human aortic vascular smooth muscle cells (HAVSMCs) 2

tag: cell type

tag: growth state


title: Normal_Healthy_Fibroblast_No_light_irradiation

description: Gene expression of Normal healthy fibroblast cell line as a control group

source_name: GM03440, No light irradiation


title: Diabetics_Type_II_Fibroblast_10_min_GREEN_light_LED_irradiation

description: Gene expression of Diabetic fibroblast cell line with 10 min Green light LED irradiation

source_name: AG06083 with artificial wounds, irradiated with GREEN light for 10 min.


title: fhm_F_ovary_5 ug TCC per L_-2

tag: treatment

tag: date sampled

tag: rep (tank within treatment)


title: fhm_F_ovary_1 ug TCC per L_-2

source_name: ovary from female fish exposed continuously to 1 ug triclocarban per liter via water for 22 d

value: TCC 1

tag: time of day sampled

tag: FISH wet weight (g)

tag: gonad wet wt (g)

tag: plasma estradiol (ng/ml)


title: fhm_F_ovary_1 ug TCC per L_-4

tag: gonadal somatic index (%)

tag: plasma testosterone (ng/ml)

tag: plasma vitellogenin (mg/ml)

tag: tubercle score


title: fhm_F_ovary_1 ug TCC per L_-1

tag: tissue

tag: ex vivo e2 production (ng/ml/12h)

tag: ex vivo t production (ng/ml/12h)


title: fhm_F_ovary_1 ug TCC per L_-5

tag: ctid (sample id)


title: fhm_F_ovary_CON-5

source_name: ovary from female fish exposed to control water for 22 d

value: con

tag: color

value: light banding color


title: fhm_F_ovary_MIX-1

source_name: ovary from female fish exposed continuously to a mixture 0.5 ug 17beta-trenbolone and 5 ug triclocarban per liter via water for 22 d

value: TRB-TCC 5

value: banding color


title: fhm_F_ovary_MIX-3


title: fhm_F_ovary_5 ug TCC per L_-1

tag: notes

value: ovulating eggs


title: fhm_F_ovary_MIX-2

tag: treatment


title: SAMPLE_101_CD4

status: Public on May 29 2015

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

country: Estonia

institute: University of Tartu

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

scan_protocol: Arrays were imaged using Illumina HiScan scanner using standard recommended Illumina scanner setting      HiScan v.3& Illumina AutoLoader2X v. 2.3.0.0

data_processing:
Bioconductor package’s minfi option ‘Raw’ pre-processing was used to convert the intensities from the red and the green channels from the original IDAT ﬁles extracted from the HiScanSQ scanner into methylated and unmethylated signals. Beta values were computed using Illumina’s formula [beta = M/(M+U+100)] and normalized using method SWAN as implemented in minfi. Detection p-values were obtained for every CpG probe in each sample using detectionP option in minfi. Samples with detection p-value > 0.01 in more than 10% of the CpG sites and possibly contaminated or mixed up samples (determined using the 65 SNPs present on the methylation beadchip) were discarded. All the probe sequences were mapped to the human genome (build hg19) and all probes that did not map uniquely, mapped to CpG sites with SNPs up to 3 bp upstream of the site, or mapped to the X/Y chromosomes were discarded.
The 'MatrixSignalIntensities.csv' contains unmethylated and methylated signal intensities
The 'MatrixProcessed.csv' file contains SWAN normalized Average Beta

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood mononuclear cells (PBMC) were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD8 T-cells and CD4 T-cells were extracted from PBMCs by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. Genomic DNA was isolated from the purified cell pellets using the QIAmp DNA Mini Kit (Qiagen) according to the manufacturer's protocol. Genomic DNA was treated with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research Corporation) according to the manufacturer’s instructions

tag: gender

value: female

tag: age (yr)

tag: agegroup

value: Old

tag: cell/tissue type


title: fhm_F_ovary_MIX-4

tag: date sampled

tag: rep (tank within treatment)

tag: time of day sampled

tag: FISH wet weight (g)

tag: gonad wet wt (g)


title: SAMPLE_101

source_name: Female_Old_Peripheral blood

value: Peripheral blood


title: fhm_F_ovary_500 ng TRB per L-4

source_name: ovary from female fish exposed continuously to 0.5 ug 17beta-trenbolone per liter via water for 22 d

