title: Uterus_I

city: Tokyo

first: Fuyuki

description: uterus Human Tiling 1.0R chip I

data_processing:
The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.

source_name: pooled Human uterus total RNA

value: uterus


title: Male 8week AJ sham rep1

status: Public on Dec 31 2013

type: RNA

city: Baltimore

first: Susan

middle: G

last: Dorsey

state: MD

address: 655 West Lombard Street

department: School of Nursing

country: USA

institute: University of Maryland Baltimore

description: Gene expression data from jejunum

hyb_protocol: 10ug of cRNA were hybridized for 16 hours at 45degrees on Mouse Gene 1.0 ST Arrays.

scan_protocol: Scanned on an Affymetrix scanner.

data_processing: The data were normalized by Affymetrix Expression Console using RMA method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: AJSHAM

label_protocol: Biotinylated cRNA was prepared per standard Affymetrix protocol from 1ug total RNA.

growth_protocol: 7 days following CBDL or sham surgery, the animals were euthanized and the jejunum was harvested under sterile conditions.

extract_protocol: Trizol extraction of total RNA performed per manufacturer instructions.

treatment_protocol: Either CBDL surgery or sham surgery.

tag: strain/background

value: A/J

tag: tissue

value: jejunum

tag: gender

value: male

tag: age

value: 8 weeks

tag: treatment

value: sham surgery


title: MLN1

city: Barcelona

first: Alba

last: Dalmases

address: Dr.Aiguader 88

country: Spain

institute: IMIM

description: Gene expression data from MDA-MB-231 breast cancer cell line

hyb_protocol: Sample was hybridized to Affymetrix Human Exon 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

organism: Homo sapiens

source_name: Total RNA from MDA-MB-231 breast cancer cell line

label_protocol: 100ng of total RNA from each sample, isolated from MDA-MB-231 breast cancer cells under different experimental conditions was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

extract_protocol: RNA was extracted following Qiagen protocol

value: MLN

tag: cell line


title: 100µM VX 1hr cardiomyocyte replicate 1

city: Aberdeen Proving Ground

first: E Chepchumba

middle: K

last: Yego

address: 3100 Ricketts Point Road

department: Research

institute: US Army Medical Research Institute of Chemical Defense

description: Cells maintained in humidified incubator at 37 degres C during treatment

hyb_protocol: Labelled RNA was hybridized for 16 hrs at 48 degrees C on miRNA 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_0003

scan_protocol: GeneChips were scanned using Affymetrix 7G GeneChip Scanner using Affymetrix GeneChip Command Console Scan Control 3.1.01228 (Affymetrix 2009)

data_processing: Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

source_name: Cardiomyocyte 100uM VX treatment for 1hr

label_protocol: 500ng total RNA was labeled using the RNA biotin labeling flashtag biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA) as per manufacturer’s instructions

growth_protocol: iPSC-derived cardiomyocytes (Cellular Dynamics, WI) were seeded at a density of 1.0 X10E6 per well in 6-well plates and maintained according to manufucturer's specifications

extract_protocol: Following treatment, cells were gently rinsed five times with hanks buffered salt solution. Total RNA was isolated from exposed and control cells using miRNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: One week after plating cells were treated with VX  or saline control

tag: cell type

value: iPSC-deived Cardiomyocyte

value: 100µM VX

tag: time


title: MLN_Dox2

value: MLN + Dox


title: 0.1µM VX 1hr cardiomyocyte replicate 1

source_name: Cardiomyocyte 0.1uM VX treatment for 1hr

value: 0.1µM VX


title: Male 8week BL6 CBDLrep1

description: Gene expression data from jejunum

value: cholestatic intestinal injury


title: MLN_Dox1


title: 0.1µM VX 1hr cardiomyocyte replicate 4


title: 0.1µM VX 6hr cardiomyocyte replicate 2

source_name: Cardiomyocyte 0.1uM VX treatment for 6hr


title: 0.1µM VX 6hr cardiomyocyte replicate 1


title: 0µM VX 6hr cardiomyocyte replicate 2

source_name: Cardiomyocyte saline treatment for 6hr

value: 0µM VX


title: Control2

value: Control


title: 0.1µM VX 6hr cardiomyocyte replicate 4


title: Male 8week AJ sham rep3

description: Gene expression data from jejunum


title: 0µM VX 1hr cardiomyocyte replicate 3

source_name: Cardiomyocyte saline treatment for 1hr


title: 0.1µM VX 1hr cardiomyocyte replicate 2


title: 0µM VX 6hr cardiomyocyte replicate 3


title: 0µM VX 1hr cardiomyocyte replicate 4


title: MLN2


title: Dox3

value: Dox


title: Control3


title: 100µM GD 6hr cardiomyocyte replicate 4

source_name: Cardiomyocyte 100uM GD treatment for 6hr

treatment_protocol: One week after plating cells were treated with GD or saline control

value: 100µM GD


title: 0µM VX 6hr cardiomyocyte replicate 1


title: 0.1µM VX 1hr cardiomyocyte replicate 3


title: 0µM VX 1hr cardiomyocyte replicate 1


title: MLN_Dox3


title: Male 8week BL6 CBDLrep3

description: Gene expression data from jejunum


title: Control1


title: Dox1


title: Dox2


title: 0µM VX 1hr cardiomyocyte replicate 2


title: UAS-Mdr65-RNAi, whole brain, rep3

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

institute: UC San Francisco

description:
UAS_control_3
4 brains total containing both male and female flies
amplified total RNA

hyb_protocol: The entire fragmented, labeled cDNA fraction was placed into a hyb cocktail volume of 150uL; 130uL were hybridized for 18-20 hr at 45C on GeneChip Drosophila Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: Using the R package affy, raw data was processed using RMA. P/M/A calls were extracted using affy, and probes were kept for statistical analyses if greater than 50% of replicates in at least one sample were called present. Of the 18,952 total probes, 13,290 were used for statistical analyses. Differentially expressed genes were determined using the R package limma with an FDR-adjusted p-value of 0.05 as the cutoff for determining statistical significance. Given the presence of batch effects and genetic background effects, we took the lists of differentially expressed genes for WT_new/C17 and WT_new/PMdr65 and subtracted genes that also showed up in the lists of differentially expressed genes between WT_new/WT_old and WT_new/UAS_control.

organism: Drosophila melanogaster

source_name: Drosophila adult_UAS-Mdr65-RNAi, whole brain

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module kit from 3.5ug amplified RNA.

growth_protocol: All flies were raised and maintained on standard cornmeal molasses agar at 16˚C or room temperature.

extract_protocol: RNA was isolated using Ambion RNAqueous Micro columns and amplified using the NuGEN Ovation FFPE WTA System V3.

treatment_protocol: Brains were dissected under PBS and transferred directly to a chilled tube containing RNA lysis buffer.

value: female and male

tag: developmental stage

value: adult

tag: genotype/variation

value: brain


title: UAS-Mdr65-RNAi, whole brain, rep2

description:
UAS_control_2
4 brains total containing both male and female flies
amplified total RNA


title: OVCAR-3_exp3

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data were analysed using BeadStudio version 1.5.1.3;  rank invariant normalization was performed

label: Biotin

label_protocol: Biotilinated cRNA were prepared with the Ambion messageAmp for Illumina array

extract_protocol: Total RNA was extracted after 12 or 24 hours using the SV total RNA Isolation System (Promega,USA).

treatment_protocol: Exponentially growing cells were cultured for 48 hours in the presence of pure recombinant HGF at the concentration of 50 ng/mL or control medium. Apoptosis was then induced by adding fresh medium, with or without HGF, supplemented with 10 microM cisplatin

tag: ovarian cancer cell line

tag: agent

value: untreated


title: 0µM VX 6hr cardiomyocyte replicate 4


title: 100µM GD 1hr cardiomyocyte replicate 3

source_name: Cardiomyocyte 100uM GD treatment for 1hr


title: TOV21-G  treated with HGF and CDDP_exp2

description: TOV-21G_48h hgf_24h CDDP_exp2

source_name: TOV-21G_48h hgf_24h CDDP

value: HGF CDDP


title: OVCAR-3 treated with HGF and CDDP_exp2

description: OVCAR-3_48h hgf_24h CDDP_exp2

source_name: OVCAR-3_48h hgf_24h CDDP


title: OVCAR-3 treated with HGF and CDDP_exp1

description: OVCAR-3_48h hgf_24h CDDP_exp1


title: OVCAR-3_exp2


title: OVCAR-3_exp1


title: PMdr65, Mdr65 null, whole brain, rep2

description:
PMdr65_2
4 brains total containing both male and female flies
amplified total RNA

source_name: Drosophila adult_PMdr65, Mdr65 null, whole brain

value: PMdr65 (Mdr65 null)


title: Male 8week BL6 CBDLrep2

description: Gene expression data from jejunum

value: jejunum

value: male

value: 8 weeks


title: SK-OV-3 treated with HGF and CDDP_exp3

description: SK-OV-3_48h hgf_24h CDDP_exp3

source_name: SK-OV-3_48h hgf_24h CDDP


title: 100µM GD 1hr cardiomyocyte replicate 4

value: iPSC-deived Cardiomyocyte


title: TOV21-G  treated with HGF and CDDP_exp1

description: TOV-21G_48h hgf_24h CDDP_exp1


title: SK-OV-3 cells expressing Dominant Negative-p38MAPK treated with HGF and CDDP_exp2

description: SK-OV-3 p38DN_48h hgf_24h CDDP_exp2

source_name: SK-OV-3 p38DN_48h hgf_24h CDDP

value: SK-OV-3 p38DN


title: Smarcb1 deficient p53 null cancer cell line 365 - Smarcb1

city: jerusalem

first: jonatan

last: darr

address: mavo qidda

department: cellulal and developmental biology

country: Israel

institute: huji

description: Expression profiling of a Smarcb1 deficient cancer cell line, 365 derived from a p53 null Smarcb1 heterozygot mouse, infected with a retroviral vector for the re-expression of Smarcb1

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit, according to  manufacturer's instructions. Washing and Staining on Fluidics Station 450 with protocol “FS450_0007”

scan_protocol: Scanning was performed with GeneChip® Scanner 3000 7G controlled by GeneChip® Operating Software (GCOS)

data_processing: Raw probe intensities were normalized by the robust multiarray average (RMA) method using the Affymetrix expression console program.

