title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 1, metastasis

description:
Patient 1, metastatic biopsy #1
CRC1-M1

value: Metastatic colorectal cancer (liver)


title: Ctrl 7h_R2

status: Public on Jun 16 2014

type: RNA

city: Coimbra

first: Joana

middle: Filipa

last: Fernandes

state: -- Please Select --

address: Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra

department: Life Sciences

country: Portugal

institute: Center for Neuroscience and Cell Biology

description: Gene expression of non-stimulated neurons after 7h

hyb_protocol: Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using whole-genome Rat GE 4x44K v3 Microarrays.

scan_protocol: Images were obtained using Agilent G2565AA microarray scanner and fluorescence quantization was performed using Agilent Feature Extraction 10.5.1.1 software and GE1_105_Dec08 protocol.

data_processing: The signal intensity was aligned and normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1.

molecule: total RNA

organism: Rattus norvegicus

source_name: Control 7h_R2

label_protocol: Equal amounts of RNA extract (200 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: The cultures were maintained in Neurobasal medium in a humidified incubator with 5% CO2/95% air, at 37°C, for 14-15 days.

extract_protocol: Total RNA from three rat hippocampal neuronal cultures submitted to control or OGD conditions were collected after 7h and 24h of recovery

treatment_protocol: For the OGD challenge, hippocampal cultures were incubated in a glucose-free saline buffer (in mM: 10 HEPES, 116 NaCl, 5.4 KCl, 0.8 MgSO4, 1 NaH2PO4, 1.8 CaCl2, 25 NaHCO3, 25 sucrose, pH 7.3) in an anaerobic chamber (Forma Anaerobic System, Thermo Fisher Scientific), at 37C, for the indicated times. Control neurons were placed in a similar saline buffer with 25 mM glucose instead of sucrose and kept in an air/CO2 incubator, at 37C, for the same period of time. After the stimulus periods, the saline buffers were replaced by conditioned medium and the cultures returned to the air/CO2 incubator, where they were kept to recover for the indicated times.

tag: strain background

value: Wistar

tag: develpmetal stage

value: E18 rat embryos

tag: tissue

value: Primary hippocampal neurons

tag: exposed to

value: none (non-stimulated control)

tag: time point

value: after 7h recovery


title: PRKO oviduct, biological rep5

city: St Lucia

first: Lisa

last: Akison

state: QLD

address: Sir William MacGregor Building

department: Biomedical Sciences

country: Australia

institute: University of Queensland

description: Gene expression data from oviducts collected from homozygous progesterone receptor mutants (PRKO) at 8h post-hCG

hyb_protocol: Following fragmentation and biotinylation, samples were hybridised at 45C for 16-18 h on Affymetrix Mouse Gene 1.0 ST arrays.  Arrays were washed and then stained using a fluorescently-labelled antibody using the GeneChip® Fluidics Station 450/250.

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

data_processing: Microarray data were analysed using Partek Genomics Suite software (Partek Inc.). Background correction was performed by robust multichip averaging followed by probe affinity adjustment for the variable G-C content of probes. Quantile normalisation was performed to remove systematic variations resulting from array preparation or sample hybridization conditions. A mean probe-set summary was obtained by averaging the intensity values for the multiple probes representing an individual gene.

label: biotin

organism: Mus musculus

source_name: Mouse oviduct, PRKO genotype, 8h post-hCG

label_protocol: Biotinylated cRNA were prepared using the GeneChip® Whole-Transcript (WT) cDNA Synthesis and Amplification kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: All mice were injected i.p. with 5IU of equine chorionic gonadotropin and 5IU of human chorionic gonadotropin prior to collection of oviducts.  Oviducts were collected at 8h post-hCG.

extract_protocol: Oviducts were homogenised in 1 ml Tri Reagent (Sigma-Aldrich Pty. Ltd.) using a Precellys 24 tissue homogeniser (Sapphire Bioscience).  Total RNA was extracted using a modified Tri Reagent protocol, which included an overnight precipitation step at -20C and the addition of 1 μl Ambion GlycoBlue (15 mg/ml; Applied Biosystems) during precipitation.

value: oviduct

tag: genotype

value: PRKO


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 3, primary

type: genomic

city: Seoul

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

country: South Korea

institute: The Catholic University of Korea, College of Medicine

description:
Patient 1, primary biopsy #3
CRC1-P3

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor

label_protocol: DNA labelling and hybridization was performed according to the manufacturer's instruction

extract_protocol: Genomic DNA was extracted using phenol-chloroform extraction method.  The purity and quantity of the DNA was estimated using Nanodrop spectrophotometer.

value: Primary colorectal cancer

tag: individual

value: Patient 1

source_name: Matched normal

value: Matched normal (adjacent)


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 2, primary

description:
Patient 1, primary biopsy #2
CRC1-P2


title: PRKO oviduct, biological rep1


title: PRKO oviduct, biological rep2


title: OGD 24h_R3

description: Gene expression of OGD-stimulated neurons after 24h

source_name: Oxygen and Glucose Deprivation 24h_R3

value: Oxygen and Glucose deprivation (OGD)

value: after 24h recovery


title: PR+/- oviduct, biological rep4

description: Gene expression data from oviducts collected from heterozygous progesterone receptor mutants (PR+/-) at 8h post-hCG

source_name: Mouse oviduct, PR+/- genotype, 8h post-hCG


title: PR+/- oviduct, biological rep5


title: PR+/- oviduct, biological rep2


title: PR+/- oviduct, biological rep3


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 1, primary

description:
Patient 1, primary biopsy #1
CRC1-P1


title: Ctrl 24h_R2

description: Gene expression of non-stimulated neurons after 24h

source_name: Control 24h_R2


title: OGD 24h_R1

source_name: Oxygen and Glucose Deprivation 24h_R1


title: Ctrl 7h_R1

source_name: Control 7h_R1


title: Ctrl 24h_R1

source_name: Control 24h_R1


title: Ctrl 7h_R3

source_name: Control 7h_R3


title: SUP-HD1-FOXO1(3A)ER_4OHT_rep2

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description: SUP-HD1-FOXO1(3A)ER cells incubated with 4OHT for 24 hours

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (Perkin Elmers) using RMA normalization protocol.

source_name: SUP-HD1-FOXO1(3A)ER, 4OHT, 24 h

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: KM-H2, L428, L1236, UHO-1. and SUP-HD1 cHL cell lines stably expressing FOXO1(3A)ER were grown in  RPMI1640 medium with addition of 10% FCS, glutamine and antibiotics at 37 ºC, 5% CO2

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.

treatment_protocol: KM-H2-KLF4ER and L428-KLF4ER cells were incubated with 200 µM 4-OHT or with relevant amount of the vehicle (ethanol).  The experiment was done twice. After 24 h of incubation total RNA was isolated with RNeasy mini kit (QIAGEN).

tag: cell type

value: cHL cell line

tag: cell line

tag: treatment


title: SUP-HD1-FOXO1(3A)ER_4OHT_rep1

value: SUP-HD1-FOXO1(3A)ER cells incubated with 4OHT for 24 hours


title: Ctrl 24h_R3

source_name: Control 24h_R3


title: SUP-HD1-FOXO1(3A)ER_con_rep1

description: SUP-HD1-FOXO1(3A)ER cells incubated with vehicle for 24 hours

source_name: SUP-HD1-FOXO1(3A)ER, vehicle, 24 h


title: SUP-HD1-FOXO1(3A)ER_con_rep2

value: SUP-HD1-FOXO1(3A)ER cells incubated with vehicle for 24 hours


title: PR+/- oviduct, biological rep1


title: Wild_Type_rep3

city: East Lansing

first: Christoph

last: Benning

state: MI

address: 1066 Bogue St

department: Great Lakes Bioenergy Research Center

country: USA

institute: Michigan State University

hyb_protocol: Double-strand cDNA was labeled with the Cy3 fluorophore for hybridization to the 4-plex array by NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per µL DNA ligase (Invitrogen), 0.27 units per µL DNA polymerase I (Invitrogen), 0.013 units per µL RNase (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27 ng/ µL of RNase A for 10 minutes at 37°C.  Treated cDNA was then purified using an equal volume of phenol:chloroform:isoamyl alcohol, ethanol precipitated, washed with 80% ethanol, and resuspended in 20 µL water.  One µg of each cDNA sample was amplified and labeled with 1 unit per µL of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C.  Array hybridization was carried out with 6 µg of labeled cDNA  suspended in NimbleGen hybridization solution for 17 hours at 42°C.

scan_protocol: Arrays were scanned at 5um on Axon4000B Scanner (Molecular Dynamics, Sunnyvale, CA, USA).

data_processing: Raw PAIR files were imported into Partek GS (v.6.5) and RMA-normalized using default settings

organism: Arabidopsis thaliana

source_name: Wild Type

label_protocol: Probe preparation, hybridization to the 4-plex GeneChip Arabidopsis ATH1 Genome Arrays (NimbleGen), and subsequent processing steps were performed according to the manufacturer’s procedure (Gene Expression Center, University of Wisconsin).

growth_protocol: Leaves from 6-week-old plants grown on soil at 22C under 16 h light/8 h dark  (100 µm/m2/s)  conditions were used

extract_protocol: The total RNAs by use of the RNeasy plant mini kit (Qiagen, Valencia, CA, USA). Subsequently, the total RNA samples were pretreated with RNase-free DNase I and cleaned up using the Plant Total RNA isolation kit (Qiagen).

treatment_protocol: Four biologically independent replicate RNA samples from DGTT2 line #57 and wild type plant were used microarray experiments

tag: genotype/variation

tag: age

value: 6 weeks

value: leaf

tag: array 4-plex id


title: Wild_Type_rep2


title: Wild_Type_rep4


title: Wild_Type_rep1


title: UHO-1-FOXO1(3A)ER_4OHT_rep2

description: UHO-1-FOXO1(3A)ER cells incubated with 4OHT for 24 hours

source_name: UHO-1-FOXO1(3A)ER, 4OHT, 24 h


title: Control Day0 (306R)

city: St Andrews

first: Antonis

last: Koussounadis

address: Sir Harold Mitchell Building

department: Biology

country: United Kingdom

institute: University of St Andrews

description: Sample name: 306R

hyb_protocol: standard Illumina

scan_protocol: standard Illumina

data_processing: background correction, VS, RSN using Bioconductor package lumi (Du et al., 2008)

source_name: OV1002 Control Day0

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturers’ standard procedure

extract_protocol: Qiagen miRNeasy Mini kit and TissueRaptor following manufacturer's instructions

tag: disease state

value: Ovarian cancer

tag: xenograft from ovarian cancer model

tag: agent

value: Control

tag: time


title: UHO-1-FOXO1(3A)ER_con_rep2

description: UHO-1-FOXO1(3A)ER cells incubated with vehicle for 24 hours

source_name: UHO-1-FOXO1(3A)ER, vehicle, 24 h


title: UHO-1-FOXO1(3A)ER_con_rep1

value: UHO-1-FOXO1(3A)ER cells incubated with vehicle for 24 hours


title: DGTT2_transgenic_rep4

source_name: DGTT2 transgenic


title: DGTT2_transgenic_rep3


title: UHO-1-FOXO1(3A)ER_4OHT_rep1

value: UHO-1-FOXO1(3A)ER cells incubated with 4OHT for 24 hours


title: L1236-FOXO1(3A)ER_4OHT_rep1

description: L1236-FOXO1(3A)ER cells incubated with 4OHT for 24 hours


title: DGTT2_transgenic_rep2


title: DGTT2_transgenic_rep1


title: L1236-FOXO1(3A)ER_4OHT_rep2

value: L1236-FOXO1(3A)ER cells incubated with 4OHT for 24 hours


title: L1236-FOXO1(3A)ER_con_rep2

description: L1236-FOXO1(3A)ER cells incubated with vehicle for 24 hours

source_name: L1236-FOXO1(3A)ER, vehicle, 24 h


title: HAPC 5

status: Public on Jun 15 2014

city: Chongqing

first: jiang

last: chunhua

state: Chongqing

address: No.30 Gao Tan Yan Zheng Street, Sha Ping Ba District

country: China

institute: third military medical universtiy

description: Gene expression data from peripheral blood leucocytes of Han Chinese with high altitude polycythemia long-term exposed to Qinghai-Tibetan plateau.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: peripheral blood leucocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Peripheral blood leucocytes of Han Chinese, who has been exposed to Qinghai-Tibetan plateau for more than six months, were obtained in plateau and stored in liquid nitrogen for RNA extraction.