value: TRB 500

tag: gonadal somatic index (%)

tag: plasma testosterone (ng/ml)

tag: plasma vitellogenin (mg/ml)

tag: tubercle score


title: SAMPLE_99

source_name: Female_Young_Peripheral blood

value: Young


title: SAMPLE_100


title: fhm_F_ovary_MIX-5

tag: tissue

tag: ctid (sample id)

tag: plasma estradiol (ng/ml)

tag: ex vivo e2 production (ng/ml/12h)

tag: ex vivo t production (ng/ml/12h)


title: fhm_F_ovary_500 ng TRB per L-3

tag: treatment

value: not recorded


title: SAMPLE_100_CD4

tag: gender

tag: age (yr)

tag: agegroup


title: SAMPLE_101_CD8

tag: cell/tissue type


title: SAMPLE_100_CD8


title: fhm_F_ovary_CON-4

tag: date sampled

tag: rep (tank within treatment)

tag: time of day sampled


title: SAMPLE_99_CD4


title: SAMPLE_99_CD8


title: SAMPLE_96


title: SAMPLE_98_CD4


title: fhm_F_ovary_500 ng TRB per L-2

tag: FISH wet weight (g)

tag: gonad wet wt (g)

tag: gonadal somatic index (%)

tag: color


title: SAMPLE_98_CD8


title: fhm_F_ovary_CON-1

tag: tissue

tag: plasma testosterone (ng/ml)

tag: plasma vitellogenin (mg/ml)

tag: tubercle score


title: fhm_F_ovary_CON-3

tag: ctid (sample id)

tag: plasma estradiol (ng/ml)

tag: ex vivo e2 production (ng/ml/12h)

tag: ex vivo t production (ng/ml/12h)


title: fhm_F_ovary_500 ng TRB per L-1

tag: treatment

tag: notes

value: ovulating


title: SAMPLE_97_CD4

tag: gender

tag: age (yr)

tag: agegroup

tag: cell/tissue type


title: SAMPLE_95


title: SAMPLE_96_CD4


title: SAMPLE_97_CD8


title: SAMPLE_96_CD8


title: SAMPLE_95_CD8


title: SAMPLE_94_CD4


title: SAMPLE_3_CD4


title: SAMPLE_95_CD4


title: SAMPLE_93_CD8


title: SAMPLE_92_CD8

value: male


title: SAMPLE_93_CD4


title: SAMPLE_92

source_name: Male_Young_Peripheral blood


title: SAMPLE_94_CD8


title: SAMPLE_91_CD4


title: SAMPLE_98


title: SAMPLE_91_CD8


title: SAMPLE_91


title: fhm_F_ovary_CON-2

value: ovary

tag: date sampled

tag: rep (tank within treatment)

tag: time of day sampled

tag: FISH wet weight (g)

tag: gonad wet wt (g)