source_name: soft tissue, MRT, 3 D.P.I Smracb1 expression vector

label_protocol: GeneChip® Whole Transcript (WT) Sense Target Labeling Assay was employed in accordance with the  manufacturer's instructions

growth_protocol: DMEM supplemented with 10% Hyclone fetal bovine serum (FBS), penicillin (50 mg/ml), streptomycin (50 mg/ml), 2 mM L-Glutamine, 0.1 nM non essential amino acids, 0.1 mM β-Mercaptoethanol and 1 mM sodium pyruvate

extract_protocol: 3 days post infection total RNA was extracted using the RNA Qiagen RNeasy mini kit for purification of total RNA from animal cells using spin technology, and in accordance with the manufacturer's instructions

treatment_protocol: Cells were infected with the pMIG retroviral vector for stable re-expression of Smarcb1 or with an empty pMiG vector as control

value: Smarcb1 deficient soft tissue tumor

value: deficient

value: re-expression

value: cancer cell line 365

tag: genotype

value: Smarcb1 deficient p53 null

tag: transfection

tag: genetic background


title: TOV-21G_exp1


title: TOV-21G_exp2


title: 100µM GD 1hr cardiomyocyte replicate 1

value: 100µM GD


title: SK-OV-3 cells expressing Dominant Negative-p38MAPK_exp2

description: SK-OV-3 p38DN_exp2

source_name: SK-OV-3 p38DN


title: 100µM GD 1hr cardiomyocyte replicate 2


title: SK-OV-3 cells expressing Dominant Negative-p38MAPK_exp1

description: SK-OV-3 p38DN_exp1


title: 100µM GD 6hr cardiomyocyte replicate 1


title: SK-OV-3 cells expressing Dominant Negative-p38MAPK treated with HGF and CDDP_exp1

description: SK-OV-3 p38DN_48h hgf_24h CDDP_exp1


title: 100µM GD 6hr cardiomyocyte replicate 3


title: PMdr65, Mdr65 null, whole brain, rep1

description:
PMdr65_1
4 brains total containing both male and female flies
amplified total RNA

value: female and male


title: PMdr65, Mdr65 null, whole brain, rep3

description:
PMdr65_3
4 brains total containing both male and female flies
amplified total RNA

value: adult


title: OVCAR-3 treated with HGF and CDDP_exp3

description: OVCAR-3_48h hgf_24h CDDP_exp3


title: UAS-Mdr65-RNAi, whole brain, rep1

description:
UAS_control_1
4 brains total containing both male and female flies
amplified total RNA

value: brain


title: Canton S, wildtype, whole brain, old rep3

description:
WT_old_3
4 brains total containing both male and female flies
amplified total RNA

source_name: Drosophila adult_Canton S, wildtype, whole brain, old

value: Canton S


title: Smarcb1 deficient p53 null cancer cell line 365 - empty vector

description: Expression profiling of a Smarcb1 deficient cancer cell line, 365 derived from a p53 null Smarcb1 heterozygot mouse, infected with an empty retroviral vector as control

source_name: soft tissue, MRT, 3 D.P.I Empty vector

value: empty vector


title: 0.1µM GD 6hr cardiomyocyte replicate 4

source_name: Cardiomyocyte 0.1uM GD treatment for 6hr

value: 0.1µM GD


title: 100µM GD 6hr cardiomyocyte replicate 2


title: Canton S, wildtype, whole brain, old rep5

description:
WT_old_5
4 brains total containing both male and female flies
amplified total RNA


title: Canton S, wildtype, whole brain, old rep2

description:
WT_old_2
4 brains total containing both male and female flies
amplified total RNA


title: Canton S, wildtype, whole brain, old rep4

description:
WT_old_4
4 brains total containing both male and female flies
amplified total RNA


title: Smarcb1 deficient p53 null cancer cell line 167 - Smarcb1

description: Expression profiling of a Smarcb1 deficient cancer cell line 167, derived from a p53 null Smarcb1 heterozygot mouse, infected with a retroviral vector for the re-expression of Smarcb1

value: cancer cell line 167


title: 0.1µM GD 1hr cardiomyocyte replicate 4

source_name: Cardiomyocyte 0.1uM GD treatment for 1hr


title: SK-OV-3_exp1

value: untreated


title: SK-OV-3_exp2


title: 0.1µM GD 6hr cardiomyocyte replicate 2


title: Mammary Gland-rtTA/Cyclin D1-KE mutant Rep3

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Mouse Gene 1.0 ST arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).  For the Mouse 430A v2.0 arrays, 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Affymetrix Expression Console 1.1 was used to compute Robust Multichip average (RMA) expression values.  For the Mouse Gene 1.0 ST microarrays. The core set of probe set clusters was used with annotation version na30, dated December 2009. The dataset was imported into Matlab version R2010b (The Mathworks, Natick, MA) and one-way ANOVA was used to evaluate the significance of differential expression between biological conditions. Genes with differential expression p-value ≤ 0.01 and absolute fold change ≥ 1.25 were clustered and visualized using a clustergram heatmap.

source_name: Mouse Mammary gland 8 week old females

label_protocol: Labeling for Mouse Gene 1.0 ST arrays was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.).   For 430A v2.0 arrays, the double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA.Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: rtTA/CCND1 KE mutant samples underwent 7 days of doxycycline treatment

tag: strain

value: FvB/N

value: mammary gland

tag: transgenic mouse

value: rtTA/CCND1 KE mutant


title: SK-OV-3_exp3


title: Canton S, wildtype, whole brain, new, rep3

description:
WT_new_3
4 brains total containing both male and female flies
amplified total RNA

source_name: Drosophila adult_Canton S, wildtype, whole brain, new


title: Mammary Gland-rtTA/Cyclin D1-KE mutant Rep1


title: Canton S, wildtype, whole brain, old rep1

description:
WT_old_1
4 brains total containing both male and female flies
amplified total RNA


title: 0.1µM GD 1hr cardiomyocyte replicate 2

value: iPSC-deived Cardiomyocyte


title: PBMC Acute IM Subj 5524 (Ref8)

city: Minneapolis

first: Samantha

last: Dunmire

state: MN

address: 2101 6th St SE

institute: University of Minnesota

hyb_protocol: cRNA was hybridized at 58C for 20 hours

scan_protocol: Chip was scanned with an Illumina 500GX scanner and data were exported through BeadStudio v1 (Illumina)

data_processing: The data were analyzed with GeneSpring GX11

source_name: Peripheral blood

label_protocol: Microarray probes were produced with the Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted using RNeasy Mini columns (Qiagen)

treatment_protocol: None.  Blood was collected from volunteers in EDTA tubes.  PBMC were isolated and frozen prior to RNA extraction.

tag: sample time

value: during acute infectious mononucleosis


title: 0.1µM GD 6hr cardiomyocyte replicate 3


title: Smarcb1 deficient p53 null cancer cell line 167 - empty vector

description: Expression profiling of a Smarcb1 deficient cancer cell line 167, derived from a p53 null Smarcb1 heterozygot mouse, infected with an empty retroviral vector as control

tag: tissue

value: Smarcb1 deficient soft tissue tumor

value: deficient


title: 0.1µM GD 6hr cardiomyocyte replicate 1

description: Cells maintained in humidified incubator at 37 degres C during treatment


title: 0.1µM GD 1hr cardiomyocyte replicate 3


title: Mammary Gland-rtTA/Cyclin D1-KE mutant Rep2


title: Canton S, wildtype, whole brain, new, rep2

description:
WT_new_2
4 brains total containing both male and female flies
amplified total RNA

tag: gender


title: PBMC Seronegative Subj 5524 (Ref8)

value: before EBV acquisition


title: SK-OV-3 treated with HGF and CDDP_exp1

description: SK-OV-3_48h hgf_24h CDDP_exp1

value: HGF CDDP


title: 0.1µM GD 1hr cardiomyocyte replicate 1


title: PBMC Acute IM Subj 5509 (Ref8)


title: Canton S, wildtype, whole brain, new, rep1

description:
WT_new_1
4 brains total containing both male and female flies
amplified total RNA

value: female and male


title: Ikbkap KO P15, rep3

city: Boston

first: Fu-Jung

last: Lin

state: MA

address: 200 Longwood Ave.

institute: Harvard Medical School

hyb_protocol: Hybridization to the Affymetrix MoGene-1_0-st-v1 array was carried out by the Functional Genomics Core Facility in UNC-CH using the standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by the Functional Genomics Core Facility in UNC-CH using the standard protocol.

data_processing: Primary analysis was carried out by the Functional Genomics Core Facility in UNC-CH using Affymetrix Expression Console software and RMA normalization.

source_name: Ikbkap KO P15 testes

label_protocol: Biotin labeling was carried out by the Functional Genomics Core Facility in UNC-CH using GeneChip WT Sense Target Labeling and Control Reagents and the standard protocol.

growth_protocol: Mouse testes were dissected from postnatal day 15 pups.

extract_protocol: Total RNA was extracted from control and Ikbkap-knockout testes using Trizol (Invitrogen), and RNA was purified with an RNeasy mini kit (QIAGEN) following manufacturer's instructions.

treatment_protocol: Not applicable.

value: Ikbkap knockout

value: testes

tag: age


title: 0µM GD 6hr cardiomyocyte replicate 4

source_name: Cardiomyocyte saline treatment for 6hr

tag: treatment

value: 0µM GD


title: C17, Moody null, whole brain, rep3

description:
C17_3
4 brains total containing both male and female flies
amplified total RNA

source_name: Drosophila adult_C17, Moody null, whole brain

value: adult

value: C17 (Moody null)

value: brain


title: SK-OV-3 treated with HGF and CDDP_exp2

description: SK-OV-3_48h hgf_24h CDDP_exp2


title: PBMC Acute IM Subj 5483 (Ref8)


title: PBMC Seronegative Subj 5509 (Ref8)


title: 0µM GD 6hr cardiomyocyte replicate 3


title: C17, Moody null, whole brain, rep2

description:
C17_2
4 brains total containing both male and female flies
amplified total RNA


title: Ikbkap KO P15, rep1


title: 0µM GD 6hr cardiomyocyte replicate 2


title: Ikbkap KO P15, rep2


title: Control P15, rep3

source_name: control P15 testes

value: control


title: PBMC Seronegative Subj 5483 (Ref8)


title: PBMC Seronegative Subj 5342 (Ref8)


title: C17, Moody null, whole brain, rep1

description:
C17_1
4 brains total containing both male and female flies
amplified total RNA


title: 0µM GD 1hr cardiomyocyte replicate 4

source_name: Cardiomyocyte saline treatment for 1hr


title: Control P15, rep2


title: Control P15, rep1


title: 0µM GD 6hr cardiomyocyte replicate 1


title: 0µM GD 1hr cardiomyocyte replicate 2


title: hdac1/2 dko lung, biological rep3

city: Philadelphia

first: Yi

last: Wang

address: 3400 Civic Center Boulevard, Bldg 421

institute: University of Pennsylvania

description: 4077_33261_Mut3 _MoGene1.1ST

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

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

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: Mouse embryonic lung at E11.5

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

growth_protocol: Timely matings were set up to obtain E11.5 embryos

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: Lung buds were disected from E11.5 embryos with appropriate genotypes and stored in RNAlater for future RNA extraction

value: Lung

value: Shhcre:Hdac1fl/fl; Hdac2 fl/fl


title: PBMC Seronegative Subj 5324 (Ref8)


title: sage overexpression_rep1

first: Deborah

middle: J

last: Andrew

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

hyb_protocol: Samples and controls were prepared using the Affymetrix GeneChip hybridization, wash and stain kit (P/N 900720). Arrays were prehybridized for 10 minutes prior to sample addition. Following sample addition, arrays were hybridized for 16 hours at 45 Celsius, and shaken at 60 rpm. Arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_002 fluidics script.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 and raw analysis was performed with Affymetrix Command Console and Expression Console.

data_processing: Data was normalized by RMA and statistical analysis was performed using Partek software. Further analysis was performed using Spotfire software.

source_name: Drosophila embryos

label_protocol: Amplification and labeling were performed using the Affymetrix GeneChip3' IVT express kit (P/N 901229) following the manufacturer's protocol.

growth_protocol: Embryos were collected and aged at 25 C.

extract_protocol: RNA was isolated by TriZol extraction and cleaned up using the Qiagen Rneasy kit.

treatment_protocol: Embryos were sorted on a COPAS biosorter prior to RNA extraction.