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

treatment_protocol: Anticoagulated peripheral blood samples were obtained at 4 550 m plateau from subjects. After centrifugated at 1 000 rpm for 10 min, gathered leucocyte beds were mixtured with three volumes of RNA preserving fluid and immediately stroed at -20℃. Admixtures were shipped to laboratory in two days at -20℃ and stored in liquid nitrogen at laboratory for RNA extraction. Finally, total RNA were extracted from the admixtures using Trizol reagent.

tag: gender

value: male

value: high altitude polycythemia

value: peripheral blood leucocytes


title: 8435

city: Brisbane

first: Divya

last: Mehta

state: Queensland

institute: The University of Queensland

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Two separate, platform-specific files for the raw data; they are missing values for few probes which we do not choose to impute according to the Genome Studio option.
Microarray expression analysis was performed in R.
The data were all normalized as follows for the CHARGE consortium as following: Illumina gene expression data has been quantile-normalized to the median distribution and subsequently log2-transformed. The probe and sample means were centered to zero.”

source_name: whole blood

label_protocol: Standard Illumina protocol, biotin

growth_protocol: RNA collection tubes

extract_protocol: TempusTM Spin RNA Isolation Kit

value: females

tag: race

value: AfricanAmericans

tag: fastingstate

value: fasting

tag: plateidhybridization

tag: ChIP

tag: rin number

tag: plateidamplification

value: whole blood


title: 8481

tag: tissue


title: 8430

value: males


title: L1236-FOXO1(3A)ER_con_rep1

tag: cell type

value: cHL cell line

tag: cell line

value: L1236-FOXO1(3A)ER cells incubated with vehicle for 24 hours


title: 8497

tag: treatment


title: control 1

description: Gene expression data from peripheral blood leucocytes of healthy Han Chinese long-term exposed to Qinghai-Tibetan plateau.


title: 8523

tag: age


title: 8369

value: non-fasting


title: 8383


title: HAPC 2


title: 8403


title: HAPC 3


title: control 5


title: 8362


title: 8502


title: 8357


title: control 2


title: 8476


title: control 3


title: 8440


title: 8343


title: HAPC 1


title: HAPC 4


title: 8392


title: 8331


title: 8293


title: 8240


title: 8237


title: 8238


title: 8269


title: 8128


title: 8025


title: 8107


title: 8229


title: 8192


title: 8176


title: 8154


title: 8158


title: 8105


title: 8266


title: 8153


title: 8200


title: 8080


title: 8313


title: 8140


title: 8152


title: 8085


title: 7861


title: control 4


title: 8308


title: 8189


title: 7811


title: 8155


title: 7817


title: 7463


title: 7417


title: 7462


title: 7454


title: 7411


title: 7427


title: 7467


title: 7421


title: 7465


title: 7422


title: 7497


title: 7528


title: 7458


title: 7536


title: 7406


title: 7470


title: 7602


title: 7464


title: 7420


title: 7397


title: 7395


title: 7382


title: 42w old FHH PDTC female, 4256273078_H

city: Utrecht

first: Sebastiaan

last: Wesseling

address: Heidelberglaan 100

department: Nephrology & Hypertension

country: Netherlands

institute: UMC Utrecht

description:
4256273078_H
Adult PDTC female.

hyb_protocol: Signal is developed with streptavidin-Cy3.

scan_protocol: The BeadChip is scanned with the Illumina BeadArray Reader, which is a two-channel, 0.8 μm resolution confocal laser scanner. During the scan process, the BeadChip barcode is scanned, ensuring effective data management.

data_processing: The raw bead files (each file contained about 1 million beads) was reorganized into non-normalized data files using T4Illumina (see www.nephrogenomics.net/UMCUtrecht/Tools/). The data were log2-transformed and quantile normalized using the program FlexArray (see gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e). The statistical program CyberT was used to signify change in gene expression between any two groups (e.g. PDTC-vs-Untreated FHH of 2 days old). P<0.05 was considered significant. In our analysis we use Array_Address_ID, instead of ID_REF, as identities for the genes because they contain more unique probe codes.

source_name: rat kidney

label_protocol: The samples were amplified and labeled using Illumina TotalPrep RNA Amplification Kit (Ambion, cat. nr. IL1791).

growth_protocol: Not applicable.

extract_protocol: Kidneys were homogenized in TRIzol using beadbeater. Then RNA was extracted from Trizol and purified using NucleoSpin® RNA II kit from Macherey-Nagel (cat. #: 740 955). The purified RNA was sent to ServiceXS.com who processed the samples as recommended by Illumina.

treatment_protocol: Fawn-Hooded Hypertensive (FHH) rats were bred. Pregnant female FHH was treated with NF-kB inhibitor PDTC in drinking water (150 mg/L) two weeks before to four weeks after birth. The offspring were sacrificed at age of 2d, 2w and adult. The kidneys were isolated from these rats and subjected to BeadChip Illumina RatRef-12. PDTC-treated rats were compared to age- and gender-matched untreated FHH rats.

tag: strain

value: Fawn-Hooded Hypertensive

value: 42 weeks

value: kidney

value: female

value: PDTC


title: 42w old FHH PDTC female, 4256273008_L

description:
4256273008_L
Adult PDTC female.


title: 7373


title: 7366


title: 36w old FHH PDTC male, 4256273008_B

description:
4256273008_B
Adult PDTC male.

value: 36 weeks


title: 7361


title: 36w old FHH PDTC male, 4256273084_G

description:
4256273084_G
Adult PDTC male.

value: male


title: 42w old FHH PDTC female, 4256273083_K

description:
4256273083_K
Adult PDTC female.


title: 42w old FHH untreated female, 4256273008_J

description:
4256273008_J
Adult untreated female.

value: Untreated


title: 7372


title: 42w old FHH untreated female, 4256273083_G

description:
4256273083_G
Adult untreated female.


title: 42w old FHH untreated female, 4256273008_I

description:
4256273008_I
Adult untreated female.


title: 42w old FHH PDTC female, 4256273084_E

description:
4256273084_E
Adult PDTC female.


title: 42w old FHH PDTC female, 4256273083_B

description:
4256273083_B
Adult PDTC female.


title: 7305


title: 36w old FHH PDTC male, 4256273078_J

description:
4256273078_J
Adult PDTC male.


title: 7326


title: 7367


title: 7316


title: 42w old FHH untreated female, 4256273078_L

description:
4256273078_L
Adult untreated female.


title: 7298


title: 7334


title: 36w old FHH PDTC male, 4256273083_E

description:
4256273083_E
Adult PDTC male.


title: 36w old FHH PDTC male, 4256273078_D

description:
4256273078_D
Adult PDTC male.


title: 42w old FHH untreated female, 4256273084_C

description:
4256273084_C
Adult untreated female.


title: 7295


title: 7293


title: 7288


title: 36w old FHH untreated male, 4256273008_D

description:
4256273008_D
Adult untreated male.


title: 36w old FHH untreated male, 4256273084_H

description:
4256273084_H
Adult untreated male.


title: 7262


title: 7239


title: 36w old FHH untreated male, 4256273078_F

description:
4256273078_F
Adult untreated male.


title: 7272


title: 7260


title: 7243


title: 36w old FHH untreated male, 4256273084_B

description:
4256273084_B
Adult untreated male.


title: 7241


title: 24h_Null(MMA-SS/Null)_blood_31

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

description: replicate 4

hyb_protocol: 20 hour hybridization at 58 degrees C

scan_protocol: Illumina BeadStation 500G-BeadArray Reader Standard

data_processing: Force positive background correction, variance stabilizing transformation, robust spline normalization

source_name: whole blood, 24h post-ITI

label_protocol: Illumina TotalPrep RNA Amolification Kit from Applied Biosystems.

extract_protocol: Whole blood RNA was isolated uisng the RiboPure Blood RNA Isolation Kit according to the manufacturer's directions and globin RNA was removed using the GLOBINclear kit from Ambion.

treatment_protocol: Rats were exposed to manual metal arc-stainless steel welding fume suspended in calcium and magnesium free phosphate buffered saline or PBS (vehicle) by intratracheal instillation. 4 or 24 h post-ITI, whole blood was collected under isoflurance anesthesia using heparin as the anticoagulant. Whole blood collected at 4 and 24 h post-exposure was challenged (a paired non-stimulant (null) and stimulant (LPS) tube) for 24 h using truCulture technology from Myriad/RBM. After the challenge, cells were recovered using RNA later for subsequent RNA isolation and microarray.

value: 24h post-ITI

value: Null(MMA-SS/Null)

value: Sprague-Dawley


title: 24h_LPS(MMA-SS/LPS)_blood_30

description: replicate 3

value: LPS(MMA-SS/LPS)


title: 24h_LPS(PBS/LPS)_blood_29

description: replicate 4

value: LPS(PBS/LPS)

value: whole blood


title: 7259

value: females

value: AfricanAmericans


title: 7552

value: males

value: fasting


title: 24h_Null(PBS/Null)_blood_28

description: replicate 3

value: Null(PBS/Null)


title: 24h_LPS(PBS/LPS)_blood_28

description: replicate 3


title: 24h_MMA-SS_blood_31

description: replicate 6

value: MMA-SS


title: 7190


title: 24h_Null(PBS/Null)_blood_29

description: replicate 4


title: 7228


title: 7216


title: 7236


title: 7178


title: 24h_Null(MMA-SS/Null)_blood_26

description: replicate 2


title: 7155


title: 24h_PBS_blood_29

description: replicate 6

value: PBS


title: 24h_MMA-SS_blood_30

description: replicate 5


title: 24h_LPS(MMA-SS/LPS)_blood_26

description: replicate 2


title: 7118


title: 24h_LPS(MMA-SS/LPS)_blood_31

description: replicate 4


title: 7142

value: non-fasting


title: 7082


title: 7108


title: 7144


title: 24h_Null(PBS/Null)_blood_27

description: replicate 2


title: 7059


title: 24h_LPS(PBS/LPS)_blood_21

description: replicate 1


title: 7055


title: 7052


title: 24h_Null(PBS/Null)_blood_21

description: replicate 1


title: 7058


title: 24h_LPS(PBS/LPS)_blood_27

description: replicate 2


title: 24h_Null(MMA-SS/Null)_blood_25

description: replicate 1


title: 24h_MMA-SS_blood_25

description: replicate 3


title: 7031


title: 24h_MMA-SS_blood_26

description: replicate 4


title: 7030


title: 7032


title: 24h_LPS(MMA-SS/LPS)_blood_25

description: replicate 1


title: 24h_PBS_blood_21

description: replicate 3


title: 7019


title: 24h_LPS_blood_24

description: replicate 4

value: LPS


title: 24h_PBS_blood_27

description: replicate 4


title: 24h_Null_blood_24

description: replicate 4


title: 7017


title: 7009


title: 7005


title: 7018


title: 24h_Null_blood_20

description: replicate 3


title: 24h_LPS_blood_20

description: replicate 3


title: 6941


title: 24h_Null_blood_18

description: replicate 2


title: 24h_LPS_blood_17

description: replicate 1


title: 36w old FHH untreated male, 4256273083_J

description:
4256273083_J
Adult untreated male.