title: SAMPLE_90

source_name: Male_Old_Peripheral blood


title: SAMPLE_90_CD4


title: SAMPLE_90_CD8


title: SAMPLE_89


title: SAMPLE_89_CD4


title: SAMPLE_89_CD8


title: SAMPLE_88


title: SAMPLE_94


title: SAMPLE_88_CD4


title: SAMPLE_93


title: SAMPLE_92_CD4


title: SAMPLE_87_CD4


title: SAMPLE_88_CD8


title: SAMPLE_87


title: SAMPLE_86_CD4


title: SAMPLE_87_CD8


title: SAMPLE_85


title: SAMPLE_84_CD8


title: SAMPLE_86


title: SAMPLE_85_CD8


title: SAMPLE_83_CD8


title: SAMPLE_83


title: SAMPLE_82


title: SAMPLE_84


title: SAMPLE_83_CD4


title: SAMPLE_85_CD4


title: SAMPLE_80


title: SAMPLE_82_CD8


title: SAMPLE_81_CD8


title: SAMPLE_81_CD4


title: SAMPLE_80_CD4


title: SAMPLE_80_CD8


title: SAMPLE_79


title: SAMPLE_79_CD4


title: SAMPLE_79_CD8


title: SAMPLE_78


title: SAMPLE_78_CD4


title: SAMPLE_78_CD8


title: SAMPLE_86_CD8


title: SAMPLE_84_CD4


title: SAMPLE_77_CD4


title: SAMPLE_77_CD8


title: SAMPLE_76


title: SAMPLE_75


title: SAMPLE_75_CD8


title: SAMPLE_74


title: SAMPLE_75_CD4


title: SAMPLE_74_CD8


title: SAMPLE_74_CD4


title: SAMPLE_73_CD8


title: SAMPLE_73_CD4


title: SAMPLE_73


title: SAMPLE_72


title: SAMPLE_72_CD8


title: SAMPLE_72_CD4


title: SAMPLE_71_CD8


title: SAMPLE_70_CD8


title: SAMPLE_69


title: SAMPLE_70_CD4


title: SAMPLE_77


title: SAMPLE_71_CD4


title: SAMPLE_68


title: SAMPLE_70


title: SAMPLE_69_CD4


title: SAMPLE_68_CD4


title: SAMPLE_69_CD8


title: SAMPLE_76_CD8


title: SAMPLE_67


title: SAMPLE_68_CD8


title: SAMPLE_76_CD4


title: SAMPLE_67_CD4


title: SAMPLE_67_CD8


title: SAMPLE_66_CD8


title: SAMPLE_71


title: SAMPLE_66


title: SAMPLE_66_CD4


title: SAMPLE_65


title: SAMPLE_64


title: SAMPLE_64_CD8


title: SAMPLE_64_CD4


title: SAMPLE_63


title: SAMPLE_63_CD4


title: SAMPLE_63_CD8


title: SAMPLE_62


title: SAMPLE_62_CD8


title: SAMPLE_61


title: SAMPLE_61_CD4


title: SAMPLE_59


title: SAMPLE_60_CD4


title: SAMPLE_60_CD8


title: SAMPLE_61_CD8


title: SAMPLE_60


title: SAMPLE_59_CD8


title: SAMPLE_59_CD4


title: SAMPLE_58


title: fhm_F_ovary_1 ug TCC per L_-3

tag: tissue

tag: gonadal somatic index (%)

tag: plasma testosterone (ng/ml)

tag: plasma vitellogenin (mg/ml)