value: embryonic stages 11-16

value: sage overexpressed tub-Gal4


title: hdac1/2 dko lung, biological rep2

description: 4077_33260_Mut2 _MoGene1.1ST


title: sage overexpression_rep3


title: PBMC Acute IM Subj 5324 (Ref8)

value: during acute infectious mononucleosis


title: 0µM GD 1hr cardiomyocyte replicate 3

value: iPSC-deived Cardiomyocyte


title: PBMC Acute IM Subj 5342 (Ref8)


title: shhcre control lung, biological rep 3

description: 4077_33258_Ctrl3 _MoGene1.1ST

value: Shhcre


title: hdac1/2 dko lung, biological rep1

description: 4077_33259_Mut1 _MoGene1.1ST


title: sage overexpression_rep2


title: shhcre control lung, biological rep 2

description: 4077_33257_Ctrl2 _MoGene1.1ST


title: tubGal4_control_3


title: 0µM GD 1hr cardiomyocyte replicate 1


title: tubGal4_control_2


title: PBMC Seronegative Subj 5088 (Ref8)

value: before EBV acquisition


title: PBMC Acute IM Subj 5036 (Ref8)


title: PBMC Seronegative Subj 5036 (Ref8)


title: tubGal4_control_1


title: PBMC Seronegative Subj 5027 (Ref8)


title: shhcre control lung, biological rep 1

description: 4077_33256_Ctrl1 _MoGene1.1ST


title: PBMC Acute IM Subj 5088 (Ref8)


title: PBMC Acute IM Subj 5027 (Ref8)


title: sage mutant_rep2

value: sage mutant


title: sage mutant_rep1


title: CRC_patient_D_16

type: genomic

city: Heidelberg

first: Odilia

last: Popanda

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Each tumor sample was cohybridized with the matched normal mucosa on a 244K Human CpG Island microarray using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies, Palo Alto, USA), following the instructions of the manufacturer.

scan_protocol: Arrays were scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1). Scanned raw data were processed using the R statistical environment. Background correction and log 2-ratio transformation were performed according to the NormExp method with offset = 50 [Ritchie, Bioinformatics, 2007]. To reduce variations between co-hybridized samples, intensity-based LOESS normalization on rank-invariant probes and negative controls was applied [Tseng, Nucleic Acids Res, 2001]. For between-array normalization, log-intensity ratios (M-values) and log-intensity averages (A-values) were scaled to have the same median-absolute-value across the arrays.

label: Alexa Fluor 5

molecule: genomic DNA

source_name: colon tumor

label_protocol: Highly methylated tumor and normal mucosa DNAs were labeled with Alexa Fluor® 5 and 3 (BioPrime Total Genomic Labeling System, Invitrogen, Karlsruhe, Germany), respectively, following the instructions of the manufacturer.

extract_protocol: High-molecular weight DNA was isolated from fresh-frozen normal and tumor tissue samples using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany). Methyl-CpG binding domain (MBD)-Fc protein was produced and MCIp performed as described previously [Schilling, Genomics, 2007] with minor modifications. Briefly, 60 µg of MBD-Fc protein was coupled to 150 µl nProtein A Sepharose beads (GE Healthcare, Neu Isenburg, Germany) at 4°C overnight. After binding of 2 µg sonicated DNA mixed with 2 pg of a mixture of in-vitro methylated and unmethylated synthetic DNA of 630 bp containing 47 CpGs, DNA elution was performed with increasing NaCl concentrations (300-1000 mM) using Ultra-free-CL centrifugal filter devices (Merck-Millipore, Billerica, USA). Low and high salt concentrations were used to enrich for lowly and highly methylated DNA, respectively.

value: F

value: colon tumor

label: Alexa Fluor 3

source_name: matched colon mucosa

value: matched colon mucosa


title: CRC_patient_D_14

value: M


title: E10.5 indivivdual embryo with NTD, 3

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

hyb_protocol: Illumina Whole Genome Expression Direct Hybridization Assay Guide- 750 ng labeled aRNA hybridized to array

data_processing: Quantile normalization and background subtraction using Illumina GenomeStudio Gene Expression Module v1.9.0

source_name: E10.5 indivivdual embryo with NTD

label_protocol: Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina (TAN07924)-Manufacturer's protocol 200ng input total RNA

growth_protocol: Animals were housed in a 12 h dark/light cycle and fed a Chow diet (LabDiet 5001). Females were monitored weekly for blood glucose levels. To induce estrus, diabetic (>250 mg/dL blood glucose) dams received an intraperitoneal injection of 5 units of Pregnant Mare's Serum Gonadotropin (Sigma). Two days after injection femals were placed with males for mating. The morning with presence of a vaginal plug being counted as 0.5 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Samples were DNase-treated and further purified using RNeasy columns (Qiagen). RNA integrity was confirmed by Agilent bioanalysis. Equal amounts of RNA from embryos derived from four separate pregnancies were pooled into one sample. In addition, four samples from individual embryos with neural tube defects were analyzed.

treatment_protocol: Whole embryos were dissected at 10.5 days of gestation and stored in Trizol (Invitrogen) at minus 80 deg Celsius.

value: NOD

tag: pregnancy

value: diabetic

value: Whole embryo


title: sage mutant_rep3


title: shHDAC6-HT1080_dsRNA-treated_rep1

city: Cleveland

first: Ganes

middle: C.

last: Sen

address: 9500 Euclid Avenue NE-20

institute: Cleveland Clinic

data_processing: The data were normalised using quantile normalisation with IlluminaGUI

source_name: HT1080 cells stably expressing HDAC6 shRNA, dsRNA-treated 6 h

label_protocol: biotinylated cRNAs prepared using Ambion’s Illumina TotalPrep-96 RNA Amplification kit

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

tag: cell line

tag: cell type

value: fibrosarcoma cells

value: HT1080 cells stably expressing HDAC6 shRNA (HDAC6 knockdown)

tag: treated with

value: dsRNA (polyIC) for 6hrs


title: shHDAC6-HT1080_untreated_rep1

source_name: HT1080 cells stably expressing HDAC6 shRNA

tag: genotype/variation


title: E10.5 indivivdual embryo with NTD, 1


title: CRC_patient_D_15


title: Wild type_rep1

value: wild type

tag: developmental stage

value: embryonic stages 11-16


title: Wild type_rep3


title: Pool of 4 embryos E10.5 from diabetic pregnancies, 3


title: E10.5 indivivdual embryo with NTD, 4


title: Wild type_rep2


title: shcontrol-HT1080_untreated_rep1

description: shctrl-

value: HT1080 cells stably expressing nontargeting shRNA (control)


title: Pool of 4 embryos E10.5 from diabetic pregnancies, 2


title: CRC_patient_D_12


title: CRC_patient_D_13


title: H0002 replicate 2

city: Berlin

first: Justyna

last: Jozefczuk

address: Ihnestrasse 63

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

description: replicate 2

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: primary dermal fibroblasts (control)

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion  (RNase-free DNase Set, Quiagen) has been applied on the columns during  isolation.

value: Fibroblasts

tag: cell passage number

value: Passage 2

value: primary dermal fibroblasts

value: female

value: 19 yr

tag: disease status

value: healthy control


title: Pool of 4 control embryos E10.5, 4

source_name: Pool of 4 control embryos E10.5

value: normal


title: E10.5 indivivdual embryo with NTD, 2


title: shcontrol-HT1080_dsRNA-treated_rep1

description: shctrl+

source_name: HT1080 cells stably expressing nontargeting shRNA, dsRNA-treated 6 h


title: H0002 replicate 1

description: replicate 1


title: Pool of 4 embryos E10.5 from diabetic pregnancies, 4


title: CRC_patient_D_9

value: F

value: colon tumor

value: matched colon mucosa


title: SHSY5Y_E

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

description: SH-SY5Y cells Human Tiling 1.0R chip E

hyb_protocol: Approximately 6.0μg of DNA was hybridized per array using the Affymetrix hybridization kit. For these 14 array sets, 7 arrays were hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The hybridized solution was removed from these arrays and reused to hybridize the remaining seven arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G. Images were quantified using GCOS software (Affymetrix). Signal values ware exported to text files using GCOS Manager software (Affymetrix).

source_name: pooled Human SH-SY5Y cells total RNA

label_protocol: Reverse transcription, amplification, fragmentation and labeling steps were performed according to Affymetrix protocol using WT Amplified Double-Strand cDNA Synthesis Kit (Affymetrix) and WT Double-Strand DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.


title: CRC_patient_D_10


title: Pool of 4 embryos E10.5 from diabetic pregnancies, 1

value: NOD

value: diabetic

value: Whole embryo


title: Cotinine low 4

city: Taipei

first: I-Jen

address: No. 1, Sec. 4, Roosevelt Road, Taipei

country: Taiwan

institute: Division of Allergy and Immunology, Department of Pediatrics, Taipei Hospital Department of Health, Taipei, Taiwan

description: Genomic DNA from samples exposed to low dose cotinine.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio v3.1 and Partek Genomic Suite 6.6

label: Cy5 and Cy3

source_name: low 4

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using QIAGENE Gentra Puregene Kit according to standard instructions

treatment_protocol: Normalized DNA concentration to 50ng/ ml and total genomic DNA (500ng) were used for DNA bisulfate conversion using EZ DNA MethylationTM kit (ZYMO RESEARCH).

value: low cotinine

value: Cord blood


title: Cotinine low 3

source_name: low 3


title: H0007 replicate 2

description: replicate 2

source_name: primary dermal fibroblasts (statosis)

value: Passage 3

value: 33 yr

value: statosis


title: CRC_patient_D_11

value: M


title: Pool of 4 control embryos E10.5, 3


title: HeLa_E

first: Fuyuki

description: HeLa cells Human Tiling 1.0R chip E

data_processing:
The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.

source_name: Human HeLa cells total RNA

value: HeLa


title: Pool of 4 control embryos E10.5, 2


title: CRC_patient_D_7


title: CRC_patient_D_8


title: Cotinine low 5

source_name: low 5


title: Uterus_E

description: uterus Human Tiling 1.0R chip E

source_name: pooled Human uterus total RNA

value: uterus

tag: race

value: caucasian


title: H0007 replicate 1

description: replicate 1

value: Fibroblasts

value: primary dermal fibroblasts

value: female


title: Cotinine low 6

source_name: low 6


title: Trachea_E

description: trachea Human Tiling 1.0R chip E

source_name: pooled Human trachea total RNA

value: trachea


title: CRC_patient_D_6

source_name: colon tumor

value: F

value: colon tumor

value: matched colon mucosa


title: Cotinine low 7

source_name: low 7


title: Thyroid_E

description: thyroid Human Tiling 1.0R chip E

source_name: pooled Human thyroid total RNA

value: thyroid


title: H0008 replicate 2

description: replicate 2

value: Passage 4

value: male

value: 60 yr


title: Thymus_E

description: thymus Human Tiling 1.0R chip E

source_name: pooled Human thymus total RNA

value: thymus


title: Cotinine low 2

source_name: low 2

value: low cotinine

value: Cord blood


title: CRC_patient_D_5

source_name: matched colon mucosa


title: Cotinine low 1

source_name: low 1


title: Pool of 4 control embryos E10.5, 1

source_name: Pool of 4 control embryos E10.5

value: NOD

value: normal

value: Whole embryo


title: CRC_patient_D_4

value: M


title: Testes_E

description: testes Human Tiling 1.0R chip E

source_name: pooled Human testes total RNA

value: testes

value: caucasian


title: Cotinine high 7

description: Genomic DNA from samples exposed to high dose cotinine.

source_name: high 7

value: high cotinine


title: CRC_patient_D_3

value: F


title: wt rep1

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction, normalization and probe summarization steps were performed according to the default setting of the RMA/affy package (v.1.38.1) as implemented in Bioconductor.

organism: Aspergillus niger

source_name: mycelium_wild type

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: Bioreactor cultivations were carried out as described previously. Fermentation medium (FM) adjusted to pH 3, is composed of 0.75 % glucose, 0.45 % NH4Cl, 0.15 % KH2PO4, 0.05% KCl, 0.05 % MgSO4, 0.1 % trace element solution  and 0.003 % yeast extract as described [41]. Freshly harvested conidia (5 x 109) from strain N402 and RD15.8#36 were used to inoculate 5 liters of FM. Cultivations were performed in a BioFlo3000 bioreactor (New Brunswick Scientific), where the temperature, pH (set to 3), and agitation speed were controlled online using the program NBS Biocommand. The cultivation program consisted of two consecutive phases: (i) 30°C, agitation speed of 250 rpm, and headspace aeration, for the first 5 h; (ii) 30°C, agitation speed of 750 rpm, and sparger aeration during the second phase. Mycelial samples were taken after specific time points for microarray, metabolic, and microscopic analyses.