value: Fawn-Hooded Hypertensive

value: 36 weeks

value: kidney

value: male


title: 6981


title: 6937


title: 6922


title: 24h_PBS_blood_18

description: replicate 2

value: 24h post-ITI

value: Sprague-Dawley


title: 24h_Null_blood_17

description: replicate 1


title: 24h_MMA-SS_blood_24

description: replicate 2


title: 24h_Null(MMA-SS/Null)_blood_30

description: replicate 3

value: Null(MMA-SS/Null)


title: 24h_PBS_blood_17

description: replicate 1

value: whole blood


title: 24h_MMA-SS_blood_20

description: replicate 1


title: 6900

value: females


title: 7335

value: AfricanAmericans


title: 6848


title: 4h_PBS_blood_47

description: replicate 6

source_name: whole blood, 4h post-ITI

value: 4h post-ITI


title: 6847

value: fasting


title: 4h_MMA-SS_blood_45

description: replicate 6


title: 4h_PBS_blood_44

description: replicate 5


title: 6837


title: 6885

value: males


title: 6828


title: 6846


title: 6809


title: 6824


title: 24h_LPS_blood_18

description: replicate 2


title: 7275


title: 4h_MMA-SS_blood_37

description: replicate 3

value: MMA-SS


title: 4h_MMA-SS_blood_38

description: replicate 4


title: 4h_PBS_blood_40

description: replicate 3

value: PBS


title: 4h_MMA-SS_blood_41

description: replicate 5


title: 6802


title: 6801


title: 4h_PBS_blood_36

description: replicate 2


title: 4h_PBS_blood_43

description: replicate 4


title: 4h_MMA-SS_blood_34

description: replicate 2


title: 4h_PBS_blood_35

description: replicate 1


title: 24h_PBS_blood_28

description: replicate 5


title: 6786


title: 6791

value: non-fasting


title: 6800


title: 6780


title: 6798


title: 6766


title: 6760


title: 6759


title: 6822


title: 2w old FHH PDTC female, 4160685013_B

description:
4160685013_B
2w old FHH PDTC female.

value: 2 weeks

value: female

value: PDTC


title: 6753


title: 6750


title: 2w old FHH PDTC female, 4160685015_K

description:
4160685015_K
2w old FHH PDTC female.

value: Fawn-Hooded Hypertensive

value: kidney


title: 2w old FHH PDTC female, 4160685010_G

description:
4160685010_G
2w old FHH PDTC female.


title: 6751


title: 2w old FHH PDTC female, 4160685018_C

description:
4160685018_C
2w old FHH PDTC female.


title: 2w old FHH PDTC male, 4160685015_E

description:
4160685015_E
2w old FHH PDTC male.

value: male


title: 6916


title: 4h_MMA-SS_blood_33

description: replicate 1

value: Sprague-Dawley


title: 6742


title: 2w old FHH PDTC male, 4160685010_C

description:
4160685010_C
2w old FHH PDTC male.


title: 2w old FHH PDTC male, 4160685013_D

description:
4160685013_D
2w old FHH PDTC male.


title: 2w old FHH PDTC female, 4160685004_F

description:
4160685004_F
2w old FHH PDTC female.


title: 2w old FHH PDTC male, 4160685004_H

description:
4160685004_H
2w old FHH PDTC male.


title: 2w old FHH untreated female, 4160685015_I

description:
4160685015_I
2w old FHH untreated female.

value: Untreated


title: 2w old FHH PDTC female, 4160685006_L

description:
4160685006_L
2w old FHH PDTC female.


title: 6711

value: whole blood


title: 2w old FHH untreated female, 4160685018_J

description:
4160685018_J
2w old FHH untreated female.


title: 6707

value: females


title: 2w old FHH untreated male, 4160685018_L

description:
4160685018_L
2w old FHH untreated male.


title: 2w old FHH untreated male, 4256273078_K

description:
4256273078_K
2w old FHH untreated male.


title: 6697

value: AfricanAmericans


title: 6741


title: 2w old FHH untreated female, 4160685013_A

description:
4160685013_A
2w old FHH untreated female.


title: 6685


title: 6687


title: 6731


title: 2w old FHH untreated male, 4160685013_L

description:
4160685013_L
2w old FHH untreated male.


title: 6683


title: 2w old FHH untreated female, 4160685006_F

description:
4160685006_F
2w old FHH untreated female.


title: 2w old FHH untreated female, 4160685004_C

description:
4160685004_C
2w old FHH untreated female.


title: 6682


title: 6729


title: 2d old FHH PDTC female, 4160685013_G

description:
4160685013_G
2d old FHH PDTC female.

value: 2 days


title: 2d old FHH PDTC female, 4160685015_J

description:
4160685015_J
2d old FHH PDTC female.


title: 2w old FHH untreated male, 4160685006_B

description:
4160685006_B
2w old FHH untreated male.


title: 6680


title: 6706

value: fasting


title: 2w old FHH untreated male, 4160685010_I

description:
4160685010_I
2w old FHH untreated male.


title: 6678


title: 6681


title: 2d old FHH PDTC female, 4160685006_C

description:
4160685006_C
2d old FHH PDTC female.


title: 6648


title: 6656


title: 2d old FHH PDTC male, 4160685015_C

description:
4160685015_C
2d old FHH PDTC male.


title: 6633


title: 2d old FHH PDTC male, 4160685013_H

description:
4160685013_H
2d old FHH PDTC male.


title: 2d old FHH PDTC female, 4160685004_L

description:
4160685004_L
2d old FHH PDTC female.


title: 2d old FHH PDTC male, 4160685010_D

description:
4160685010_D
2d old FHH PDTC male.


title: 6676


title: 6610


title: 6632

value: males


title: 2d old FHH PDTC male, 4160685006_K

description:
4160685006_K
2d old FHH PDTC male.


title: 2d old FHH untreated female, 4160685018_D

description:
4160685018_D
2d old FHH untreated female.


title: 2d old FHH untreated female, 4160685013_C

description:
4160685013_C
2d old FHH untreated female.


title: 2d old FHH untreated male, 4160685018_K

description:
4160685018_K
2d old FHH untreated male.


title: 6596


title: 6624


title: 6631


title: 2d old FHH untreated female, 4160685018_I

description:
4160685018_I
2d old FHH untreated female.


title: 2d old FHH untreated male, 4160685013_J

description:
4160685013_J
2d old FHH untreated male.


title: 2d old FHH untreated female, 4160685006_I

description:
4160685006_I
2d old FHH untreated female.


title: 6590


title: 6577


title: 2d old FHH untreated male, 4160685015_B

description:
4160685015_B
2d old FHH untreated male.


title: 6599


title: 2d old FHH untreated female, 4160685010_F

description:
4160685010_F
2d old FHH untreated female.


title: 2d old FHH untreated male, 4160685006_G

description:
4160685006_G
2d old FHH untreated male.


title: 6575


title: 6565


title: 6569


title: 6563


title: 6562


title: 6560


title: 6538


title: 9724


title: 6564


title: 2d old FHH untreated male, 4160685004_A

description:
4160685004_A
2d old FHH untreated male.


title: 9762


title: 6517


title: 6515


title: Cal-27 shScra

city: Chengdu

first: chongkui

last: sun

state: Sichuan

address: No.14, Sec. 3, Renmin Road South

department: State key laboratory of oral diseases

institute: Sichuan University

description: OSCC negative control

hyb_protocol: Standard hybridization protocol following GeneChip Hybridization, Wash, and Stain Kit in GeneChip Hybridization Oven 645.

scan_protocol: Scan the samples using GeneChip Scanner 3000 7G.

data_processing: The raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method to be normalized.

label: Biotin

source_name: human  oral squamous cell carcinoma cells

label_protocol: The label experiment was performed following GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: Culture oral squamous cell carcinoma cell Cal-27 in Dulbecco’s modified Eagle’s medium (DMEM) supplied with 10% fetal bovine serum and penicilin /streptomycin.

extract_protocol: Total RNA was extracted using Trizol isolation system (Invitrogen) according to manufacturer’s instructions. Total RNA quality was then determined and the total RNA should be more than 1µg. Reverse transcription was performed using Ambion WT Expression Kit to get cDNA.

treatment_protocol: Assemble lentivirus using shTCAB1 and shScramble plasmids respectively, and infecte Cal-27 cells with lentivirus to deplete endogenous TCAB1 while shScramble group as negative control.

value: Treated with shScramble lentivirus

tag: design

value: Negative Control

value: oral squamous cell carcimoma


title: 6534


title: 9757


title: 9692


title: Cal-27 shTCAB1

description: OSCC TCAB1 knockdown

value: Treated with shTCAB1 lenivirus

value: Test group


title: 6497


title: 9688

value: non-fasting


title: 9709


title: 9704


title: 9700


title: 6496


title: 9666


title: 6486


title: 6492


title: 9646


title: 9622


title: 9599


title: 6479


title: 6462


title: 6454


title: 9603


title: 9577


title: 6435


title: 6477


title: 6402


title: 6436


title: 9524


title: 9589


title: 6413


title: 9552


title: 9489


title: 9501


title: 9483


title: 6331


title: 2w old FHH untreated male, 4160685015_G

description:
4160685015_G
2w old FHH untreated male.

value: Fawn-Hooded Hypertensive

value: 2 weeks


title: 9510


title: 6327


title: 9487


title: 9449


title: 6290


title: 6297


title: 6285


title: 9414


title: 9465


title: 6688


title: 9474


title: 6324


title: 6291


title: 6394


title: 9433


title: 6334


title: 9385


title: 9377


title: 6264


title: 6267


title: 9372


title: 9331


title: 9350


title: 6283


title: 6278


title: 9403


title: 9321


title: 6263


title: 9304


title: 9301


title: 9318


title: 9300


title: 9286


title: 9270


title: 6228


title: 6233


title: 6246


title: 6220


title: 9269


title: 6241


title: 9268


title: 9264


title: 6216


title: 9215


title: 9233


title: 9251


title: 9197


title: 9176


title: 6208


title: 9204


title: 6203


title: 9295


title: 9257


title: 9157


title: 6522


title: 9139


title: 9167


title: 6202


title: miR-145 transfected PC3 cells at 16th hour

city: Istanbul

first: Mustafa

last: Ozen

address: Fatih

department: Medical Genetics

country: Turkey

institute: Istanbul University

hyb_protocol: Purified samples are heat denatured, spotted to Agilent Human genome 4X44K array (Agilent Technologies, CA) and covered with an Agilent 4-plex gasket chamber (Agilent Technologies, CA) for further hybridization at 55 C for 17 hr.