title: SAMPLE_65_CD8


title: SAMPLE_58_CD4


title: SAMPLE_57


title: SAMPLE_58_CD8


title: SAMPLE_65_CD4


title: SAMPLE_56_CD8


title: SAMPLE_57_CD8


title: SAMPLE_56_CD4


title: SAMPLE_56


title: SAMPLE_55


title: SAMPLE_54


title: SAMPLE_62_CD4


title: SAMPLE_55_CD8


title: SAMPLE_55_CD4


title: SAMPLE_54_CD4


title: SAMPLE_53


title: SAMPLE_53_CD4


title: SAMPLE_53_CD8


title: SAMPLE_52


title: SAMPLE_52_CD4


title: SAMPLE_51


title: SAMPLE_52_CD8


title: SAMPLE_57_CD4


title: SAMPLE_50_CD4


title: SAMPLE_50_CD8


title: SAMPLE_51_CD8


title: SAMPLE_51_CD4


title: SAMPLE_49


title: SAMPLE_49_CD4


title: SAMPLE_49_CD8


title: SAMPLE_47_CD4


title: SAMPLE_48_CD8


title: SAMPLE_48_CD4


title: SAMPLE_47_CD8


title: SAMPLE_47


title: SAMPLE_46


title: SAMPLE_46_CD8


title: SAMPLE_46_CD4


title: SAMPLE_45_CD8


title: SAMPLE_45_CD4


title: SAMPLE_54_CD8


title: SAMPLE_44


title: SAMPLE_44_CD8


title: SAMPLE_44_CD4


title: SAMPLE_43


title: SAMPLE_43_CD4


title: SAMPLE_43_CD8


title: SAMPLE_50


title: SAMPLE_42


title: SAMPLE_42_CD8


title: SAMPLE_42_CD4


title: SAMPLE_41


title: SAMPLE_41_CD4


title: SAMPLE_40_CD4


title: SAMPLE_40


title: SAMPLE_40_CD8


title: SAMPLE_39


title: SAMPLE_38


title: SAMPLE_39_CD4


title: SAMPLE_45


title: SAMPLE_38_CD4


title: SAMPLE_38_CD8


title: SAMPLE_39_CD8


title: SAMPLE_37


title: SAMPLE_37_CD8


title: SAMPLE_36


title: SAMPLE_35_CD4


title: SAMPLE_36_CD4


title: SAMPLE_34


title: SAMPLE_35


title: SAMPLE_36_CD8


title: SAMPLE_35_CD8


title: SAMPLE_33_CD4


title: SAMPLE_34_CD4


title: SAMPLE_33


title: SAMPLE_34_CD8


title: SAMPLE_32_CD4


title: SAMPLE_41_CD8


title: SAMPLE_33_CD8


title: SAMPLE_32_CD8


title: SAMPLE_31


title: SAMPLE_31_CD8


title: SAMPLE_31_CD4


title: SAMPLE_37_CD4


title: SAMPLE_27_CD4


title: SAMPLE_27_CD8


title: SAMPLE_26


title: SAMPLE_26_CD4


title: SAMPLE_26_CD8


title: SAMPLE_30


title: SAMPLE_29


title: SAMPLE_29_CD4


title: SAMPLE_28_CD8


title: SAMPLE_28


title: SAMPLE_30_CD8


title: SAMPLE_29_CD8


title: SAMPLE_27


title: SAMPLE_24


title: SAMPLE_25


title: SAMPLE_25_CD4


title: SAMPLE_22_CD4


title: SAMPLE_25_CD8


title: SAMPLE_22_CD8


title: SAMPLE_30_CD4


title: SAMPLE_23_CD8


title: SAMPLE_21_CD4


title: SAMPLE_24_CD8


title: SAMPLE_21


title: SAMPLE_23


title: SAMPLE_23_CD4


title: SAMPLE_22


title: SAMPLE_21_CD8


title: SAMPLE_28_CD4


title: SAMPLE_24_CD4


title: SAMPLE_20


title: SAMPLE_20_CD4


title: SAMPLE_19_CD4


title: SAMPLE_17_CD4


title: SAMPLE_16_CD4


title: SAMPLE_17_CD8


title: SAMPLE_16_CD8


title: SAMPLE_17


title: SAMPLE_12_CD4


title: SAMPLE_12_CD8


title: SAMPLE_18_CD8


title: SAMPLE_16


title: SAMPLE_11_CD4


title: SAMPLE_11


title: SAMPLE_15_CD4


title: SAMPLE_15_CD8


title: SAMPLE_14


title: SAMPLE_13_CD8


title: SAMPLE_14_CD8


title: SAMPLE_18_CD4


title: SAMPLE_14_CD4


title: SAMPLE_13


title: SAMPLE_15


title: SAMPLE_12


title: SAMPLE_19


title: SAMPLE_11_CD8


title: SAMPLE_18


title: SAMPLE_20_CD8


title: SAMPLE_19_CD8


title: SAMPLE_10


title: SAMPLE_10_CD8


title: SAMPLE_13_CD4


title: SAMPLE_9_CD4


title: SAMPLE_9


title: SAMPLE_8


title: SAMPLE_8_CD8


title: SAMPLE_6


title: SAMPLE_3_CD8


title: SAMPLE_5_CD4


title: SAMPLE_7


title: SAMPLE_2_CD4


title: SAMPLE_4


title: SAMPLE_6_CD4


title: SAMPLE_7_CD8


title: SAMPLE_6_CD8


title: SAMPLE_5_CD8


title: SAMPLE_1_CD4


title: SAMPLE_5


title: SAMPLE_2


title: SAMPLE_1


title: SAMPLE_4_CD8


title: SAMPLE_2_CD8


title: lung_H1838_cell_line_lung_adenocarcinoma

status: Public on May 28 2015

type: SRA

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

department: Pathology

institute: University of Michigan

description:
Sample name: MCTP_SAMPLE_154
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence alignment was performed using the Tuxedo pipeline: Bowtie2 (Bowtie2/2.0.2) and Tophat2 (TopHat/2.0.4)(Kim et al., 2013). We supplied TopHat with the set of transcript models annotated in the Homo sapiens Ensembl database version 69. The option fr-firststrand was used for the strand specific RNA-seq libraries while all other parameters were used with default values. When provided with ssRNA-seq data TopHat2 annotates aligned reads with the tag XS indicating the strand of origin in the DNA.