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen) followed column purification including a DNAse I treatment.

tag: strain background

value: wild type

tag: time point

value: whole fungal mycelium

value: exponential growth


title: Stomach_E

city: Tokyo

description: stomach Human Tiling 1.0R chip E

source_name: pooled Human stomach total RNA

value: stomach


title: wt rep2


title: Cotinine high 6

source_name: high 6


title: CRC_patient_D_2

value: colon tumor

value: matched colon mucosa


title: H0008 replicate 1

description: replicate 1

source_name: primary dermal fibroblasts (statosis)

value: Fibroblasts

value: Passage 4

value: primary dermal fibroblasts

value: male

value: 60 yr

value: statosis


title: Cotinine high 4

source_name: high 4

value: Cord blood


title: TOV-21G transfected with CSE1L siRNA_exp1

description: TOV-21G transfected with CSE1L siRNA

data_processing: data were analysed using BeadStudio version 2;  rank invariant normalization was performed

extract_protocol: Total RNA was extracted from cells transfected with CTRL or CSE1L siRNA 72h after transfection

tag: ovarian cancer cell line

tag: protocol

value: siRNA-mediated CSE1L knock down


title: SpinalCord_E

description: spinal cord Human Tiling 1.0R chip E

source_name: pooled Human spinal cord total RNA

tag: tissue

value: spinal cord

value: caucasian


title: Spleen_E

description: spleen Human Tiling 1.0R chip E

source_name: pooled Human spleen total RNA

value: spleen


title: TOV-21G transfected with scrambled siRNA_exp2

value: control


title: SkeletalMuscle_E

description: skeletal muscle Human Tiling 1.0R chip E

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: SK-OV-3 transfected with CSE1L siRNA_exp1

description: SK-OV-3 transfected with CSE1L siRNA


title: SmallIntestine_E

description: small intestine Human Tiling 1.0R chip E

source_name: pooled Human small intestine total RNA

value: small intestine


title: Cotinine high 5

source_name: high 5

value: high cotinine


title: SalivaryGland_E

description: salivary gland Human Tiling 1.0R chip E

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Cotinine high 3

source_name: high 3


title: SK-OV-3 transfected with scrambled siRNA_exp1


title: Pancreas_E

description: pancreas Human Tiling 1.0R chip E

source_name: pooled Human pancreas total RNA

value: pancreas


title: TOV-21G transfected with CSE1L siRNA_exp2

description: TOV-21G transfected with CSE1L siRNA


title: TOV-21G transfected with scrambled siRNA_exp1


title: Cotinine high 1

source_name: high 1


title: SK-OV-3 transfected with CSE1L siRNA_exp2

description: SK-OV-3 transfected with CSE1L siRNA


title: Lung_E

description: lung Human Tiling 1.0R chip E

source_name: pooled Human lung total RNA

value: lung


title: mt rep1

source_name: mycelium_TupA mutant

value: TupA mutant (UV-mutant RD15.8#36)

value: whole fungal mycelium

value: exponential growth


title: mt rep2


title: Liver_E

description: liver Human Tiling 1.0R chip E

source_name: pooled Human liver total RNA

value: liver


title: Prostate_E

description: prostate Human Tiling 1.0R chip E

source_name: pooled Human prostate total RNA

value: prostate


title: Kidney_E

description: kidney Human Tiling 1.0R chip E

source_name: pooled Human kidney total RNA

value: kidney


title: CRC_patient_D_1

source_name: colon tumor

tag: gender

value: M

value: colon tumor

source_name: matched colon mucosa

value: matched colon mucosa


title: Heart_E

description: heart Human Tiling 1.0R chip E

source_name: pooled Human heart total RNA

value: heart

value: caucasian


title: Severe-8h-Rep 2

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Replicate 2
1901185010_E

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a scan factor = 0.65

data_processing: The data were normalised using median normalisation with GeneSpring Ver 7.3

organism: Rattus norvegicus

source_name: Rat primary cortical neurons

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

growth_protocol: Cortical neurons were isolated from E17 Hooded Wistar rat embryos as described previously (Chung et al, 2005, Experimental Neurology).  Briefly, cortices from embryos were removed and cortical tissue from 8-10 pups was pooled and placed into HEPES buffer with 0.1% trypsin (Sigma) and incubated at 37C for 15 minutes.  After three washes with warm HEPES, the tissue was gently triturated and passed through a 20mm gauze filter and plated at a density of 5x105 cells per well onto 19mm2 glass coverslips.  Cells were maintained in Neurobasal medium (Gibco) supplemented with 10% B-27 supplement.

extract_protocol: RNA was extracted and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: After 21 days in culture, the neurons formed large clusters separated by fasciculated bundles of axons.  The axonal bundles were injured by either direct transection with a fine goniotomy knife (Chung et al, 2003, Journal of Neuroscience) or underwent stretch injury via puffing of sterile oxygen (Chung et al, 2005, Journal of Neurotrauma).  After the appropriate time, the cells were lysed and mRNA collected using a Qiagen RNeasy isolation kit.  At least twelve wells were pooled for each timepoint, and three different cultures from different pregnant rats was used.

tag: strain

value: Wistar

tag: age

value: Gestation day 15-16

value: Primary cortical neurons

tag: age of  culture

value: Day 21

value: Severe


title: Severe-8h-Rep 3

description:
Replicate 3
1901185010_I

tag: treatment


title: Severe-8h-Rep 1

description:
Replicate 1
1901185003_L


title: Cortex_E

description: cortex Human Tiling 1.0R chip E

source_name: pooled Human cortex total RNA

value: cortex


title: Severe-48h-Rep 3

description:
Replicate 3
1901185010_L


title: Severe-48h-Rep 1

description:
Replicate 1
1901185010_C


title: Colon_E

description: colon Human Tiling 1.0R chip E

source_name: pooled Human colon total RNA

value: colon


title: Severe-15h-Rep 1

description:
Replicate 1
1901185013_L


title: Severe-15h-Rep 2

description:
Replicate 2
1901185010_F


title: Cerebellum_E

description: cerebellum Human Tiling 1.0R chip E

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: FetalBrain_E

description: fetal brain Human Tiling 1.0R chip E

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: SK-OV-3 transfected with scrambled siRNA_exp2

value: control


title: CD8 T cells_AdP1A_rep2

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

description: CD8 T cells from lymph nodes, sorted by flow cytometry, 4 days after infection with adenovirus (AdP1At)

hyb_protocol: The Cy3- labeled cDNAs were hybridized  overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 8 x 60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1  for 1 min at room temperature followed by a second wash with preheated Agilent Gene  Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with  acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files. The software determines feature intensities (including background  subtraction), rejects outliers and calculates statistical confidences. For determination of  differential gene expression FES derived output data files were further analyzed using the  Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).

source_name: CD8 T cells, lymph nodes, infected mice, day 4

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed  according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed  procedure. Briefly, the amplification is based on a global PCR protocol using mRNA-derived  cDNA. mRNA was isolated via magnetic bead technology. The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent  Technologies). The average length of the highly amplified cDNA products ranged between 200–1,000 bp.  It’s noteworthy

treatment_protocol: For untreated samples, Naive CD8 T cells from lymph node of TCR transgenic TCRP1A B10D2 mice were sorted by flow cytometry (CD8+, CD3+, CD44-, Topro3-). For AdP1A samples,  Naive CD8 T cells from lymph node of TCR transgenic TCRP1A B10D2 (Ly5.2) were transferred into Ly5.1 B10D2 mice. One day after adoptive transfer, mice were infected intra-dermally (ears) with the adenovirus AdP1At (coding for P1A, tha antigen recognized by TCRP1A CD8 T cells). Four days after infection draining lymph nodes were recovered and activated TCRP1A CD8 T cells were sorted by flow cytometry (CD8+, Ly5.2+, CD44+, Topro3-). For TILs samples, 2 to 3 melanoma tumor from TIRP mice (Huijbers Y, Cancer Res. 2006 Mar 15;66(6):3278-86) were pooled. After a ficoll, CD8 T cells were sorted by flow cytometry (CD3+, CD8+, Topro3-).

value: female

value: lymph node

tag: cell type


title: BoneMarrow_E

description: bone marrow Human Tiling 1.0R chip E

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: Severe-24h-Rep 3

description:
Replicate 3
1901185010_K


title: Cotinine high 2

source_name: high 2

value: high cotinine

value: Cord blood


title: Severe-48h-Rep 2

description:
Replicate 2
1901185010_H


title: CD8 T cells_TILs_rep4

description: CD8 T cells sorted by flow cytometry from melanoma

source_name: CD8 T cells, melanoma

value: pooled male/female

value: melanoma


title: CD8 T cells_AdP1A_rep3

value: CD8 T cells from lymph nodes, sorted by flow cytometry, 4 days after infection with adenovirus (AdP1At)


title: Severe-24h-Rep 2

description:
Replicate 2
1901185010_G

value: Wistar

value: Gestation day 15-16


title: Mild-48h-Rep 3

description:
Replicate 3
1901185003_I

value: Primary cortical neurons

value: Day 21

value: Mild


title: Severe-15h-Rep 3

description:
Replicate 3
1901185010_J

value: Severe


title: Severe-0h-Rep 1

description:
Replicate 1
1901185010_D


title: Severe-24h-Rep 1

description:
Replicate 1
1901185002_L


title: Mild-48h-Rep 2

description:
Replicate 2
1901185002_I


title: CD8 T cells_TILs_rep3

value: CD8 T cells sorted by flow cytometry from melanoma


title: CD8 T cells_TILs_rep1


title: CD8 T cells_untreated_rep3

description: Naive TCR transgenic T cells (CD44 negative) sorted by flow cytometry

source_name: Naive T cells, Lymph node


title: CD8 T cells_TILs_rep2


title: Mild-24h-Rep 2

description:
Replicate 2
1901185002_G


title: Mild-24h-Rep 3

description:
Replicate 3
1901185003_G


title: CD8 T cells_untreated_rep2

value: Naive TCR transgenic T cells (CD44 negative) sorted by flow cytometry


title: CONTROLvsCKO P10-4_Cy5

city: Amsterdam

first: Celso

middle: Henrique

last: Freitas Alves

address: Meibergdreef 47

department: Neuromedical Genetics

institute: Netherlands Institute for Neuroscience

description:
Raw data file: US12302316_252665513715_S01_GE2-v5_95_Feb07_1_3.txt
Age matched

hyb_protocol: Prior to hybridization, equal amounts (825 ng) of Cy3- and Cy5-labelled RNA were hydrolyzed for 30 min at 60°C in 1x fragmentation buffer (Agilent Technologies). The fragmented targets were hybridized to a microarray by incubating for 17 h at 60°C in 1x target solution (Agilent Technologies) in a rotating hybridization chamber. Specifically, each hybridization consisted of two individual samples (one control and one knockout), one labelled with Cy3 and one with Cy5.