scan_protocol: After post-hybridization washes, slide was scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing:
Scanned images were analyzed with Feature Extraction v10.7.3.1 (Agilent Technologies, CA) and Bioconductor software (Agilent Technologies, CA).
Data were normalized by loess normalization, then log2 expression values for each gene were calculated and differentially expressed genes with 2-fold change in each sample compared to the control were selected.

label_protocol: Total RNA of samples and references in concentration of 150 ng are labeled with Cy5 and Cy3, respectively via a reverse transcription reaction by using “Agilent Two-Color Microarray-Based Gene Expression Analysis Kit (Low Input Quick Amp Labeling)”and the labeled and amplified RNAs were purified using “Qiagen’s RNeasy Mini Kit” according to the manufacturers’ protocols.

growth_protocol: PC3 cells were grown using RPMI medium (Gibco-BRL, Bethesda, MA) containing 10% fetal bovine serum (FBS) and 1% PSA at 37°C in a humidified and 5% CO2 incubator.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.

treatment_protocol: Precursor-miR-145 (pre-miR-145) was purchased from Ambion Inc. and non-targeting miRNA was purchased from SwitchGear Genomics. Transfection experiments were optimized and performed using X-treme Gene Transfection Kit (Roche, Switzerland) according to the manufacturer’s instructions.

source_name: Universal Human Reference RNA

tag: vendor and part number

value: Stratagene p/n 740000


title: miR-145 transfected PC3 cells at 24th hour


title: 9081


title: 6183


title: 9116


title: 6204


title: 6163


title: 6160


title: 9083


title: 9076


title: miR-145 transfected PC3 cells at 8th hour


title: 9065


title: Control

source_name: PC3 cells


title: p5 mouse palatal epithelium 5

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

hyb_protocol: Affymetrix standard wash protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

source_name: mouse oral hard palate epithelium

label_protocol: Affymetrix 3 IVT standard labeling protocol

extract_protocol: Total RNA was extracted from the whole epithelial sheets using TriZol and purified by RNeasy kit. The integrity (18S/28S) and concentrations of RNA was determined using an Experion  per the manufacturer’s instruction.

treatment_protocol: Four female Balb/c mice were sacrificed and skin epidermal tissues were obtained from the tail of mice, and oral epidermal tissues were obtained from the hard palate. Epithelium was separated from the dermis by 0.2% dispase treatment for 2 hrs at room temperature.

value: mouse oral hard palate epithelium

value: 6-8 weeks

tag: genotype

value: Balb/c


title: p4 mouse palatal epithelium 4


title: 6153

value: females

value: whole blood


title: 9050

value: AfricanAmericans


title: 9048

value: fasting


title: p2 mouse palatal epithelium 2


title: 6152

value: males


title: 9080


title: p1 mouse palatal epithelium 1


title: 8993


title: 8985


title: 6145


title: 8977


title: 8996


title: 8962


title: m4 mouse skin epithelium 4

source_name: mouse tail epithelium

value: mouse tail epithelium


title: m2 mouse skin epithelium 2


title: 6144


title: 8905


title: 6121


title: 8874


title: 8883


title: 8857


title: 8855


title: m5 mouse skin epithelium 5


title: m1 mouse skin epithelium 1


title: 8897


title: KS patient 6 versus pooled control

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

country: Italy

institute: University G.d'Annunzio

description: Experiment 6

hyb_protocol: 2 µg of respectively Cy3-Cy5 labeled aRNA, from each patient and control pool, were fragmented and then hybridized on a Phalanx Human OneArray™ V5 using 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs.

scan_protocol: After hybridization, Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner ScanArray Express (Perkin Elmer, Waltham, MA, USA) and analysed using the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer, Waltham, MA, USA). The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of sample vs. reference signal.

data_processing: A gene was considered to be significantly expressed when showing an absolute value of log-ratio higher or equal to 0.5, an index that translates to a fold-change > 0.7 or < 1.4 in transcript quantity, a present call in at least the 50% of experiments and a p-Value <0.05. False Discovery Rate (FDR) was used to adjust p-values and to correct for the multiple testing issues; FDR was set < 10%. The resulting gene lists underwent a clustering analysis (Cluster 3.0 and TreeView, Stanford University Labs) to unravel Genes Differentially Expressed (DEGs). Identified DEGs were, then, analysed by Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, Redwood City, CA, USA) to disclose the biological functions and the functional networks they are involved in.

source_name: Testicular biopsy of patient 1 (K6) affected by Klinefelter Syndrome

label_protocol: Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA), following the 2 rounds amplification protocol. 10 to 20 µg of amplified aRNA were fluorescently labeled with Cy3 or Cy5 cyanins.

extract_protocol: Total RNA was extracted from KS and control testicular biopsies using the RNeasy Microarray Tissue Mini Kit (Quiagen, Hilden, Germany) after homogenization of the samples, following the manufacturer’s instructions. The RNAs extracted from controls were pooled.

value: testicular biopsy

value: male

tag: pathology

value: Klinefelter Syndrome

source_name: Control testicular biopsies from 3 patients with normal spermatogenesis and obstructive infertility

value: normal spermatogenesis, obstructive infertility


title: 6111

tag: gender


title: 8834

tag: race


title: 6110

tag: fastingstate


title: 6114

tag: plateidhybridization


title: 8798

tag: ChIP


title: 8804

tag: rin number


title: 8845

tag: plateidamplification


title: KS patient 5 versus pooled control replicate

description: Experiment 5 technical replicate

source_name: Testicular biopsy of patient 1 (K5) affected by Klinefelter Syndrome

tag: tissue


title: 8793


title: 6099


title: 8761

value: non-fasting


title: 8736


title: KS patient 6 versus pooled control replicate

description: Experiment 6 technical replicate


title: 6100


title: 8928


title: KS patient 5 versus pooled control

description: Experiment 5


title: KS patient 4 versus pooled control replicate

description: Experiment 4 technical replicate

source_name: Testicular biopsy of patient 1 (K4) affected by Klinefelter Syndrome


title: 8722


title: KS patient 4 versus pooled control

description: Experiment 4


title: 6104


title: 8697


title: 8622


title: 8710


title: 8689


title: 6094


title: KS patient 3 versus pooled control

description: Experiment 3

source_name: Testicular biopsy of patient 1 (K3) affected by Klinefelter Syndrome


title: KS patient 3 versus pooled control replicate

description: Experiment 3 technical replicate


title: 8533


title: 8586


title: 6096


title: 8518


title: 8521


title: 6078


title: KS patient 2 versus pooled control replicate

description: Experiment 2 technical replicate

source_name: Testicular biopsy of patient 1 (K2) affected by Klinefelter Syndrome


title: 8494


title: 8593


title: 6070


title: 6077


title: KS patient 2 versus pooled control

description: Experiment 2


title: 6098


title: 8597


title: 8467


title: KS patient 1 versus pooled control

description: Experiment 1

source_name: Testicular biopsy of patient 1 (K1) affected by Klinefelter Syndrome


title: 6088


title: 8178


title: 6056


title: Forelimb autopod_mesenchyme_Sox9EGFP negative cells_rep3

city: Barcelona

first: Jelena

last: Raspopovic

address: Calle Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: CRG

description:
all cells are mesenchymal
FL_P6_190312_1_2

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: forelimb autopod, stage E11.5, Sox9-EGFP negative cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was harvested from FACS sorted Sox9-EGFP negative and Sox9-EGFP positive cells, using RNAeasy(QIAGEN) according to the manufacturer’s instructions. RNA quality was examined on a Bioanalyzer2100 (Agilent). 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions. Briefly: mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA.

tag: transgenic mouse

value: SoxEGFP mouse

tag: embryo stage

tag: limb region

value: forelimb autopod

tag: cell type

value: Sox9-EGFP negative mesenchymal cells


title: 8018

source_name: whole blood

tag: age

tag: treatment


title: 8167


title: 7941


title: 6054


title: 7858


title: Forelimb autopod_mesenchyme_Sox9EGFP negative cells_rep1

description:
all cells are mesenchymal
FL_P6_270212_1_1

tag: strain


title: 7795


title: Forelimb autopod_mesenchyme_Sox9EGFP positive cells_rep3

description:
all cells are mesenchymal
FL_P5_190312_1_4

source_name: forelimb autopod, stage E11.5, Sox9-EGFP positive cells

value: Sox9-EGFP positive mesenchymal cells


title: 8453


title: Forelimb autopod_mesenchyme_Sox9EGFP negative cells_rep2

description:
all cells are mesenchymal
FL_P6_050312_2_3


title: 6519


title: 7620


title: 6302


title: 6053


title: Forelimb autopod_mesenchyme_Sox9EGFP positive cells_rep2

description:
all cells are mesenchymal
FL_P5_130312_1_3


title: 6025


title: 7733


title: 6026


title: KS patient 1 versus pooled control replicate

description: Experiment 1 technical replicate


title: H4 treated with GANT61 48hr

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

institute: The Frist Affiliated Hospital of Nanchang University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: ovary;adenocarcinoma;derived from metastatic site:ascites

label_protocol: Each biotinylated cRNA (750 ng) was hybridized to an Illumina Human HT expression BeadChip V4 (Illumina Inc., San Diego, CA). Following standard washing steps and staining with Streotavidin-Cy3, the arrays were scanned using an Illumina BeadArray Reader.

growth_protocol: Cells were cultured as recommended by the supplier in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from each sample was isolated by TRIzol (Invitrogen) according to the manufacturer's instructions. Double-stranded cDNA and biotin-labeled cRNA were synthesized from RNA (300 ng) using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: ES2 and H4 cells were treated with GANT61 (20 μM for 32hr and 48hr) and control vehicle DMSO, respectively.

tag: cell line

value: adenocarcinoma

tag: morphology

value: epithelial

tag: growth properties

value: adherent


title: 6044

tag: gender

value: females

tag: race

value: whole blood


title: 5965

value: AfricanAmericans

tag: fastingstate

tag: plateidhybridization


title: 6019

value: males

value: fasting

tag: ChIP

tag: rin number


title: Forelimb autopod_mesenchyme_Sox9EGFP positive cells_rep1

description:
all cells are mesenchymal
FL_P5_200212_1_2


title: 6033

tag: plateidamplification

tag: tissue


title: ES2 treated with GANT61 48hr

description: replicate 1


title: 5988


title: 6023


title: 5996


title: atnp02 control

city: Parma

first: Luca

last: Pagano

address: Parco Area delle Scienze 11/A

department: Chemistry Life Sciences and Environmental Sustainability

institute: University of Parma

description:
Gene expression data from atnp02 resistant mutant plant grown on MS medium for 21 days.
NP02 CONT: Resistant mutant atnp02 Arabidopsis thaliana accession Ler-0 treated with 0 mg/l of CdS QDs (control).

hyb_protocol: Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression 3' Amplification Reagent Hybridization Controls (Cat# 900454; Lot# 4140132) and the Hybridization Module of GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720; Lot# 4139834) and mixed with aRNA samples. Hybridization was performed over night for 16 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays were done in the GeneChip®Fluidics Station 450. Biolitix AG (Witterswill, Switzerland).

scan_protocol: Scanning was done with GeneChip® Scanner 3000 (Affymetrix). Biolitix AG (Witterswill, Switzerland).