We used Ensembl v69 as the reference transcriptome to reconstruct the longest annotation for each gene based on the transcript and exon information provided by this assembly. We only included transcript isoforms that satisfied the following criteria: gene and transcript biotypes were annotated with the same type; transcript isoform annotation level was manual or automatic followed by manual revision (annotation levels 1 or 2) and transcript isoform was not reported as a problematic in the Encode-Gencode attributes table (e.g: transcript biotype is retained_intron, to be experimentally confirmed, or disruptive_domain).  Moreover, each transcript isoform used for our gene models was annotated with their “isoform expression rank” across the tissue cohorts, and their support level (tsl) provided by the Genecode project. Tsl equal to 1 indicates that all splice junctions of that transcript are supported by at least one non-suspect mRNA; any other number suggests that the transcript is supported by suspicious ESTs. These final gene models were used as the reference loci, or features, for downstream analysis.
The final gene models in the summarized transcriptome were used to compute strand specific expression. Paired-end reads mapping to the forward or opposite strand of a feature were counted in order to quantify the raw amount of forward and opposite transcription on a particular locus.  In order to determine what DNA strand a read pair was originated from, we first used the reads’ XS tag, provided by TopHat2, to identify the strand for each read in the pair. Then, we use the fact that in our ssRNA-seq protocol the second read is complementary to original mRNA and therefore the second read has to be on the same strand than the feature, while the first read on the opposite strand. These criteria unambiguously define a read pair DNA strand of origin. We discard all pairs in which one or both reads map to multiple locations in the genome, and all read pairs in which any of the reads was improperly mapped or did not have the XS flag provided by TopHat2 to indicate the strand of origin.
Genome_build: hg19
Supplementary_files_format_and_content: Feature (e.g. gene) raw read count over sense and antisense strands. Processed data files linked to SuperSeries record.

extract_protocol:
Total RNA from frozen tissues or cell lines were isolated using miRNeasy mini kit (Qiagen Valencia, CA) while RNA was isolated from FFPE sections using FFPE RNAeasy kit (Qiagen).  For RNA from frozen sections and cell lines only samples with RNA integrity number (RIN) >8.0, upon 2100 Bioanalyzer analysis (Agilent Santa Clara, CA) were subjected to RNA sequencing.
Transcriptome libraries were prepared following a modified protocol previously described for generating strand specific RNASeq libraries 8.  Briefly 2.5 μg of total RNA was subjected to polyA selection using oligodT beads (Invitrogen, Carlsbad, CA).  Purified polyA RNA was fragmented and reverse transcribed using Superscipt-II (Invitrogen, Carlsbad CA).  Second strand synthesis was performed with DNA Ploymerase I (New England Biolabs, Ipswich, MA) in the presence of dNTP mix containing dUTP instead of dTTP.  The product was then subjected to end repair, A base addition and adaptor ligation steps.  Libraries were next size selected in the range of 350 bps after resolving in a 3% Nusieve 3:1 (Lonza, Basel, Switzerland) agarose gel and DNA recovered using QIAEX II gel extraction reagent (Qiagen, Valencia, CA). Libraries were barcoded during the 14-cycle PCR amplification with Phusion DNA polymerase (New England Biolabs, Ipswich, MA) and purified using AMPure XP beads (Beckman Coulter, Brea, CA).

tag: age

value: not collected

value: MCTP

value: lung

tag: disease

value: cancer

value: LUCL


title: lung_H1975_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_155
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_A427_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_85
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: SAMPLE_10_CD4


title: SAMPLE_8_CD4


title: SAMPLE_9_CD8


title: lung_A549_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_89
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: SAMPLE_3


title: SAMPLE_7_CD4


title: lung_SKMES1_cell_line_lung_squamous_carcinoma

description:
Sample name: MCTP_SAMPLE_218
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Normal_Prostate_HSPH0249