scan_protocol: After hybridization, the arrays were washed at room temperature for 5 min in 6x saline-sodium phosphate–EDTA (SSPE)/0.005% N-Lauroylsarcosine (Sigma-Aldrich, St Louis, MO, USA), 1 min in 0.06x SSPE/0.005% N-Lauroylsarcosine and 30 s in acetonitrile (Sigma-Aldrich), then dried in a nitrogen flow. Microarrays were scanned using an Agilent DNA Microarray Scanner at 5 µm resolution and 10% (low) and 100% (high) photomultiplier tube setting. Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1).

data_processing:
Raw expression data were analyzed in R statistical processing software (version 2.6.0) using the LIMMA package  in Bioconductor (http://www.bioconductor.org). All features that were flagged as saturated or as a nonuniformity outlier by the feature extraction software on 1 or more arrays were excluded from further analysis. Data were normalized using LIMMA by applying a background correction (using the ‘normexp’ algorithm) followed by normalization of intensity distributions within and between arrays (using the ‘quantile’ algorithm). It was recently demonstrated that the analysis of the separate intensity channels (the individual Cy3 and Cy5 signals) yields more reproducible results than the standard ratio-based approach (the ratio between the Cy3 and Cy5 channels) for dual-color microarray datasets, so we also applied this approach for the present dataset. Thus, the 2log-transformed intensity measurements per sample were extracted from the normalized ratio data and used in all following analyses.
To detect genes with a significant interaction between age and genotype, we performed a 2-way analysis of variance (ANOVA) using age and genotype as grouping factors. To compare gene expression between Crb2 cKO and control retinas at each timepoint separately t-tests were used. The Benjamini–Hochberg method was used to correct for multiple testing. P-values < 0.05 after correction were considered significant.

source_name: neuro-retina

label_protocol: Briefly, for each sample, 200 ng of RNA were linearly amplified and fluorescently labelled with either Cy3-CTP or Cy5-CTP (Perkin Elmer) using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: RNeasy Mini Kit, catalogue number: 74106; Qiagen Benelux, Venlo, The Netherlands

tag: sample id

value: CKO

value: retina


title: Mild-48h-Rep 1

description:
Replicate 1
1901185013_I


title: CONTROLvsCKO P10-4_Cy3

tag: genotype/variation

value: CONTROL


title: Mild-15h-Rep 3

description:
Replicate 3
1901185003_E


title: CD8 T cells_AdP1A_rep1

value: female

value: lymph node


title: Cortical neurons-OGD-24h-Rep 1

description:
Replicate 1
1745080079_C

scan_protocol: Standard Illumina scanning protocol with a pmt value=478

source_name: Murine primary cortical neurons

growth_protocol: Neocortical neurons (gestational days 15 or 16) obtained from foetal cortices of Swiss albino mice were used to prepare the primary cultures employing previous described procedures with modifications [Cheung NS, Beart PM, Pascoe CJ, John CA, Bernard O. Human Bcl-2 protects against AMPA receptor-mediated apoptosis. J Neurochem. 2000; 74: 1613-1620.].

treatment_protocol: OGD was induced in neuronal cortical cell cultures. This hypoxic (PO2 <50 mm Hg) condition was maintained continuously (10min,5h, 8h, 15h and 24h). Neuronal samples then collected for global gene expression analyses.

value: Swiss Albino mice

tag: agent

value: OGD

tag: age of culture

tag: treatment time-point


title: CONTROLvsCKO P10-3_Cy3

description:
Raw data file: US12302316_252665513715_S01_GE2-v5_95_Feb07_1_2.txt
Age matched


title: Cortical neurons-OGD-15h-Rep 3

description:
Replicate 3
1745080079_H


title: Mild-15h-Rep 2

description:
Replicate 2
1901185002_E


title: Mild-8h-Rep 3

description:
Replicate 3
1901185003_C


title: CD8 T cells_untreated_rep1


title: CONTROLvsCKO P10-3_Cy5


title: striatum-HI+PC-24h-Rep3

description:
Replicate 3
4514990160_H

source_name: Infarct striatum

growth_protocol: All animal work conducted in this study was approved by the University of New South Wales (UNSW) Animal Ethics and Experimentation Committee and performed in accordance with the guidelines of the National Health and Medical Research Council (Australia). C57 Black 6 mouse pups were obtained from Animal Resources Centre (Perth, WA) and were housed under standard housing conditions in the UNSW Biological Resources Centre animal facility throughout experiments.

extract_protocol: RNA was extracted and cleaned up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Pups were anesthetized with 1.5% isoflurane in 30% O2/70% N2 mixture and underwent unilateral HI. The right common carotid artery was exposed through a ventral midline neck incision and permanently occluded by electrocoagulation (Aaron Medical Industries Inc, Florida, USA), where the occlusion was verified The wound was sutured and mouse pups were returned to their mother for 1.5–2 h. Sham control rats (n = 4) underwent the identical procedure, without carotid artery occlusion.  Pups were then placed in an 8% O2/92% N2 humidified chamber at 37°C for 1 h. This combined procedure results in select neuronal damage or infarction in the hemisphere ipsilateral to the carotid occlusion, whereas hypoxia alone (contralateral hemisphere) does not produce any significant brain injury (reference). Following the HI or sham surgery procedure, all pups were returned to their dam and kept under standard housing conditions for the remainder of the study.

value: 8 days

value: Pre-conditioning+Hypoxic ischemia

value: brain striatum


title: striatum-HI+PC-24h-Rep2

description:
Replicate 2
4514990161_G


title: Cortical neurons-OGD-24h-Rep 2

description:
Replicate 2
1745080079_D

value: Gestation day 15-16


title: Cortical neurons-OGD-15h-Rep 2

description:
Replicate 2
1745080079_G

value: Primary cortical neurons


title: striatum-HI-24h-Rep4

description:
Replicate 4
4514990160_E

value: Hypoxic ischemia


title: CONTROLvsCKO P10-2_Cy5

description:
Raw data file: US12302316_252665513715_S01_GE2-v5_95_Feb07_1_1.txt
Age matched


title: striatum-HI+PC-24h-Rep4

description:
Replicate 4
4514990160_G


title: Mild-15h-Rep 1

description:
Replicate 1
1901185013_E

value: Wistar

value: Day 21

value: Mild


title: CONTROLvsCKO P10-2_Cy3


title: Cortical neurons-OGD-24h-Rep 3

description:
Replicate 3
1745080079_E


title: Mild-24h-Rep 1

description:
Replicate 1
1901185013_G


title: striatum-HI-24h-Rep3

description:
Replicate 3
4514990160_F


title: Cortical neurons-OGD-15h-Rep 1

description:
Replicate 1
1745080079_F


title: Mild-8h-Rep 2

description:
Replicate 2
1901185002_C


title: striatum-HI+PC-24h-Rep1

description:
Replicate 1
4514990161_H


title: Mild-8h-Rep 1

description:
Replicate 1
1901185013_C


title: Cortical neurons-OGD-8h-Rep 2

description:
Replicate 2
1745080069_D


title: striatum-HI-24h-Rep1

description:
Replicate 1
4514990161_F


title: Mild-0h-Rep 2

description:
Replicate 2
1901185002_A


title: Mild-0h-Rep 3

description:
Replicate 3
1901185003_A


title: CONTROLvsCKO P10-1_Cy3

description:
Raw data file: US12302316_252665513714_S01_GE2-v5_95_Feb07_1_4.txt
Age matched


title: striatum-HI-24h-Rep2

description:
Replicate 2
4514990161_E


title: CONTROLvsCKO P10-1_Cy5


title: striatum-Sham-24h-Rep4

description:
Replicate 4
4514990160_A

value: Ctrl


title: Mild-0h-Rep 1

description:
Replicate 1
1901185013_A


title: Cortical neurons-OGD-5h-Rep 3

description:
Replicate 3
1745080069_H


title: CONTROLvsCKO P6-5_Cy3

description:
Raw data file: US12302316_252665513714_S01_GE2-v5_95_Feb07_1_3.txt
Age matched

value: CKO


title: striatum-PC-24h-Rep2

description:
Replicate 2
4514990161_C

value: Hypoxic pre-conditioning


title: striatum-PC-24h-Rep1

description:
Replicate 1
4514990161_D


title: Cortical neurons-OGD-5h-Rep 2

description:
Replicate 2
1745080069_G


title: Cortical neurons-OGD-10min-Rep 3

description:
Replicate 3
1745080072_G


title: CONTROLvsCKO P6-5_Cy5

value: CONTROL

value: retina


title: CONTROLvsCKO P6-4_Cy3

description:
Raw data file: US12302316_252665513714_S01_GE2-v5_95_Feb07_1_2.txt
Age matched


title: CONTROLvsCKO P6-4_Cy5


title: striatum-Sham-24h-Rep3

description:
Replicate 3
4514990160_B


title: CONTROLvsCKO P6-3_Cy5

description:
Raw data file: US12302316_252665513714_S01_GE2-v5_95_Feb07_1_1.txt
Age matched


title: Cortical neurons-OGD-8h-Rep 1

description:
Replicate 1
1745080069_C


title: striatum-PC-24h-Rep3

description:
Replicate 3
4514990160_D


title: Ctrl-Rep 6

description:
Replicate 6
1901185010_B


title: Ctrl-Rep 5

description:
Replicate 5
1901185010_A


title: Cortical neurons-OGD-10min-Rep 2

description:
Replicate 2
1745080072_F


title: Cortical neurons-OGD-5h-Rep 1

description:
Replicate 1
1745080069_F


title: CONTROLvsCKO P6-3_Cy3


title: Ctrl-Rep 4

description:
Replicate 4
1901185003_K


title: Ctrl-Rep 3

description:
Replicate 3
1901185003_H


title: Ctrl-Rep 2

description:
Replicate 2
1901185003_F


title: Cortical neurons-OGD-10min-Rep 1

description:
Replicate 1
1745080072_E


title: Ctrl-Rep 1

description:
Replicate 1
1901185002_H


title: striatum-HI+PC-8h-Rep2

description:
Replicate 2
4514990155_D


title: Cortical neurons-Ctrl-Rep 3 [OGD]

description:
Replicate 3
1745080079_B


title: Cortical neurons-Ctrl-Rep 5 [OGD]

description:
Replicate 5
1745080069_B


title: CONTROLvsCKO P6-2_Cy5

description:
Raw data file: US12302316_252665513713_S01_GE2-v5_95_Feb07_1_4.txt
Age matched


title: CONTROLvsCKO P6-2_Cy3


title: Cortical neurons-Ctrl-Rep 4 [OGD]

description:
Replicate 4
1745080069_A


title: striatum-HI+PC-8h-Rep3

description:
Replicate 3
4514990043_D


title: CONTROLvsCKO P3-5_Cy5

description:
Raw data file: US12302316_252665513713_S01_GE2-v5_95_Feb07_1_2.txt
Age matched


title: Cortical neurons-Ctrl-Rep 1 [OGD]

description:
Replicate 1
1745080072_H


title: 10_Baso

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: TORAY Industries, Inc.