data_processing: Raw microarray data were analyzed using the Affymetrix Program Suite Expression Console v1.1 (www.affymetrix.com/analysis/). A gene expression model was obtained from normalized CEL intensities based on a perfect match only model (RMA). The RMA algorithm used a robust multi-array average for background adjustment, normalization, and log2 transformation of signal intensities.

source_name: atnp02 resistant mutant untreated

label_protocol: 100 ng of total RNA were used for amplification, which was performed with the GeneChip 3' IVT Express Kit (Cat # 901228, Lot# 0907014, Affymetrix). For fragmentation, 15 μg aRNA were used. aRNA were labeled with biotin. Biolitix AG (Witterswill, Switzerland).

growth_protocol: Seeds were germinated on MS medium at 24°C, a relative humidity of 30% and under a 16 h photoperiod.

extract_protocol: Total RNA was extracted from 0.1 g of plant material using a Sigma-Aldrich Spectrum Plant Total RNA kit.

treatment_protocol: After 14 days, plants were transferred on Murashige and Skoog (MS) medium supplemented with 0 mg/L, 40 mg/L or 80 mg/L CdS QDs, for other 21 days at 24°C, a relative humidity of 30% and under a 16 h photoperiod.

tag: accession

tag: genotype/variation

value: mutant atnp02 tolerant to cadmium sulfide quantum dots (CdS QDs)

value: seedling


title: H4 treated with DMSO 48hr

description: replicate 1

tag: cell type


title: ES2 treated with DMSO 48hr

description: replicate 1


title: atnp01 treated 80

description:
Gene expression data from atnp01 resistant mutant plant grown on MS medium supplemented with 80 mg/L of CdS QDs for 21 days.
NP01 80: Resistant mutant atnp01 Arabidopsis thaliana accession Ler-0, treated with 80 mg/l of CdS QDs.

source_name: atnp01 resistant mutant treated with 80 mg/L of CdS QDs (MIC)

value: mutant atnp01 tolerant to cadmium sulfide quantum dots (CdS QDs)

value: 80 mg/L of CdS QDs for 21 days


title: 5949

tag: age


title: atnp01 control

description:
Gene expression data from atnp01 resistant mutant plant grown on MS medium for 21 days.
NP01 CONT: Resistant mutant atnp01 Arabidopsis thaliana accession Ler-0, treated with 0 mg/l CdS QDs (control).

source_name: atnp01 resistant mutant untreated

tag: treatment


title: wt treated 80

description:
Gene expression data from WT plant grown on MS medium supplemented with 80 mg/L of CdS QDs for 21 days.
WT 80: Wild type Arabidopsis thaliana accession Ler-0 treated with 80 mg/l of CdS QDs.

source_name: WT treated with 80 mg/L of CdS QDs (MIC)

value: WT


title: wt treated 40

description:
Gene expression data from WT plant grown on MS medium supplemented with 40 mg/L of CdS QDs for 21 days.
WT 40: Wild type Arabidopsis thaliana accession Ler-0 treataed with 40 mg/l of CdS QDs.

source_name: WT treated with 40 mg/L of CdS QDs (1/2MIC)

value: 40 mg/L of CdS QDs for 21 days


title: atnp02 treated 80

description:
Gene expression data from atnp02 resistant mutant plant grown on MS medium supplemented with 80 mg/L of CdS QDs for 21 days.
NP02 80: Resistant mutant atnp02 Arabidopsis thaliana accession Ler-0, treated with 80 mg/l of CdS QDs.

source_name: atnp02 resistant mutant treated with 80 mg/L of CdS QDs (MIC)


title: 5915


title: wt control

description:
Gene expression data from WT plant grown on MS medium for 21 days.
WT CONT: Wild type Arabidopsis thaliana accession Ler-0, treated with 0 mg/l CdS QDs (control).

source_name: WT untreated


title: 5881


title: 5896


title: TTA alone_dentate-gyrus_mouse4570

status: Public on Jun 14 2014

city: Wallingford

first: John

last: Corradi

state: CT

address: 5 Research Parkway

institute: Bristol-Myers Squibb Company

hyb_protocol: Labeled cDNA was hybridized on the Affymetrix Genechip HT-MG-430A (Affymetrix, Santa Clara, CA).  All array hybridization and washing was performed according to the manufacturer’s recommendations.

scan_protocol: Scanning was performed according to the manufacturer’s recommendations.

data_processing: Gene expression values were normalized with the RMA Irizarry algorithm

source_name: DG

label_protocol: All total RNA were amplified and labeled with Ovation® Pico WTA System and Encore Biotin Module (Nugen INC, San Carlos, CA, USA).

extract_protocol: RNA was isolated from frozen laser captured hippocampal subfields using Micro RNeasy Kit Plus (Qiagen, Valencia, CA), according to the manufacturer’s protocol.

tag: genotype

value: TTA alone

value: 6.1 months

tag: Sex

value: female


title: TTA alone_CA3_mouse4626


title: TTA alone_dentate-gyrus_mouse4580


title: TTA alone_dentate-gyrus_mouse4626


title: TTA alone_dentate-gyrus_mouse4592


title: TTA alone_CA3_mouse4637


title: 8489

value: non-fasting


title: TTA alone_CA1_mouse4580


title: TTA alone_CA1_mouse4626


title: TTA alone_CA3_mouse4580


title: TTA alone_CA3_mouse4592


title: TTA alone_CA1_mouse4570


title: TTA alone_dentate-gyrus_mouse4637


title: TTA alone_CA1_mouse4637


title: TTA alone_CA1_mouse4592


title: Tg4510_dentate-gyrus_mouse4666


title: Tg4510_dentate-gyrus_mouse4600


title: Tg4510_dentate-gyrus_mouse4653


title: Tg4510_dentate-gyrus_mouse4621


title: Tg4510_dentate-gyrus_mouse4549


title: Tg4510_CA3_mouse4666


title: Tg4510_CA3_mouse4653


title: Tg4510_CA3_mouse4549


title: TTA alone_CA3_mouse4570


title: Tg4510_CA3_mouse4600


title: Tg4510_dentate-gyrus_mouse4535


title: Tg4510_CA1_mouse4600


title: Tg4510_CA1_mouse4666


title: Tg4510_CA1_mouse4535


title: double-negative_dentate-gyrus_mouse4883

value: Dbl Neg


title: double-negative_dentate-gyrus_mouse4866


title: double-negative_dentate-gyrus_mouse4825


title: double-negative_CA3_mouse4866


title: Tg4510_CA1_mouse4549


title: Tg4510_CA3_mouse4621


title: Tg4510_CA3_mouse4535


title: double-negative_CA3_mouse4886


title: double-negative_dentate-gyrus_mouse4806


title: double-negative_CA3_mouse4797


title: double-negative_CA3_mouse4883


title: double-negative_CA3_mouse4825


title: double-negative_dentate-gyrus_mouse4797


title: double-negative_CA1_mouse4886


title: Tg4510_CA1_mouse4653


title: double-negative_CA1_mouse4883


title: double-negative_dentate-gyrus_mouse4886


title: double-negative_CA1_mouse4806


title: double-negative_CA1_mouse4797


title: double-negative_CA1_mouse4825


title: double-negative_CA1_mouse4866


title: TTA alone_CA3_mouse8552

tag: age(months)

value: 4.5 months


title: TTA alone_dentate-gyrus_mouse8522


title: TTA alone_CA3_mouse8521


title: TTA alone_dentate-gyrus_mouse8543


title: TTA alone_CA1_mouse8521


title: Tg4510_dentate-gyrus_mouse8565


title: Tg4510_CA1_mouse8599


title: TTA alone_CA1_mouse8522


title: TTA alone_CA3_mouse8584


title: TTA alone_CA3_mouse8543


title: TTA alone_CA1_mouse8543


title: TTA alone_dentate-gyrus_mouse8552


title: Tg4510_dentate-gyrus_mouse8587


title: Tg4510_CA3_mouse8691


title: Tg4510_dentate-gyrus_mouse8599


title: TTA alone_CA1_mouse8552


title: TTA alone_dentate-gyrus_mouse8521


title: Tg4510_dentate-gyrus_mouse8569


title: TTA alone_CA3_mouse8522


title: Tg4510_CA3_mouse8596


title: Tg4510_dentate-gyrus_mouse8596


title: Tg4510_CA3_mouse8565


title: TTA alone_CA1_mouse8584


title: Tg4510_CA1_mouse8691


title: Tg4510_CA3_mouse8569


title: TTA alone_dentate-gyrus_mouse8584


title: Tg4510_dentate-gyrus_mouse8691


title: Tg4510_CA3_mouse8587


title: Tg4510_CA3_mouse8599


title: Tg4510_CA1_mouse8565


title: double-negative_dentate-gyrus_mouse8531


title: double-negative_dentate-gyrus_mouse8715


title: Tg4510_CA1_mouse8587


title: Tg4510_CA1_mouse8569


title: double-negative_dentate-gyrus_mouse8578


title: double-negative_CA3_mouse8715


title: double-negative_CA1_mouse8563


title: double-negative_CA3_mouse8578


title: double-negative_dentate-gyrus_mouse8540


title: double-negative_CA1_mouse8577


title: double-negative_CA1_mouse8578


title: double-negative_CA3_mouse8531


title: Tg4510_CA1_mouse8596


title: double-negative_CA3_mouse8577


title: double-negative_CA1_mouse8540


title: double-negative_CA1_mouse8715


title: hippocampus_tTA alone_10.7 months_mouse115

source_name: hippocampus

extract_protocol: RNA was isolated from frozen cortices and hippocampi using RNeasy Mini Kits (Qiagen, Valencia, CA), according to the manufacturer’s protocol.

value: tTA alone

value: hippocampus


title: hippocampus_tTA alone_10.7 months_mouse112


title: hippocampus_tTA alone_10.8 months_mouse113


title: double-negative_CA3_mouse8540


title: double-negative_dentate-gyrus_mouse8563


title: double-negative_CA1_mouse8531


title: double-negative_dentate-gyrus_mouse8577


title: hippocampus_tTA alone_10.8 months_mouse114


title: hippocampus_tTA alone_6.2 months_mouse18


title: double-negative_CA3_mouse8563


title: hippocampus_tTA alone_10.8 months_mouse116


title: hippocampus_tTA alone_6.2 months_mouse16


title: hippocampus_tTA alone_6.2 months_mouse14


title: hippocampus_tTA alone_6.1 months_mouse21


title: TBI 3 days ipsilateral neocortex, PBS i.p. wildtype B6 mouse_4

city: Uppsala

first: Ted

last: Ebendal

address: Husargatan 3

department: Neuroscience

country: Sweden

institute: Uppsala University

description: Gene expression data from injured mouse neocortex

hyb_protocol: Affymetrix GeneChip®  Mouse Genome 430 2.0 arrays were hybridized for 16 hours in a 45°C incubator and rotated at 60 rpm.  Washing and staining was performed with the Fluidics Station 450 according to the GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 2).   User Manual

scan_protocol: Scanning was done according to the GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 2), using the Affymetrix®GeneChip® Scanner 3000.

data_processing: The raw data was normalized in Expression Console provided by Affymetrix (http://www.affymetrix.com), using the MAS 5.0 algorithm.

source_name: Injured mouse neocortex, saline

label_protocol: 250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® 3’ IVT Express Kit User Manual (P/N 702646 Rev. 1, Affymetrix Inc., Santa Clara, CA).

growth_protocol: Adult male mice were used as control and for inflicting controlled cortical impact injury.