status: Public on Dec 01 2014

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

source_name: FFPE normal prostate

label_protocol: Not provided

extract_protocol: Not provided


title: Normal_Prostate_HSPH0256


title: Normal_Prostate_HSPH0264


title: Normal_Prostate_HSPH0232


title: Normal_Prostate_HSPH0259


title: Normal_Prostate_HSPH0263


title: Normal_Prostate_HSPH0251


title: Normal_Prostate_HSPH0248


title: Normal_Prostate_HSPH0247


title: Normal_Prostate_HSPH0262


title: Normal_Prostate_HSPH0229


title: Normal_Prostate_HSPH0219


title: Normal_Prostate_HSPH0254


title: Normal_Prostate_HSPH0238


title: Normal_Prostate_HSPH0218


title: Normal_Prostate_HSPH0244


title: Normal_Prostate_HSPH0255


title: Normal_Prostate_HSPH0240


title: Normal_Prostate_HSPH0217


title: Normal_Prostate_HSPH0216


title: Normal_Prostate_HSPH0245


title: Normal_Prostate_HSPH0214


title: Normal_Prostate_HSPH0260


title: Normal_Prostate_HSPH0212


title: Normal_Prostate_HSPH0246


title: Normal_Prostate_HSPH0211


title: Normal_Prostate_HSPH0220


title: Normal_Prostate_HSPH0210


title: Normal_Prostate_HSPH0234


title: Normal_Prostate_HSPH0213


title: Normal_Prostate_HSPH0194


title: Normal_Prostate_HSPH0192


title: Normal_Prostate_HSPH0203


title: Normal_Prostate_HSPH0199


title: Normal_Prostate_HSPH0207


title: Normal_Prostate_HSPH0185


title: Normal_Prostate_HSPH0164


title: Normal_Prostate_HSPH0176


title: Normal_Prostate_HSPH0206


title: Normal_Prostate_HSPH0186


title: Normal_Prostate_HSPH0179


title: Normal_Prostate_HSPH0208


title: Normal_Prostate_HSPH0178


title: Normal_Prostate_HSPH0165


title: Normal_Prostate_HSPH0190


title: Normal_Prostate_HSPH0172


title: Normal_Prostate_HSPH0169


title: Normal_Prostate_HSPH0181


title: Normal_Prostate_HSPH0157


title: Normal_Prostate_HSPH0163


title: Normal_Prostate_HSPH0177


title: Normal_Prostate_HSPH0170


title: Normal_Prostate_HSPH0187


title: Normal_Prostate_HSPH0180


title: Normal_Prostate_HSPH0161


title: Normal_Prostate_HSPH0159


title: Normal_Prostate_HSPH0175


title: Normal_Prostate_HSPH0166


title: Normal_Prostate_HSPH0155


title: Normal_Prostate_HSPH0151


title: Normal_Prostate_HSPH0148


title: Normal_Prostate_HSPH0152


title: Normal_Prostate_HSPH0144


title: Normal_Prostate_HSPH0130


title: Normal_Prostate_HSPH0149


title: Normal_Prostate_HSPH0136


title: Normal_Prostate_HSPH0133


title: Normal_Prostate_HSPH0141


title: Normal_Prostate_HSPH0116


title: Normal_Prostate_HSPH0139


title: Normal_Prostate_HSPH0138


title: Normal_Prostate_HSPH0146


title: Normal_Prostate_HSPH0135


title: Normal_Prostate_HSPH0125


title: Normal_Prostate_HSPH0134


title: Normal_Prostate_HSPH0114


title: Normal_Prostate_HSPH0122


title: Normal_Prostate_HSPH0121


title: Normal_Prostate_HSPH0137


title: Normal_Prostate_HSPH0120


title: Normal_Prostate_HSPH0113


title: Normal_Prostate_HSPH0129


title: Normal_Prostate_HSPH0115


title: Normal_Prostate_HSPH0142


title: Normal_Prostate_HSPH0112


title: Normal_Prostate_HSPH0111


title: Normal_Prostate_HSPH0110


title: Normal_Prostate_HSPH0119


title: Normal_Prostate_HSPH0098


title: Normal_Prostate_HSPH0109


title: Normal_Prostate_HSPH0106


title: Normal_Prostate_HSPH0093


title: Normal_Prostate_HSPH0073