description: TLR-mediated production of cytokines in human basophils sample

hyb_protocol: Supported by manufacturer's protocol (TORAY Industries. Inc) Labeled aRNA samples are dissolved in the hybridization buffer supplied by the manufacturer. The solution was applied to the microarray, and hybridized for over-night on the shaking apparatus. After hybridization, microarray was washed 3 kinds of washing buffer supplied by the manufacturer sequencially, and dried for scanning.

scan_protocol: Supported by manufacturer's protocol (TORAY Industries. Inc) ScanArrayExpress(PerkinElmer) was used for scanning and GenePixPro v.5 was used for data digitalization. PMT gain was calibrated for scanning without the saturated spots.

data_processing: Blank value (calculated from inteisity of blank spots ) was reduced from each spot intensity. Ratio-VALUE was corrected with global normalization method.

label: Labeled with Cy3 (GE Healthcare Life-Sciences)

source_name: LPS-stimulated cells

label_protocol: Amino allyl-modified aRNA was amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kits (Applied Biosystems)

extract_protocol: Extracted with RNeasy(QIAGEN)

tag: LPS-stimulated cells

label: Labeled with Cy5 (GE Healthcare Life-Sciences)

source_name: non-LPS-stimulated cells

tag: non-LPS-stimulated cells


title: striatum-HI+PC-8h-Rep4

description:
Replicate 4
4514990041_D

tag: time point


title: 12_Baso

data_processing: Blank value (calculated from inteisity of blank spots ) was reduced from each spot intensity. Ratio-VALUE was corrected with global normalization methord.


title: CONTROLvsCKO P6-1_Cy3

description:
Raw data file: US12302316_252665513713_S01_GE2-v5_95_Feb07_1_3.txt
Age matched


title: 11_Baso


title: 9_Baso


title: striatum-HI-8h-Rep3

description:
Replicate 3
4514990041_C


title: striatum-Sham-24h-Rep2

description:
Replicate 2
4514990161_A


title: striatum-HI+PC-8h-Rep1

description:
Replicate 1
4514990159_D


title: striatum-Sham-24h-Rep1

description:
Replicate 1
4514990161_B


title: CONTROLvsCKO P3-4_Cy5

description:
Raw data file: US12302316_252665513713_S01_GE2-v5_95_Feb07_1_1.txt
Age matched


title: CONTROLvsCKO P6-1_Cy5


title: CONTROLvsCKO P3-5_Cy3


title: striatum-HI-8h-Rep2

description:
Replicate 2
4514990043_C


title: striatum-HI-8h-Rep1

description:
Replicate 1
4514990159_C


title: 8_Baso


title: Cortical neurons-Llac-24h-Rep 2

description:
Replicate 2
4173865027_H

treatment_protocol: Lactacystin (Sigma, Louis, MO) were freshly prepared in dimethyl sulfoxide upon usage to get a stock concentration of 1mM respectively. Desired concentrations were achieved through dilution with NB medium. Day 5 cultured murine cortical neurons were treated with 0.1uM and 1uM lactacystin (achieved via dilution with Neurobasal medium) over a time course of 5- 24h. Neuronal samples then collected for global gene expression analyses.

value: Day 5

value: 0.1uM Lactacystin


title: 7_PBMC

description: TLR-mediated production of cytokines in human PBMCs-depleted basophils sample


title: Cortical neurons-Ctrl-Rep 2 [OGD]

description:
Replicate 2
1745080079_A

value: Swiss Albino mice


title: Cortical neurons-Llac-24h-Rep 3

description:
Replicate 3
4173865007_H


title: CONTROLvsCKO P3-3_Cy5

description:
Raw data file: US12302316_252665513712_S01_GE2-v5_95_Feb07_1_4.txt
Age matched


title: 4_PBMC

hyb_protocol: Supported by manufacturer's protocol (TORAY Industries. Inc) ScanArrayExpress(PerkinElmer) was used for scanning and GenePixPro v.5 was used for data digitalization. PMT gain was calibrated for scanning without the saturated spots.

scan_protocol: Supported by manufacturer's protocol (TORAY Industries. Inc) Labeled aRNA samples are dissolved in the hybridization buffer supplied by the manufacturer. The solution was applied to the microarray, and hybridized for over-night on the shaking apparatus. After hybridization, microarray was washed 3 kinds of washing buffer supplied by the manufacturer sequencially, and dried for scanning.


title: striatum-PC-8h-Rep1

description:
Replicate 1
4514990159_B

value: 8 days


title: 5_PBMC


title: striatum-Sham-8h-Rep4

description:
Replicate 4
4514990041_A


title: 6_PBMC


title: Cortical neurons-OGD-8h-Rep 3

description:
Replicate 3
1745080069_E

value: OGD


title: CONTROLvsCKO P3-4_Cy3


title: Cortical neurons-Llac-15h-Rep 1

description:
Replicate 1
4173865026_G


title: 3_PBMC


title: CONTROLvsCKO P3-2_Cy3

description:
Raw data file: US12302316_252665513712_S01_GE2-v5_95_Feb07_1_3.txt
Age matched


title: striatum-PC-8h-Rep3

description:
Replicate 3
4514990041_B

value: brain striatum


title: striatum-PC-8h-Rep2

description:
Replicate 2
4514990043_B


title: Cortical neurons-Llac-24h-Rep 1

description:
Replicate 1
4173865026_H

value: Gestation day 15-16


title: CONTROLvsCKO P3-2_Cy5


title: Cortical neurons-Llac-15h-Rep 3

description:
Replicate 3
4173865007_G

value: Primary cortical neurons


title: CONTROLvsCKO P3-1_Cy5

description:
Raw data file: US12302316_252665513712_S01_GE2-v5_95_Feb07_1_2.txt
Age matched


title: CONTROLvsCKO P3-3_Cy3


title: Cortical neurons-Hlac-8h-Rep 3

description:
Replicate 3
4173865007_D

value: 1uM Lactacystin


title: striatum-Sham-8h-Rep3

description:
Replicate 3
4514990043_A


title: SHSY5Y_D

description: SH-SY5Y cells Human Tiling 1.0R chip D

source_name: pooled Human SH-SY5Y cells total RNA

tag: cell line


title: Cortical neurons-Llac-15h-Rep 2

description:
Replicate 2
4173865027_G


title: Cortical neurons-Hlac-8h-Rep 2

description:
Replicate 2
4173865027_D


title: HeLa_D

description: HeLa cells Human Tiling 1.0R chip D

source_name: Human HeLa cells total RNA

value: HeLa


title: striatum-Sham-8h-Rep2

description:
Replicate 2
4514990155_A


title: Uterus_D

description: uterus Human Tiling 1.0R chip D

source_name: pooled Human uterus total RNA

value: uterus

tag: race

value: caucasian


title: CONTROLvsCKO P3-1_Cy3

tag: tissue


title: Trachea_D

description: trachea Human Tiling 1.0R chip D

source_name: pooled Human trachea total RNA

value: trachea


title: 2_PBMC

data_processing: Blank value (calculated from inteisity of blank spots ) was reduced from each spot intensity. Ratio-VALUE was corrected with global normalization.

extract_protocol: Extracted with RNeasy (QIAGEN)


title: Thyroid_D

description: thyroid Human Tiling 1.0R chip D

source_name: pooled Human thyroid total RNA

value: thyroid


title: striatum-HI+PC-3h-Rep3

description:
Replicate 3
4625024047_D

value: Pre-conditioning+Hypoxic ischemia


title: striatum-HI+PC-3h-Rep2

description:
Replicate 2
4625024048_D


title: Thymus_D

description: thymus Human Tiling 1.0R chip D

source_name: pooled Human thymus total RNA

value: thymus


title: CONTROLvsCKO P0-4_Cy5

description:
Raw data file: US12302316_252665513711_S01_GE2-v5_95_Feb07_1_4.txt
Age matched

value: CONTROL

value: retina


title: 1_PBMC

data_processing: Mean blank value (calculated from inteisity of blank spots ) was reduced from each spot intensity. Ratio-VALUE (Cy3/Cy5) was corrected with global normalization method.


title: CONTROLvsCKO P0-3_Cy3

description:
Raw data file: US12302316_252665513711_S01_GE2-v5_95_Feb07_1_3.txt
Age matched

value: CKO


title: Cortical neurons-Hlac-24h-Rep 3

description:
Replicate 3
4173865007_F

value: Swiss Albino mice

value: Day 5


title: CONTROLvsCKO P0-5_Cy3

description:
Raw data file: US12302316_252665513712_S01_GE2-v5_95_Feb07_1_1.txt
Age matched


title: CONTROLvsCKO P0-5_Cy5


title: striatum-HI-3h-Rep2

description:
Replicate 2
4625024054_C

value: 8 days

value: Hypoxic ischemia


title: striatum-HI+PC-3h-Rep1

description:
Replicate 1
4625024054_D

value: brain striatum


title: Testes_D

description: testes Human Tiling 1.0R chip D

source_name: pooled Human testes total RNA

value: testes


title: CONTROLvsCKO P0-4_Cy3


title: CONTROLvsCKO P0-3_Cy5


title: Cortical neurons-Hlac-5h-Rep 2

description:
Replicate 2
4173865027_C

value: Gestation day 15-16

value: Primary cortical neurons

value: 1uM Lactacystin


title: Cortical neurons-Hlac-5h-Rep 1

description:
Replicate 1
4173865026_C


title: Cortical neurons-Hlac-8h-Rep 1

description:
Replicate 1
4173865026_D


title: striatum-HI-3h-Rep4

description:
Replicate 4
4625024047_C


title: Cortical neurons-Hlac-24h-Rep 1

description:
Replicate 1
4173865026_F


title: Cortical neurons-Hlac-24h-Rep 2

description:
Replicate 2
4173865027_F


title: Cortical neurons-Hlac-5h-Rep 3

description:
Replicate 3
4173865007_C


title: striatum-HI-3h-Rep3

description:
Replicate 3
4625024048_C


title: Spleen_D

description: spleen Human Tiling 1.0R chip D

source_name: pooled Human spleen total RNA

value: spleen

value: caucasian


title: CONTROLvsCKO P0-2_Cy5

description:
Raw data file: US12302316_252665513711_S01_GE2-v5_95_Feb07_1_2.txt
Age matched


title: Stomach_D

description: stomach Human Tiling 1.0R chip D

source_name: pooled Human stomach total RNA

value: stomach


title: striatum-Sham-8h-Rep1

description:
Replicate 1
4514990159_A

value: Ctrl


title: striatum-HI-3h-Rep1

description:
Replicate 1
4625024059_C


title: Cortical neurons-Hlac-15h-Rep 2

description:
Replicate 2
4173865027_E


title: SmallIntestine_D

description: small intestine Human Tiling 1.0R chip D

source_name: pooled Human small intestine total RNA

value: small intestine


title: SkeletalMuscle_D

description: skeletal muscle Human Tiling 1.0R chip D

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: SalivaryGland_D

description: salivary gland Human Tiling 1.0R chip D

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Cortical neurons-Hlac-15h-Rep 3

description:
Replicate 3
4173865007_E


title: CONTROLvsCKO P0-2_Cy3

source_name: neuro-retina

value: CONTROL

value: retina


title: striatum-PC-3h-Rep4

description:
Replicate 4
4625024047_B

value: Hypoxic pre-conditioning


title: CONTROLvsCKO P0-1_Cy5

description:
Raw data file: US12302316_252665513711_S01_GE2-v5_95_Feb07_1_1.txt
Age matched