extract_protocol: Dissected brain tissue was protected in the RNAlater reagent (Qiagen), homogenized and total RNA isolated using Rneasy Mini kit (Qiagen).

treatment_protocol: Wildtype B6 mice were subjected to injury for post-treatment with cyclophosphamide or saline and sacrificed after three days. Brains from uninjured mice and injured, untreated mice served as controls. Experimental protocol followed approved ethical regulations.

value: cerebral neocortex

value: male

tag: strain

value: wildtype


title: hippocampus_tTA alone_6 months_mouse22


title: hippocampus_tTA alone_6 months_mouse17


title: hippocampus_tTA alone_6.1 months_mouse20


title: hippocampus_tTA alone_6.2 months_mouse13


title: hippocampus_tTA alone_6.1 months_mouse19


title: TBI 3 days ipsilateral neocortex, PBS i.p. wildtype B6 mouse_3

tag: gender


title: TBI 3 days ipsilateral neocortex, PBS i.p. wildtype B6 mouse_2


title: TBI 3 days ipsilateral neocortex cyclophosphamide i.p. wildtype B6 mouse_5

source_name: Injured mouse neocortex, cyclophosphamide


title: TBI 3 days ipsilateral neocortex cyclophosphamide i.p. wildtype B6 mouse_4


title: TBI 3 days ipsilateral neocortex, PBS i.p. wildtype B6 mouse_1


title: Neocortex uninjured wildtype B6 mouse_3

description: Gene expression data from uninjured mouse neocortex

source_name: Uninjured wt mouse neocortex


title: hippocampus_tTA alone_6 months_mouse15


title: TBI 3 days ipsilateral neocortex cyclophosphamide i.p. wildtype B6 mouse_3


title: hippocampus_tTA alone_5 months_mouse66


title: hippocampus_tTA alone_5 months_mouse60


title: TBI 3 days ipsilateral neocortex cyclophosphamide i.p. wildtype B6 mouse_2


title: hippocampus_tTA alone_5 months_mouse61


title: hippocampus_tTA alone_4.7 months_mouse68


title: TBI 3 days ipsilateral neocortex cyclophosphamide i.p. wildtype B6 mouse_1


title: Neocortex uninjured wildtype B6 mouse_2


title: Neocortex uninjured wildtype B6 mouse_1


title: TBI 3 days ipsilateral neocortex wildtype B6 mouse_2

source_name: Injured wt mouse neocortex


title: hippocampus_tTA alone_5 months_mouse63


title: hippocampus_tTA alone_4.7 months_mouse65


title: TBI 3 days ipsilateral neocortex wildtype B6 mouse_3


title: hippocampus_tTA alone_4.7 months_mouse64


title: TBI 3 days ipsilateral neocortex Ccr2-/- mouse_5

source_name: Injured Ccr2-/- mouse neocortex

extract_protocol: Dissected tissues were protected by RNAlater reagent (Qiagen), homogenized and total RNA isolated using Rneasy Mini kit (Qiagen).

treatment_protocol: Two strains of chemokine signalling-deficient mice were compared after injury. Experimental protocol followed approved ethical regulations.


title: hippocampus_Tg4510_6.3 months_mouse7


title: TBI 3 days ipsilateral neocortex Ccr2-/- mouse_4


title: hippocampus_tTA alone_4.6 months_mouse67


title: hippocampus_Tg4510_6.3 months_mouse12


title: TBI 3 days ipsilateral neocortex wildtype B6 mouse_1


title: hippocampus_Tg4510_6.3 months_mouse11


title: hippocampus_tTA alone_4.6 months_mouse69


title: hippocampus_Tg4510_6.1 months_mouse75


title: hippocampus_Tg4510_5.9 months_mouse8


title: hippocampus_Tg4510_6 months_mouse10


title: TBI 3 days ipsilateral neocortex Ccr2-/- mouse_3


title: hippocampus_tTA alone_4.7 months_mouse62


title: Neocortex uninjured Ccr2-/- mouse_1

source_name: Uninjured Ccr2-/- mouse neocortex


title: Neocortex uninjured Ccr2-/- mouse_2


title: TBI 3 days ipsilateral neocortex Ccr2-/- mouse_2


title: hippocampus_Tg4510_4.9 months_mouse38


title: TBI 3 days ipsilateral neocortex Ccr2-/- mouse_1


title: TBI 3 days ipsilateral neocortex Ccl3-/- mouse_2

source_name: Injured Ccl3-/- mouse neocortex


title: TBI 3 days ipsilateral neocortex Ccl3-/- mouse_3


title: hippocampus_Tg4510_4.7 months_mouse44


title: Neocortex uninjured Ccl3-/- mouse_1

source_name: Uninjured Ccl3-/- mouse neocortex


title: hippocampus_Tg4510_4.7 months_mouse36


title: AIC strain dilution rate at 0.2 biological rep1

city: Gothenburg

first: Zihe

last: Liu

address: Kemivägen 10

institute: Chalmers University of Technology

description: Gene expression data from AIC strain_dilution rate at 0.2_biological rep1

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Images were analyzed using R 2.10.1 software and Bioconductor packages. Briefly, data normalization was carried out using the method of Probe Logarithmic Intensity Error (PLIER) with perfect match probe only (PM-only).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae strain with insulin productions at dilution rate of 0.2 in chemostat cultivation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: All fermentations were performed in DasGip 1.0-liter stirrer-pro vessels (Drescher Amold Schneider, Germany) with a working volume of 400ml of SD-SCAA media, at 30°C, 600 rpm agitation.

extract_protocol: RNA was isolated using the RNeasy Minikit (Qiagen) and processed to cRNA using the Genechip 3’ IVT Express Kit (Affymetrix) and hybridized/scanned on the Yeast Genome 2.0 Array (Affymetrix) to create CEL files.

treatment_protocol: Samples for microarray analysis were taken at approximatly OD=1, and centrifuged at 4 degree for 3min, depleted supernatant, and stored in liquid nitrogen for short time and stored at -80 °C until processing

value: CEN. PK 530-1C with pTPI1-alpha factor leader insulin (2 μm POT1)

value: dilution rate at 0.2 biological rep1

value: AIC


title: TBI 3 days ipsilateral neocortex Ccl3-/- mouse_4


title: AIC strain dilution rate at 0.2 biological rep3

description: Gene expression data from AIC strain_dilution rate at 0.2_biological rep3

value: dilution rate at 0.2 biological rep3


title: hippocampus_Tg4510_4.9 months_mouse35


title: AAC strain dilution rate at 0.2 biological rep3

description: Gene expression data from AAC strain_dilution rate at 0.2_biological rep3

source_name: Saccharomyces cerevisiae strain with amyalse productions at dilution rate of 0.2 in chemostat cultivation

value: CEN. PK 530-1C with pTPI1-alpha factor leader amylase (2 μm POT1)

value: AAC


title: AIC strain dilution rate at 0.2 biological rep2

description: Gene expression data from AIC strain_dilution rate at 0.2_biological rep2

value: dilution rate at 0.2 biological rep2


title: hippocampus_Tg4510_4.6 months_mouse43


title: hippocampus_Tg4510_4.6 months_mouse41


title: hippocampus_Tg4510_4.5 months_mouse40


title: AIC strain dilution rate at 0.1 biological rep3

description: Gene expression data from AIC strain_dilution rate at 0.1_biological rep3

source_name: Saccharomyces cerevisiae strain with insulin productions at dilution rate of 0.1 in chemostat cultivation

value: dilution rate at 0.1 biological rep3


title: hippocampus_Tg4510_2 months_mouse88

value: female


title: Neocortex uninjured Ccl3-/- mouse_2


title: AAC strain dilution rate at 0.2 biological rep1

description: Gene expression data from AAC strain_dilution rate at 0.2_biological rep1


title: AIC strain dilution rate at 0.1 biological rep2

description: Gene expression data from AIC strain_dilution rate at 0.1_biological rep2

value: dilution rate at 0.1 biological rep2


title: hippocampus_Tg4510_4.6 months_mouse39


title: AIC strain dilution rate at 0.1 biological rep1

description: Gene expression data from AIC strain_dilution rate at 0.1_biological rep1

value: dilution rate at 0.1 biological rep1


title: AAC strain dilution rate at 0.2 biological rep2

description: Gene expression data from AAC strain_dilution rate at 0.2_biological rep2


title: hippocampus_Tg4510_2 months_mouse87


title: hippocampus_Tg4510_4.6 months_mouse42


title: TBI 3 days ipsilateral neocortex Ccl3-/- mouse_1


title: AAC strain dilution rate at 0.1 biological rep3

description: Gene expression data from AAC strain_dilution rate at 0.1_biological rep3

source_name: Saccharomyces cerevisiae strain with amyalse productions at dilution rate of 0.1 in chemostat cultivation


title: hippocampus_Tg4510_2 months_mouse85


title: hippocampus_Tg4510_1.9 months_mouse89


title: hippocampus_Tg4510_1.9 months_mouse90


title: AAC strain dilution rate at 0.1 biological rep1

description: Gene expression data from AAC strain_dilution rate at 0.1_biological rep1


title: AIC strain dilution rate at 0.05 biological rep3

description: Gene expression data from AIC strain_dilution rate at 0.05_biological rep3

source_name: Saccharomyces cerevisiae strain with insulin productions at dilution rate of 0.05 in chemostat cultivation

value: dilution rate at 0.05 biological rep3


title: AIC strain dilution rate at 0.05 biological rep2

description: Gene expression data from AIC strain_dilution rate at 0.05_biological rep2

value: dilution rate at 0.05 biological rep2


title: AAC strain dilution rate at 0.05 biological rep3

description: Gene expression data from AAC strain_dilution rate at 0.05_biological rep3

source_name: Saccharomyces cerevisiae strain with amyalse productions at dilution rate of 0.05 in chemostat cultivation


title: hippocampus_Tg4510_1.7 months_mouse82

value: hippocampus


title: hippocampus_Tg4510_1.9 months_mouse86


title: AAC strain dilution rate at 0.1 biological rep2

description: Gene expression data from AAC strain_dilution rate at 0.1_biological rep2


title: AIC strain dilution rate at 0.05 biological rep1

description: Gene expression data from AIC strain_dilution rate at 0.05_biological rep1

value: dilution rate at 0.05 biological rep1


title: hippocampus_Tg4510_1.8 months_mouse83


title: hippocampus_Tg4510_1.7 months_mouse81


title: hippocampus_double negative_10.7 months_mouse119

value: DN


title: AAC strain dilution rate at 0.05 biological rep1

description: Gene expression data from AAC strain_dilution rate at 0.05_biological rep1


title: hippocampus_double negative_10.8 months_mouse121


title: hippocampus_double negative_10.8 months_mouse120


title: hippocampus_Tg4510_1.7 months_mouse84


title: hippocampus_double negative_10.7 months_mouse118


title: phc98071

city: Bethesda

first: Henry

last: Zhang

state: MD

address: 49 Convent Drive

department: NICHD Bioinformatics and Scientific Programming Core

institute: NICHD

description: Gene expresion data from sample phc98071

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 high resolution scanner (M10).

data_processing: The data were analyzed with the software of RMAExpress with custom CDF file, quantile normalization, background adjust, and median polish.