title: Normal_Prostate_HSPH0087


title: Normal_Prostate_HSPH0099


title: Normal_Prostate_HSPH0107


title: Normal_Prostate_HSPH0075


title: Normal_Prostate_HSPH0072


title: Normal_Prostate_HSPH0080


title: Normal_Prostate_HSPH0081


title: Normal_Prostate_HSPH0092


title: Normal_Prostate_HSPH0096


title: Normal_Prostate_HSPH0066


title: Normal_Prostate_HSPH0065


title: Normal_Prostate_HSPH0079


title: Normal_Prostate_HSPH0102


title: Normal_Prostate_HSPH0064


title: Normal_Prostate_HSPH0105


title: Normal_Prostate_HSPH0067


title: Normal_Prostate_HSPH0100


title: Normal_Prostate_HSPH0104


title: Normal_Prostate_HSPH0088


title: Normal_Prostate_HSPH0071


title: Normal_Prostate_HSPH0069


title: Normal_Prostate_HSPH0070


title: Normal_Prostate_HSPH0063


title: Normal_Prostate_HSPH0103


title: Normal_Prostate_HSPH0062


title: Normal_Prostate_HSPH0058


title: Normal_Prostate_HSPH0060


title: Normal_Prostate_HSPH0057


title: Normal_Prostate_HSPH0044


title: Normal_Prostate_HSPH0059


title: Normal_Prostate_HSPH0049


title: Normal_Prostate_HSPH0047


title: Normal_Prostate_HSPH0053


title: Normal_Prostate_HSPH0050


title: Normal_Prostate_HSPH0023


title: Normal_Prostate_HSPH0032


title: Normal_Prostate_HSPH0046


title: Normal_Prostate_HSPH0035


title: Normal_Prostate_HSPH0025


title: Normal_Prostate_HSPH0012


title: Normal_Prostate_HSPH0019


title: Normal_Prostate_HSPH0052


title: Normal_Prostate_HSPH0016


title: Normal_Prostate_HSPH0036


title: Normal_Prostate_HSPH0017


title: Normal_Prostate_HSPH0022


title: Normal_Prostate_HSPH0171


title: Normal_Prostate_HSPH0030


title: Normal_Prostate_HSPH0039


title: Normal_Prostate_HSPH0043


title: Normal_Prostate_HSPH0037


title: Normal_Prostate_HSPH0051


title: Normal_Prostate_HSPH0009


title: Normal_Prostate_HSPH0006


title: Normal_Prostate_HSPH0020


title: Normal_Prostate_HSPH0004


title: Prostate_Tumor_HSPH0264

source_name: FFPE prostate tumor


title: Prostate_Tumor_HSPH0257


title: Prostate_Tumor_HSPH0253


title: Prostate_Tumor_HSPH0262


title: Prostate_Tumor_HSPH0255


title: Prostate_Tumor_HSPH0259


title: Prostate_Tumor_HSPH0248


title: Prostate_Tumor_HSPH0258


title: Prostate_Tumor_HSPH0251


title: Prostate_Tumor_HSPH0254


title: Prostate_Tumor_HSPH0252


title: Prostate_Tumor_HSPH0244


title: Prostate_Tumor_HSPH0249


title: Prostate_Tumor_HSPH0245


title: Prostate_Tumor_HSPH0240


title: Prostate_Tumor_HSPH0246


title: Prostate_Tumor_HSPH0243


title: Normal_Prostate_HSPH0008


title: Normal_Prostate_HSPH0001


title: Prostate_Tumor_HSPH0241


title: Prostate_Tumor_HSPH0263


title: Prostate_Tumor_HSPH0242


title: Prostate_Tumor_HSPH0250


title: Prostate_Tumor_HSPH0256


title: Prostate_Tumor_HSPH0239


title: Prostate_Tumor_HSPH0247


title: Prostate_Tumor_HSPH0237


title: Prostate_Tumor_HSPH0236


title: Prostate_Tumor_HSPH0235


title: Prostate_Tumor_HSPH0229


title: Prostate_Tumor_HSPH0228


title: Prostate_Tumor_HSPH0233


title: Prostate_Tumor_HSPH0238


title: Prostate_Tumor_HSPH0224


title: Prostate_Tumor_HSPH0232


title: Prostate_Tumor_HSPH0221


title: Prostate_Tumor_HSPH0230


title: Prostate_Tumor_HSPH0219


title: Prostate_Tumor_HSPH0260


title: Prostate_Tumor_HSPH0226


title: Prostate_Tumor_HSPH0234


title: Prostate_Tumor_HSPH0223