value: CKO


title: Prostate_D

description: prostate Human Tiling 1.0R chip D

source_name: pooled Human prostate total RNA

value: prostate


title: striatum-PC-3h-Rep3

description:
Replicate 3
4625024048_B

source_name: Infarct striatum

value: 8 days

value: brain striatum


title: striatum-PC-3h-Rep1

description:
Replicate 1
4625024059_B


title: Cortical neurons-Hlac-15h-Rep 1

description:
Replicate 1
4173865026_E

source_name: Murine primary cortical neurons

value: Swiss Albino mice

value: Gestation day 15-16

value: Day 5


title: SpinalCord_D

description: spinal cord Human Tiling 1.0R chip D

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Cortical neurons-Ctrl-Rep 6 [H and L Lact]

description:
Replicate 6
4173865007_B

value: Primary cortical neurons

value: No treatment


title: Pancreas_D

description: pancreas Human Tiling 1.0R chip D

source_name: pooled Human pancreas total RNA

value: pancreas

value: caucasian


title: Cortical neurons-Ctrl-Rep 5 [H and L Lact]

description:
Replicate 5
4173865007_A

value: Ctrl


title: Cortical neurons-Ctrl-Rep 4 [H and L Lact]

description:
Replicate 4
4173865027_B


title: Cortical neurons-Ctrl-Rep 2 [H and L Lact]

description:
Replicate 2
4173865026_B


title: Cortical neurons-Ctrl-Rep 3 [H and L Lact]

description:
Replicate 3
4173865027_A


title: striatum-Sham-3h-Rep3

description:
Replicate 3
4625024048_A


title: striatum-Sham-3h-Rep4

description:
Replicate 4
4625024047_A


title: 4 dpf-E2-rep3

city: houston

first: Ruixin

last: Hao

state: TX

address: 3605 Cullen Blvd, Room 3005

department: Department of biology and biochemistry

institute: University of Houston

description:
Gene expression of 4 dpf embryos after 4 days  of 1 µM E2 treatment
Sample name: 29281

hyb_protocol: The Agilent’s Hybridization Kit was used for the hybridization. After Cy3 labeling, the samples were fragmented and 1.65 µg of sample and hybridization mix was loaded onto each of the 4x44K Expression arrays. The slide was hybridized in Agilent Hybridization Chamber at 65C at a 10rpm rotation for 17 hours. The slide was washed using the Agilent Expression Wash Buffer Set 1 and 2 as per the Agilent protocol. Performed by Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

scan_protocol: The slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

data_processing: The Agilent Feature Extraction Software Version 11.0.1.1 was used to analyze the scanned images and processed Signal intensities were obtained after background substraction. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

organism: Danio rerio

source_name: Whole embryo, 4 dpf, 1 µM E2 treatment, replicate 3

label_protocol: The Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.5 was used.  The Labeling Kit (Agilent p/n 5190-0442) was used along with Agilent’s RNA Spike-In Kit and Agilent’s Wash Buffers 1 and 2. The RNA Spike-Ins was added to the sample. The sample was simultaneously amplified and Cy3 dye labeled as cRNA was generated using T7 RNA Polymerase. The cRNA was purified using Qiagen RNeasy mini spin columns. Samples were then measured again on the Nanodrop for yield and dye incorporation. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

growth_protocol: Zebrafish embryos were collected after spawning and allowed to develop in a Petri dish in embryo medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) at 28.5˚C with 14:10 LD (14:10 LD; lights on 8 AM; lights off 10 PM.) .

extract_protocol: Total RNA from pooled embryos was extracted using Trizol (Invitrogen Corporation, Carlsbad, CA) and RNeasy spin columns (Qiagen, Chatsworth, CA) according to the manufacturer’s protocols. On-column DNase I (Qiagen, Chatsworth, CA) digestion was performed to remove remaining DNA. RNA concentrations were measured with NanoDrop 1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and RNA integrity was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: 17β-estradiol (E2) at a 1 mM stock solution in 100% dimethylsulfoxide (DMSO) was diluted in embryo medium to obtain 1 μM concentrations. A clutch of zebrafish embryos from several pairs of adult fish were divided and transferred into 6 well plates. 30 embryos were pooled as one sample and exposed to 3 ml 1 μM E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). Embryo media containing E2 were changed every day. At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for RNA extractions.

tag: time

value: 4 days

tag: developmental stage

value: 4 dpf embryo

value: Whole embryo


title: Lung_D

description: lung Human Tiling 1.0R chip D

source_name: pooled Human lung total RNA

value: lung


title: 4 dpf-E2-rep4

description:
Gene expression of 4 dpf embryos after 4 days  of 1 µM E2 treatment
Sample name: 29285

source_name: Whole embryo, 4 dpf, 1 µM E2 treatment, replicate 4


title: Liver_D

description: liver Human Tiling 1.0R chip D

source_name: pooled Human liver total RNA

value: liver


title: 4 dpf-DMSO-rep4

description:
Gene expression of 4 dpf embryos after 4 days  of 0.1% DMSO treatment
Sample name: 29284

source_name: Whole embryo, 4 dpf, 0.1% DMSO control treatment, replicate 4

value: DMSO


title: Kidney_D

description: kidney Human Tiling 1.0R chip D

source_name: pooled Human kidney total RNA

value: kidney


title: Heart_D

description: heart Human Tiling 1.0R chip D

source_name: pooled Human heart total RNA

value: heart


title: FetalBrain_D

description: fetal brain Human Tiling 1.0R chip D

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Cortical neurons-Ctrl-Rep 1 [H and L Lact]

description:
Replicate 1
4173865026_A

tag: strain

value: Swiss Albino mice

tag: age

value: Gestation day 15-16


title: Cortex_D

description: cortex Human Tiling 1.0R chip D

source_name: pooled Human cortex total RNA

value: cortex


title: 4 dpf-E2-rep1

description:
Gene expression of 4 dpf embryos after 4 days  of 1 µM E2 treatment
Sample name: 24984

source_name: Whole embryo, 4 dpf, 1 µM E2 treatment, replicate 1


title: striatum-PC-3h-Rep2

description:
Replicate 2
4625024054_B

value: 8 days

tag: treatment

value: Hypoxic pre-conditioning

value: brain striatum


title: striatum-HI+PC-0h-Rep4

description:
Replicate 4
4625024017_D

value: Pre-conditioning+Hypoxic ischemia


title: CONTROLvsCKO P0-1_Cy3

value: CONTROL

value: retina


title: striatum-Sham-3h-Rep1

description:
Replicate 1
4625024059_A

value: Ctrl


title: Colon_D

description: colon Human Tiling 1.0R chip D

source_name: pooled Human colon total RNA

value: colon

value: caucasian


title: striatum-Sham-3h-Rep2

description:
Replicate 2
4625024054_A


title: 4 dpf-DMSO-rep2

description:
Gene expression of 4 dpf embryos after 4 days  of 0.1% DMSO treatment
Sample name: 24995

source_name: Whole embryo, 4 dpf, 0.1% DMSO control treatment, replicate 2

value: 4 days

value: 4 dpf embryo

value: Whole embryo


title: 4 dpf-E2-rep2

description:
Gene expression of 4 dpf embryos after 4 days  of 1 µM E2 treatment
Sample name: 24994

source_name: Whole embryo, 4 dpf, 1 µM E2 treatment, replicate 2


title: Cortical neurons-Rot-24h-Rep 3

description:
4165582011_F
Replicate 3

treatment_protocol: Rotenone (95-98%, Sigma- Aldrich, R8875) was dissolved in DMSO to give a 10mM stock concentration which was stored at -20°C for not more than 6 months. The stock solution was further diluted down to 10uM in DMSO and added into NeuroBasal medium to obtain 10nM for drug treatment on neuron cultures. Neuronal samples then collected for global gene expression analyses.

value: Primary cortical neurons

tag: age of  culture

value: Day 5

value: 10nM rotenone


title: Cortical neurons-Rot-15h-Rep 2

description:
4165582015_F
Replicate 2

value: Swiss Albino mice

value: Gestation day 15-16


title: striatum-HI+PC-0h-Rep2

description:
Replicate 2
4625024032_D

source_name: Infarct striatum

value: 8 days


title: 4 dpf-DMSO-rep3

description:
Gene expression of 4 dpf embryos after 4 days  of 0.1% DMSO treatment
Sample name: 29280

source_name: Whole embryo, 4 dpf, 0.1% DMSO control treatment, replicate 3

value: DMSO


title: 3 dpf-E2-rep1

description:
Gene expression of 3 dpf embryos after 3 days  of 1 µM E2 treatment
Sample name: 24983

source_name: Whole embryo, 3 dpf, 1 µM E2 treatment, replicate 1

value: 3 days

value: 3 dpf embryo


title: Cortical neurons-Rot-15h-Rep 3

description:
4165582011_D
Replicate 3

source_name: Murine primary cortical neurons


title: striatum-HI+PC-0h-Rep1

description:
Replicate 1
4625024044_D

value: Pre-conditioning+Hypoxic ischemia

value: brain striatum


title: Cortical neurons-Rot-24h-Rep 2

description:
4165582011_E
Replicate 2


title: Cortical neurons-Rot-24h-Rep 1

description:
4165582015_G
Replicate 1


title: 4 dpf-DMSO-rep1

description:
Gene expression of 4 dpf embryos after 4 days  of 0.1% DMSO treatment
Sample name: 24985

source_name: Whole embryo, 4 dpf, 0.1% DMSO control treatment, replicate 1


title: striatum-HI-0h-Rep3

description:
Replicate 3
4625024017_C

value: Hypoxic ischemia


title: striatum-HI+PC-0h-Rep3

description:
Replicate 3
4625024023_D


title: Cerebellum_D

description: cerebellum Human Tiling 1.0R chip D

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: BoneMarrow_D

description: bone marrow Human Tiling 1.0R chip D

source_name: pooled Human bone marrow total RNA

value: bone marrow

value: caucasian


title: 3 dpf-E2-rep4

description:
Gene expression of 3 dpf embryos after 3 days  of 1 µM E2 treatment
Sample name: 29283

source_name: Whole embryo, 3 dpf, 1 µM E2 treatment, replicate 4


title: 3 dpf-E2-rep3

description:
Gene expression of 3 dpf embryos after 3 days  of 1 µM E2 treatment
Sample name: 29279

source_name: Whole embryo, 3 dpf, 1 µM E2 treatment, replicate 3


title: 3 dpf-E2-rep2

description:
Gene expression of 3 dpf embryos after 3 days  of 1 µM E2 treatment
Sample name: 25057

source_name: Whole embryo, 3 dpf, 1 µM E2 treatment, replicate 2


title: striatum-HI-0h-Rep1

description:
Replicate 1
4625024044_C


title: SHSY5Y_M

description: SH-SY5Y cells Human Tiling 1.0R chip M

source_name: pooled Human SH-SY5Y cells total RNA


title: HeLa_M

description: HeLa cells Human Tiling 1.0R chip M

source_name: Human HeLa cells total RNA

value: HeLa


title: striatum-HI-0h-Rep2

description:
Replicate 2
4625024023_C


title: Cortical neurons-Rot-15h-Rep 1

description:
4165582015_E
Replicate 1


title: Uterus_M

description: uterus Human Tiling 1.0R chip M

source_name: pooled Human uterus total RNA

value: uterus


title: 3 dpf-DMSO-rep4

description:
Gene expression of 3 dpf embryos after 3 days  of 0.1% DMSO treatment
Sample name: 29282