source_name: liver tissue of subject 36, non-tumor

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

value: liver


title: AAC strain dilution rate at 0.05 biological rep2

description: Gene expression data from AAC strain_dilution rate at 0.05_biological rep2


title: phc98074

description: Gene expresion data from sample phc98074

source_name: liver tissue of subject 37, tumor


title: phc98070

description: Gene expresion data from sample phc98070

source_name: liver tissue of subject 35, tumor


title: hippocampus_double negative_10.7 months_mouse117

source_name: hippocampus


title: phc98072

description: Gene expresion data from sample phc98072

source_name: liver tissue of subject 36, tumor


title: hippocampus_double negative_6.4 months_mouse26


title: hippocampus_double negative_6.4 months_mouse27


title: phc98073

description: Gene expresion data from sample phc98073

source_name: liver tissue of subject 37, non-tumor


title: hippocampus_double negative_6.3 months_mouse29


title: hippocampus_double negative_6.4 months_mouse24


title: phc98067

description: Gene expresion data from sample phc98067

source_name: liver tissue of subject 34, non-tumor


title: hippocampus_double negative_6.3 months_mouse25


title: phc98068

description: Gene expresion data from sample phc98068

source_name: liver tissue of subject 34, tumor


title: phc98065

description: Gene expresion data from sample phc98065

source_name: liver tissue of subject 33, non-tumor


title: hippocampus_double negative_6.3 months_mouse23


title: phc98066

description: Gene expresion data from sample phc98066

source_name: liver tissue of subject 33, tumor


title: phc98064

description: Gene expresion data from sample phc98064

source_name: liver tissue of subject 32, tumor


title: hippocampus_double negative_6.1 months_mouse79


title: hippocampus_double negative_6.3 months_mouse28


title: phc98063

description: Gene expresion data from sample phc98063

source_name: liver tissue of subject 32, non-tumor


title: hippocampus_double negative_6.1 months_mouse80


title: phc98060

description: Gene expresion data from sample phc98060

source_name: liver tissue of subject 30, tumor


title: phc98044

description: Gene expresion data from sample phc98044

source_name: liver tissue of subject 22, tumor


title: phc98059

description: Gene expresion data from sample phc98059

source_name: liver tissue of subject 30, non-tumor


title: phc98043

description: Gene expresion data from sample phc98043

source_name: liver tissue of subject 22, non-tumor


title: phc98069

description: Gene expresion data from sample phc98069

source_name: liver tissue of subject 35, non-tumor


title: hippocampus_double negative_6.1 months_mouse78


title: phc98042

description: Gene expresion data from sample phc98042

source_name: liver tissue of subject 21, tumor


title: hippocampus_double negative_4.9 months_mouse59


title: hippocampus_double negative_4.9 months_mouse58


title: hippocampus_Tg4510_5 months_mouse37


title: phc98039

description: Gene expresion data from sample phc98039

source_name: liver tissue of subject 20, non-tumor


title: hippocampus_double negative_4.7 months_mouse72


title: phc98040

description: Gene expresion data from sample phc98040

source_name: liver tissue of subject 20, tumor


title: phc98037

description: Gene expresion data from sample phc98037

source_name: liver tissue of subject 19, non-tumor


title: hippocampus_double negative_4.7 months_mouse71

source_name: hippocampus


title: hippocampus_double negative_4.7 months_mouse74


title: phc98038

description: Gene expresion data from sample phc98038

source_name: liver tissue of subject 19, tumor


title: phc98034

description: Gene expresion data from sample phc98034

source_name: liver tissue of subject 17, tumor


title: hippocampus_double negative_4.7 months_mouse73


title: phc98035

description: Gene expresion data from sample phc98035

source_name: liver tissue of subject 18, non-tumor


title: phc98036

description: Gene expresion data from sample phc98036

source_name: liver tissue of subject 18, tumor


title: hippocampus_double negative_4.8 months_mouse70


title: TBI 3 days ipsilateral neocortex Ccl3-/- mouse_5

source_name: Injured Ccl3-/- mouse neocortex

value: cerebral neocortex

value: male


title: hippocampus_double negative_4.6 months_mouse56


title: phc98032

description: Gene expresion data from sample phc98032

source_name: liver tissue of subject 16, tumor


title: hippocampus_double negative_4.6 months_mouse55


title: mandible 05 JPS

city: Daegu

first: Tae-Geon

last: Kwon

address: Samduck 2 Ga, Jung Gu

department: Department of Oral & Maxillofacial Surgery

institute: School of Dentistry Kyungpook National University

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 1.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Affymetrix Human Gene 1.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

source_name: mandibular bone-derived cell

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using Ambion WT Expression Kit(4411973) and GeneChip WT Terminal Labeling and Controls Kit(Affymetrix 901525).    The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using Ambion WT Expression Kit(4411973) and GeneChip WT Terminal Labeling and Controls Kit(Affymetrix 901525).    The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using Ambion WT Expression Kit(4411973) and GeneChip WT Terminal Labeling and Controls Kit(Affymetrix 901525).The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using Ambion WT Expression Kit(4411973) and GeneChip WT Terminal Labeling and Controls Kit(Affymetrix 901525).

growth_protocol: The particulated bone were then transferred into culture flasks and cultured with DMEM supplemented with 20% fetal bovine serum (FBS, GIBCO-Invetrogen, Carlsbad, CA), 100 U/ml penicillin, 100 mg/ml streptomycin sulphate and 2 mM glutamine incubated at 37°C in a humidified atmosphere of 5% CO2 in air. The medium was first changed 2 days after seeding to remove non-adherent cells and the media (DMEM - 20% FBS) was changed every 2 days until the cells migrated out from the explants and reached confluency.   Subconfluent primary cells were trypsinized and replated to 75 Cm2 flask. At passage 2, the cells were harvested to extract RNA for cDNA microarray.

extract_protocol: Total RNA extraction with TRIzol reagent(Invetrogen, Carlsbad, CA, USA) was performed according to the manufacturer's instructions.

treatment_protocol: There was no prior treatment to cells before RNA extraction.

tag: diagnosis

value: healthy

tag: age, yrs

value: Cortico-cancellous bone chip


title: CHX-treated LNCaP versus CHX/R1881-treated LNCaP

city: Lyon Cedex 07

first: Nathalie

last: ALLIOLI

address: 46 Allée d'Italie

department: Institut de Génomique Fonctionnelle de Lyon (IGFL)

country: France

institute: Ecole Normale Supérieure de Lyon (ENS)

description:
Biological replicate DC1.
DC_17603

hyb_protocol: 1 µg of combined Cy3/Cy5 dye-labeled aRNA were hybridized competitively to microarray slides for 18 h at 62°C in hybridization buffer (5185-5973, Agilent) and under Agilent Gasket slide coverslip (Agilent hybridization chamber, G2534A, Agilent) in a rotative Agilent hybridization oven. Several post-hybridization washes were performed.

scan_protocol: Fluorescent microarray TIFF images were collected for both Cy3 and Cy5 by scanning washed and dried glass slides with a GenePix 4000B microarray scanner (Axon Instruments).

data_processing:
Image intensity data were extracted and analysed with GenePixPro6.0 microarray analysis software. After visual inspection, spots of insufficient quality were flagged and excluded from further analysis. GenePix data files (gpr format) were then generated.
Signal intensities were log2-transformed (Cy3/Cy5) and normalization was performed by the intensity-dependent Lowess method. Data were imported and analyzed into the R Bioconductor software in order to identify genes with potentially significant change in expression in response to R1881/CHX treatment.

source_name: CHX-treated LNCaP

label_protocol: 1 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA amplification kit (1752, Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine Cy3 or Cy5 dyes. Fluorescent probes were purified using Rneasy mini kit (Qiagen).

growth_protocol: 5x10^5 LNCaP cells were plated onto 25 cm2 flasks in RPMI-1640 complete medium for 36 h and steroid-deprived by culturing for 48 h in phenol red-free RPMI-1640 medium supplemented with 5% dextran-coated charcoal-stripped FBS.

extract_protocol: Total RNA were extracted using the Rneasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: LNCaP cells were then treated with 1 nM R1881 and/or 25 µg/ml of cycloheximide for 24 h. When cycloheximide treatment was combined with androgen stimulation, cycloheximide was added into the medium simultaneously with R1881.

tag: cell line

value: LNCaP

value: prostatic tumoral cells

value: steroid-depleted for 48h and treated with 25µgml CHX for 24h

source_name: CHX/R188-treated LNCaP

value: steroid-depleted for 48h and treated with 25µgml CHX and 1nM R1881 for 24h


title: phc98031

description: Gene expresion data from sample phc98031

source_name: liver tissue of subject 16, non-tumor

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


title: mandible 03 NBC

value: female


title: mandible 06 PJH


title: mandible 04 HJH


title: phc98029

description: Gene expresion data from sample phc98029

source_name: liver tissue of subject 15, non-tumor


title: phc98033

description: Gene expresion data from sample phc98033

source_name: liver tissue of subject 17, non-tumor


title: CHX/R1881-treated LNCaP versus CHX-treated LNCaP

description:
Biological replicate CD1.
CD_17604


title: phc98030

description: Gene expresion data from sample phc98030

source_name: liver tissue of subject 15, tumor


title: mandible 01 SBS


title: iliac 06 PJH

source_name: iliac bone-derived cell, human


title: control LNCaP versus CHX-treated LNCaP, rep2

description:
Biological replicate BD2.
BD_41156

source_name: control non-stimulated LNCaP

value: steroid-depleted for 48h

tag: sample type

value: control


title: iliac 01 SBS


title: CHX-treated LNCaP versus control LNCaP, rep2

description:
Biological replicate DB2.
DB_41155


title: mandible 02 HKT


title: control LNCaP versus CHX-treated LNCaP, rep1

description:
Biological replicate BD1.
BD_17602


title: phc98027

description: Gene expresion data from sample phc98027

source_name: liver tissue of subject 14, non-tumor


title: iliac 05 JPS


title: phc98028

description: Gene expresion data from sample phc98028

source_name: liver tissue of subject 14, tumor


title: iliac 03 NBC


title: phc98026

description: Gene expresion data from sample phc98026

source_name: liver tissue of subject 13, tumor


title: iliac 02 HKT


title: control LNCaP versus CHX/R1881-treated LNCaP, rep2

description:
Biological replicate BC2.
BC_41071


title: CHX-treated LNCaP versus control LNCaP, rep1

description:
Biological replicate DB1.
DB_17741


title: phc98024

description: Gene expresion data from sample phc98024

source_name: liver tissue of subject 12, tumor


title: phc98025

description: Gene expresion data from sample phc98025

source_name: liver tissue of subject 13, non-tumor


title: iliac 04 HJH


title: Wut

type: SRA

city: Shanghai

first: Liu

last: Xuxin

address: 300 Fengling Road

institute: Institute of Plant and Physiology & Ecology

description:
small RNA sequencing
wild type

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Removing adaptor and remove off low quality reads to generate data for analysis, for each genotype,two datas generated, Huaq generated data huaq_small_RNA.txt, Wut generated data wut_small_RNA.txt.
the small RNA with length of 17~36 nt were mapped to genomic sequences (BRAD, Brassica Database, http://brassicadb.org/brad/) of Chinese cabbage (B. rapa ssp. pekinensis. cv Chiifu-401-42) by SOAP2 (short oligonucleotide alignment program) with the 0 or 1 mismatch, it generated data small_RNA_soap_all.txt.
after comparing with Brassica genome with annotated sequence, to generate small RNAs mapped on gene regeion, the final data of small RNAs is gene_derived_small_RNAs.txt.
after comparing with Arabidopsis and Brassica miRNAs, to generate small RNAs matched with sequence of conserved miRNAs, the final data of small RNAs miRNAs.txt.
Genome_build: Brassica genome version 1.2, (http://brassicadb.org/brad)
Supplementary_files_format_and_content: in text files include RPKM values for each small RNAs sequence.huaq_small_RNA.txt and wut_small_RNA.txt, each file have two columns, one is small RNAs sequence another is abundance; in file of small_RNA_soap_all.txt, every row has 13 columns, they present as sequence with aboundance,sequence or reverse sequence,quality number, matched number, a/b derived file name,length of reads,+/- sense or antisense strand, number of chromosome, start position on reference chromosome,number of mismatch, detail information of mismatch, matched number of small RNA sequence,detail information of matched reads; in file of gene_derived_small_RNAs.txt, evry row has 22 columns, they present as sequence with aboundance,sequence or reverse sequence,quality number, matched number, a/b derived file name,length of reads,+/- sense or antisense strand, number of chromosome, start position on reference chromosome,number of mismatch, detail information of mismatch, matched number of small RNA sequence,detail information of matched reads, cis/trans, ID of chromosome, source, type, start position, end position, score(E-values or P-values), strand, phase, attributes;in file of miRNAs.txt, evry row has 5 columns, they are ID, brassica ID,Huaq abundance, Wut abundance,ratio(huaq/wut). in file of matched_gene.txt, every row has  5 columns, they are Brassica gene ID, Ortholog gene of Arabidopsis, Gene name, Foldchang(ratio=huaq/wut), Abstract of gene Function.