source_name: Whole embryo, 3 dpf, 0.1% DMSO control treatment, replicate 4

value: Whole embryo


title: Trachea_M

description: trachea Human Tiling 1.0R chip M

source_name: pooled Human trachea total RNA

value: trachea


title: Cortical neurons-Rot-8h-Rep 3

description:
4165582011_C
Replicate 3

value: Primary cortical neurons

value: Day 5

value: 10nM rotenone


title: Thyroid_M

description: thyroid Human Tiling 1.0R chip M

source_name: pooled Human thyroid total RNA

value: thyroid


title: 3 dpf-DMSO-rep2

description:
Gene expression of 3 dpf embryos after 3 days  of 0.1% DMSO treatment
Sample name: 24993

source_name: Whole embryo, 3 dpf, 0.1% DMSO control treatment, replicate 2

value: DMSO


title: striatum-PC-0h-Rep3

description:
Replicate 3
4625024023_B

source_name: Infarct striatum

value: 8 days

value: Hypoxic pre-conditioning


title: Thymus_M

description: thymus Human Tiling 1.0R chip M

source_name: pooled Human thymus total RNA

value: thymus


title: striatum-PC-0h-Rep4

description:
Replicate 4
4625024017_B

value: brain striatum


title: 2 dpf-E2-rep2

description:
Gene expression of 2 dpf embryos after 2 days  of 1 µM E2 treatment
Sample name: 24990

source_name: Whole embryo, 2 dpf, 1 µM E2 treatment, replicate 2

value: 2 days

value: 2 dpf embryo


title: 3 dpf-DMSO-rep3

description:
Gene expression of 3 dpf embryos after 3 days  of 0.1% DMSO treatment
Sample name: 29278

source_name: Whole embryo, 3 dpf, 0.1% DMSO control treatment, replicate 3

value: 3 days

value: 3 dpf embryo


title: Cortical neurons-Rot-8h-Rep 2

description:
4165582015_D
Replicate 2

source_name: Murine primary cortical neurons

value: Swiss Albino mice

value: Gestation day 15-16


title: Cortical neurons-Rot-8h-Rep 1

description:
4165582015_C
Replicate 1


title: 3 dpf-DMSO-rep1

description:
Gene expression of 3 dpf embryos after 3 days  of 0.1% DMSO treatment
Sample name: 24982

source_name: Whole embryo, 3 dpf, 0.1% DMSO control treatment, replicate 1

value: Whole embryo


title: striatum-Sham-0h-Rep3

description:
Replicate 3
4625024023_A

value: Ctrl


title: striatum-PC-0h-Rep1

description:
Replicate 1
4625024044_B


title: Cortical neurons-EGCG-Rep 1

description:
4165582015_H
Replicate 1

treatment_protocol: EGCG from green tea (≥ 95%, cat# E4143, Sigma-Aldrich, USA) was dissolved in Milli-Q water to make a 10mM stock solution. The stock solution was further diluted to 1uM in NeuroBasal medium before treatment. Fresh stock solution was prepared from the powder for each 24h neuronal treatment. Neuronal samples then collected for global gene expression analyses.

value: Primary cortical neurons

value: 1uM EGCG


title: Testes_M

description: testes Human Tiling 1.0R chip M

source_name: pooled Human testes total RNA

value: testes

value: caucasian


title: Cortical neurons-EGCG-Rep 2

description:
4165582011_G
Replicate 2

value: Day 5


title: striatum-Sham-0h-Rep4

description:
Replicate 4
4625024017_A

value: 8 days


title: 2 dpf-DMSO-rep3

description:
Gene expression of 2 dpf embryos after 2 days  of 0.1% DMSO treatment
Sample name: 29276

source_name: Whole embryo, 2 dpf, 0.1% DMSO control treatment, replicate 3

value: DMSO


title: 2 dpf-E2-rep3

description:
Gene expression of 2 dpf embryos after 2 days  of 1 µM E2 treatment
Sample name: 29277

source_name: Whole embryo, 2 dpf, 1 µM E2 treatment, replicate 3


title: Stomach_M

description: stomach Human Tiling 1.0R chip M

source_name: pooled Human stomach total RNA

value: stomach


title: Spleen_M

description: spleen Human Tiling 1.0R chip M

source_name: pooled Human spleen total RNA

value: spleen


title: Cortical neurons-EGCG-Rep 3

description:
4165582011_H
Replicate 3


title: striatum-Sham-0h-Rep2

description:
Replicate 2
4625024032_A

value: brain striatum


title: Cortical neurons-Ctrl-Rep 3 [EGCG, Rot]

description:
4165582011_A
Replicate 3

value: vehicle control


title: striatum-Sham-0h-Rep1

description:
Replicate 1
4625024044_A


title: 2 dpf-DMSO-rep2

description:
Gene expression of 2 dpf embryos after 2 days  of 0.1% DMSO treatment
Sample name: 25056

source_name: Whole embryo, 2 dpf, 0.1% DMSO control treatment, replicate 2

value: 2 days

value: 2 dpf embryo


title: striatum-PC-0h-Rep2

description:
Replicate 2
4625024032_B

value: Hypoxic pre-conditioning


title: SpinalCord_M

description: spinal cord Human Tiling 1.0R chip M

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Cortical neurons-KA-24h-Rep 3

description:
4068838003_H
Replicate 3

treatment_protocol: Kainate (Sigma- Aldrich) was dissolved in 100mM NaOH to give a 100mM stock concentration which was stored at -20°C. The stock solution was further diluted down to 100uM in NeuroBasal medium for drug treatment on neuron cultures. Neuronal samples then collected for global gene expression analyses.

value: Swiss Albino mice

value: Gestation day 15-16

value: 100uM kainate


title: SmallIntestine_M

description: small intestine Human Tiling 1.0R chip M

source_name: pooled Human small intestine total RNA

value: small intestine


title: 2 dpf-E2-rep1

description:
Gene expression of 2 dpf embryos after 2 days  of 1 µM E2 treatment
Sample name: 24980

source_name: Whole embryo, 2 dpf, 1 µM E2 treatment, replicate 1

value: Whole embryo


title: 1 dpf-E2-rep3

description:
Gene expression of 1 dpf embryos after 1 day  of 1 µM E2 treatment
Sample name: 29275

source_name: Whole embryo, 1 dpf, 1 µM E2 treatment, replicate 3

value: 1 day

value: 1 dpf embryo


title: Cortex-HI+PC-24h-Rep3

description:
Replicate 3
4514990040_H

source_name: Infarct Cortex

value: 8 days

value: Pre-conditioning+Hypoxic ischemia

value: brain cortex


title: 2 dpf-DMSO-rep1

description:
Gene expression of 2 dpf embryos after 2 days  of 0.1% DMSO treatment
Sample name: 24981

source_name: Whole embryo, 2 dpf, 0.1% DMSO control treatment, replicate 1

value: DMSO


title: SkeletalMuscle_M

description: skeletal muscle Human Tiling 1.0R chip M

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle

value: caucasian


title: Cortical neurons-Ctrl-Rep 4 [EGCG, Rot]

description:
4165582011_B
Replicate 4

value: Primary cortical neurons

value: Day 5

value: vehicle control

value: Ctrl


title: 1 dpf-E2-rep2

description:
Gene expression of 1 dpf embryos after 1 day  of 1 µM E2 treatment
Sample name: 24988

source_name: Whole embryo, 1 dpf, 1 µM E2 treatment, replicate 2


title: Cortical neurons-Ctrl-Rep 2 [EGCG, Rot]

description:
4165582015_B
Replicate 2

value: Swiss Albino mice


title: Cortical neurons-Ctrl-Rep 1 [EGCG, Rot]

description:
4165582015_A
Replicate 1

value: Gestation day 15-16


title: Cortical neurons-KA-24h-Rep 2

description:
4068838002_H
Replicate 2

value: 100uM kainate


title: Cortex-HI+PC-24h-Rep1

description:
Replicate 1
4514990042_H


title: Prostate_M

description: prostate Human Tiling 1.0R chip M

source_name: pooled Human prostate total RNA

value: prostate


title: Cortex-HI-24h-Rep4

description:
Replicate 4
4514990040_E

value: Hypoxic ischemia


title: 1 dpf-DMSO-rep3

description:
Gene expression of 1 dpf embryos after 1 day of 0.1% DMSO treatment
Sample name: 29274

source_name: Whole embryo, 1 dpf, 0.1% DMSO control treatment, replicate 3

value: 1 day

value: Whole embryo


title: Cortex-HI+PC-24h-Rep4

description:
Replicate 4
4514990040_G

value: 8 days


title: Cortical neurons-KA-24h-Rep 1

description:
4068838001_H
Replicate 1

source_name: Murine primary cortical neurons


title: Pancreas_M

description: pancreas Human Tiling 1.0R chip M

source_name: pooled Human pancreas total RNA

value: pancreas


title: 1 dpf-DMSO-rep2

description:
Gene expression of 1 dpf embryos after 1 day  of 0.1% DMSO treatment
Sample name: 25054

source_name: Whole embryo, 1 dpf, 0.1% DMSO control treatment, replicate 2

value: 1 dpf embryo


title: Cortical neurons-KA-15h-Rep 2

description:
4068838002_F
Replicate 2


title: SalivaryGland_M

description: salivary gland Human Tiling 1.0R chip M

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Lung_M

description: lung Human Tiling 1.0R chip M

source_name: pooled Human lung total RNA

value: lung


title: Cortical neurons-KA-15h-Rep 1

description:
4068838001_F
Replicate 1


title: Cortex-HI+PC-24h-Rep2

description:
Replicate 2
4514990042_G

value: Pre-conditioning+Hypoxic ischemia

value: brain cortex


title: 1 dpf-E2-rep1

description:
Gene expression of 1 dpf embryos after 1 day  of 1 µM E2 treatment
Sample name: 24978

source_name: Whole embryo, 1 dpf, 1 µM E2 treatment, replicate 1


title: Liver_M

description: liver Human Tiling 1.0R chip M

source_name: pooled Human liver total RNA

value: liver

value: caucasian


title: Cortex-HI-24h-Rep3

description:
Replicate 3
4514990040_F


title: Cortical neurons-KA-5h-Rep 2

description:
4068838002_D
Replicate 2

value: Primary cortical neurons

value: Day 5


title: Cortical neurons-KA-15h-Rep 3

description:
4068838003_F
Replicate 3

value: Swiss Albino mice

value: Gestation day 15-16


title: Kidney_M

description: kidney Human Tiling 1.0R chip M

source_name: pooled Human kidney total RNA

value: kidney


title: Cortex-HI-24h-Rep1

description:
Replicate 1
4514990042_F

value: Hypoxic ischemia


title: Heart_M

description: heart Human Tiling 1.0R chip M

source_name: pooled Human heart total RNA

value: heart


title: Cortical neurons-KA-5h-Rep 1

description:
4068838001_D
Replicate 1

value: 100uM kainate


title: Cortical neurons-KA-5h-Rep 3

description:
4068838003_D
Replicate 3


title: FetalBrain_M

description: fetal brain Human Tiling 1.0R chip M

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Cortex_M

description: cortex Human Tiling 1.0R chip M

source_name: pooled Human cortex total RNA

value: cortex


title: Cortex-HI-24h-Rep2

description:
Replicate 2
4514990042_E

source_name: Infarct Cortex

value: 8 days


title: Cortex-PC-24h-Rep4

description:
Replicate 4
4514990040_C

value: Hypoxic pre-conditioning