organism: Brassica rapa subsp. chinensis

source_name: above ground portions of seedling

growth_protocol: All plants were grown under a 16/8 h light/dark photoperiod at 22 ℃ for 3 weeks, the above-ground portions of the seedlings were harvested, quick-frozen immediately with liquid nitrogen and stored at -80°C.

extract_protocol: Total RNAs were extracted using TRIzol Reagent (Invitrogen). RNA concentration was measured by Eppendorf Biophotometer 6121. DNA was removed by digestion using TURBO DNA-free kit (Ambion). RNA samples were sent to Keygene N.V., Wageningen in Netherlands where the samples were prepared by using the MIRVana MIRNA Isolation Kit (Ambion, Austin, TX, USA)and sequenced on Illumina GAII sequencer, according to the Alternative v1.5 Protocol (Illumina, San Diego, CA, USA).

treatment_protocol: The above-ground part of seedling of samples were collected and frozen in liquid nitrogen immediately, Total RNAs were extracted using TRIzol Reagent (Invitrogen). RNA concentration was measured by Eppendorf Biophotometer 6121. DNA was removed by digestion of using TURBO DNA-free kit (Ambion).

value: Wut

value: 21 day

value: above ground portions of seedling


title: phc98023

description: Gene expresion data from sample phc98023

source_name: liver tissue of subject 12, non-tumor


title: CHX/R1881-treated LNCaP versus control LNCaP, rep2

description:
Biological replicate CB2.
CB_41069


title: control LNCaP versus CHX/R1881-treated LNCaP, rep1

description:
Biological replicate BC1.
BC_17610


title: phc98018

description: Gene expresion data from sample phc98018

source_name: liver tissue of subject 9, tumor


title: phc98022

description: Gene expresion data from sample phc98022

source_name: liver tissue of subject 11, tumor


title: control LNCaP versus R1881-treated LNCaP, rep2

description:
Biological replicate BA2.
BA_41068

source_name: R1881-treated LNCaP

value: steroid-depleted for 48h and treated with 1nM R1881 for 24h


title: phc98017

description: Gene expresion data from sample phc98017

source_name: liver tissue of subject 9, non-tumor


title: control LNCaP versus R1881-treated LNCaP, rep1

description:
Biological replicate BA1.
BA_17609


title: BarleyKoji_44hr_40°C_rep3

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

description: Gene expression after 44 hr in barley koji at 40°C

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custum array for Aspergillus kawachii for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed and died.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters protocol GE1_107_Sep09 and Grid: 036226_D_F_20110830) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Aspergillus luchuensis

source_name: barley koji, 44 hr, 40°C, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: A white koji mold Aspergillus kawachii SH46 from Higuchi Matsunosuke Shoten Co., Ltd (Osaka, Japan) and barley polished to the extent of 70% were used for koji making. The barley was steamed (water adsorption rate, 35%) and the barley koji were made under two different preset temperature; (1) rising from 36°C to 40°C for 25 hr and then lowering to 30°C, and (2) rising from 36°C to 40°C for 25 hr and maintaining it. The barley koji (100 g) was made in triplicate and used for following experiments.

extract_protocol: The barley koji was collected and frozen immediately at −80°C until use. The koji was disrupted by hammering with liquid nitrogen to keep the frozen condition and 2 g of crushed koji was incubated with 5 ml of RNAiso (Takara Bio, Shiga, Japan) at 50 °C for 10 min. During the incubation, the solution was vigorously mixed by vortex mixer every 2 min. The solution was placed at room temperature for 5 min. The solution was frozen at -80°C over 1 hr. The freezed samples were melted at room temperature and centrifuged at 1,580 × g for 15 min at room temperature. The upper phase was retrieved and 0.2 times volume of chloroform was added and vigorously mixed and centrifuged at 1,580 × g for 15 min at room temperature. The upper phase was retrieved and further purified by SV total RNA isolation system according to manufacturer’s protocol (Promega, Madison, WI). The quality of RNA sample for DNA microarray analysis was confirmed by electrophoresis with BioAnalyzer Instruments (Agilent Technologies).


title: R1881-treated LNCaP versus control LNCaP, rep1

description:
Biological replicate AB1.
AB_17607


title: Huaq

description:
small RNA sequencing
wild type

value: Huaq


title: R1881-treated LNCaP versus control LNCaP, rep2

description:
Biological replicate AB2.
AB_41067


title: BarleyKoji_44hr_40°C_rep2

source_name: barley koji, 44 hr, 40°C, replicate 2


title: BarleyKoji_44hr_40°C_rep1

source_name: barley koji, 44 hr, 40°C, replicate 1


title: BarleyKoji_26.5hr_40°C_rep3

description: Gene expression after 26.5 hr in barley koji at 40°C

source_name: barley koji, 26.5 hr, 40°C, replicate 3


title: BarleyKoji_26.5hr_40°C_rep1

source_name: barley koji, 26.5 hr, 40°C, replicate 1


title: BarleyKoji_44hr_30°C_rep3

description: Gene expression after 44 hr in barley koji at 30°C

source_name: barley koji, 44 hr, 30°C, replicate 3


title: phc98016

description: Gene expresion data from sample phc98016

source_name: liver tissue of subject 8, tumor

value: liver


title: CHX/R1881-treated LNCaP versus control LNCaP, rep1

description:
Biological replicate CB1.
CB_17608

source_name: CHX/R188-treated LNCaP

source_name: control non-stimulated LNCaP


title: phc98015

description: Gene expresion data from sample phc98015

source_name: liver tissue of subject 8, non-tumor


title: Corrected Fanconi Anemia-iPSC-derived NSC 3

city: La Jolla

first: Fei

last: Yi

state: CA

address: 10010 North Torrey Pines Road

institute: Salk Institute

description: Gene expression data from LRRK2 (G2019S) homozygous iPSC

hyb_protocol: After hybridization cocktails preparation, the Affymetrix PrimeView arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The statistical analysis of the data was performed using GenePattern platform from Broad Institute. Briefly, raw CEL files were imported into GenePattern platform and normalized using RMA algorithm. The Hierarchical Clustering analysis was performed using the HierarchicalClustering module of the software. The dendrograms and the heat map of the clustered gene expression data were visualized by the HierarchicalClusteringViewer module.

label_protocol: The Affymetrix GeneChip microarray was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 10ug fragmented and labeled aRNA (final concentration of the aRNA on the array is 0.05ug/ul) were hybridized to the Affymetrix PrimeView chips

growth_protocol: Cells were cultured in NSC maintainance medium.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Qiagen).

treatment_protocol: The induced NSC were cultured at passage 2

value: iPSC

tag: disease state

value: Fanconi Anemia


title: BarleyKoji_26.5hr_40°C_rep2

source_name: barley koji, 26.5 hr, 40°C, replicate 2


title: BarleyKoji_44hr_30°C_rep2

source_name: barley koji, 44 hr, 30°C, replicate 2


title: phc98012

description: Gene expresion data from sample phc98012

source_name: liver tissue of subject 6, tumor


title: Corrected Fanconi Anemia-iPSC-derived NSC 2

description: Gene expression data from wildtype iPSC


title: BarleyKoji_26.5hr_30°C_rep3

description: Gene expression after 26.5 hr in barley koji at 30°C

source_name: barley koji, 26.5 hr, 30°C, replicate 3


title: Corrected Fanconi Anemia-iPSC-derived NSC 1

description: Gene expression data from wildtype iPSC


title: phc98008

description: Gene expresion data from sample phc98008

source_name: liver tissue of subject 4, tumor


title: phc98004

description: Gene expresion data from sample phc98004

source_name: liver tissue of subject 2, tumor


title: phc98011

description: Gene expresion data from sample phc98011

source_name: liver tissue of subject 6, non-tumor


title: phc98003

description: Gene expresion data from sample phc98003

source_name: liver tissue of subject 2, non-tumor


title: BarleyKoji_26.5hr_30°C_rep2

source_name: barley koji, 26.5 hr, 30°C, replicate 2


title: Fanconi Anemia-iPSC-derived NSC 3

description: Gene expression data from LRRK2 (G2019S) heterozygous fibroblasts

source_name: Fanconi Anemia-iPSC-derived NSC 3


title: BarleyKoji_44hr_30°C_rep1

source_name: barley koji, 44 hr, 30°C, replicate 1


title: BarleyKoji_26.5hr_30°C_rep1

source_name: barley koji, 26.5 hr, 30°C, replicate 1


title: Fanconi Anemia-iPSC-derived NSC 1

description: Gene expression data from LRRK2 (G2019S) homozygous fibroblasts

source_name: Fanconi Anemia-iPSC-derived NSC 1


title: Control-iPSC-derived NSC 3

source_name: Control-iPSC-derived NSC 3

value: FANCA(+/+)


title: phc98007

description: Gene expresion data from sample phc98007

source_name: liver tissue of subject 4, non-tumor


title: hippocampus_double negative_4.9 months_mouse57

source_name: hippocampus

value: DN

value: hippocampus


title: BarleyKoji_25hr_40°C_rep3

description: Gene expression after 25 hr in barley koji at 40°C

source_name: barley koji, 25 hr, 40°C, replicate 3


title: BarleyKoji_25hr_40°C_rep2

source_name: barley koji, 25 hr, 40°C, replicate 2


title: Fanconi Anemia-iPSC-derived NSC 2

source_name: Fanconi Anemia-iPSC-derived NSC 2


title: Control-iPSC-derived NSC 2

description: Gene expression data from wildtype fibroblasts

source_name: Control-iPSC-derived NSC 2


title: phc98041

description: Gene expresion data from sample phc98041

source_name: liver tissue of subject 21, non-tumor


title: BarleyKoji_25hr_40°C_rep1

source_name: barley koji, 25 hr, 40°C, replicate 1


title: Control-iPSC-derived NSC 1

source_name: Control-iPSC-derived NSC 1