title: pre-meiotic [S2_30_100_3]


title: pre-meiotic [S2_30_100_6]

status: Public on Feb 04 2015

type: genomic

city: Leicester

first: Adeolu

last: Adewoye

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

description: NimbleGen high resolution mouse aCGH data

hyb_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)

data_processing:
Data was QC and processed in R using  DNAcopy package
normalised log2 (test/control) ratio provided in *segMNT.txt file.

molecule: genomic DNA

organism: Mus musculus

extract_protocol: DNA was extracted from spleen by phenol-chloroform following standard protocols with 1% SDS and 300 μg/ml proteinase K (Roche Diagnostics limited)

tag: strain background

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)

tag: sample group

value: offspring of 3 Gy whole-body acute irradiated paternal and non-exposed maternal

tag: exposed status of the sperm (that gave rise to the offspring)

value: pre meiotic

tag: tissue

value: spleen

source_name: spleen_DNA from maternal and paternal

treatment_protocol: mixture of equal spleen_DNA concentration from maternal and paternal hybridised against DNA from each offspring

tag: strain

value: C57BL6/J (male) and CBA/Ca (female)

tag: sample type

value: reference; equal mixture of paternal and maternal DNA


title: pre-meiotic [S2_16_71_7]

scan_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)


title: pre-meiotic [S2_27_94_6]

label_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)


title: pre-meiotic [S2_30_100_5]


title: pre-meiotic [S2_24_88_3]


title: pre-meiotic [S2_16_72_3]


title: pre-meiotic [S2_13_65_2]


title: pre-meiotic [S2_30_96_1]


title: pre-meiotic [S2_30_100_4]


title: pre-meiotic [S2_24_87_3]


title: pre-meiotic [S2_24_87_6]


title: pre-meiotic [S2_27_94_2]


title: pre-meiotic [S2_27_94_4]


title: pre-meiotic [S2_16_71_3]


title: pre-meiotic [S2_27_93_1]


title: pre-meiotic [S2_16_72_5]


title: pre-meiotic [S2_16_71_4]


title: pre-meiotic [S2_30_96_2]


title: pre-meiotic [S2_27_94_5]


title: pre-meiotic [S2_27_93_3]


title: pre-meiotic [S2_21_82_3]


title: pre-meiotic [S2_24_87_1]


title: pre-meiotic [S2_24_87_2]


title: pre-meiotic [S2_21_82_4]


title: pre-meiotic [S2_27_94_1]


title: pre-meiotic [S2_16_71_1]


title: pre-meiotic [S2_21_82_5]


title: pre-meiotic [S2_15_69_1]


title: pre-meiotic [S2_30_96_4]


title: Infant No Shock. Adult  FST with no Odor rep1

type: RNA

city: Philadelphia

first: Gordon

middle: A.

last: Barr

state: PA

address: 3615 Civic Center Blvd

department: Anesthesiology and Critical Care Medicine

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: According to protocols provided by the manufacturer.

scan_protocol: Arrays were scanned with the Affymetrix GeneArray Scanner 3000 7G.

data_processing: Preprocessing, background correction and normalization (RMA) for perfect match probes only. All infant treated groups were normalized together with other experimental conditions not reported here. Differential expression between controls and the depressive phenotype groups and the depressive and rescue phenotype groups conditions was determined on logged (base 2) data by Ranked Products. Correction for multiple testing was with pfp as described.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Brain:Bilateral Amygdala

label_protocol: Nugen Linear RNA Amplification(Part #: 3100-12) and Fragmentation & Labeling(Part #: 4200-12) methods.

growth_protocol: After infant treatment, animals were weaned and allowed to grow up without intervention until adult testing.

extract_protocol: Approximately 60 milligrams fresh frozen tissue from each sample was used in this experiment. Total RNA was isolated using Trizol Reagent (Invitrogen, Cat. No: 15596), which contains phenol and guanidine isothiocyanate, to maintain the integrity of the RNA during sample homogenization. Addition of chloroform followed by centrifugation separated the solution into a RNA-containing aqueous phase and an organic phase. Total RNA was then recovered from the aqueous phase using isopropanol. The precipited RNA pellet, after washed with 75% Ethanol and Air-Dried, was redissolved in DEPC H2O. The quality of the RNA was tested by Gel Analysis and 260/280 ratio of OD (Optical Density) which should be between 1.8 and 2.0.The quantity of the RNA was measured by the OD reading at 260 nm (1 OD equals 40 _g / ml of RNA).

treatment_protocol: Infant Olfactory Conditioning: Pups were placed in individual 600mL beakers and given a 10 min acclimation period prior to conditioning to allow for recovery from experimental handling. During a conditioning session, pups received 9-11 pairings of a 30 second peppermint odor with 0.5mA hindlimb shock during the last 1 second of odor, with an intertrial interval (ITI) of 4 minutes. The odor (peppermint, McCormick & Co Inc.,) was delivered by a flow dilution olfactometer (2 liters/min flow rate) at a concentration of 1:10 peppermint vapor. The control group did not receive shock. Pups were returned to the home cage immediately after conditioning. Adult FST testing with and without odor: Depressive-like behavior was tested in a cylinder that was filled with water (25±1°C and changed for each test) to achieve a depth that prevented both escape and the tail from touching the bottom. Animals were habituated for 15 minutes one day prior to testing (day 1), and tested for a duration of 5 minutes on the next day (day 2). The time the animal spent immobile (passive floating without struggling, in a slightly hunched but upright position with the head slightly immersed and minor movements necessary to maintain the head above water) was recorded. For odor presentation during the FST, a Plexiglas lid containing an odor tube covered the FST apparatus to ensure the odor did not dissipate. This, in part, was intended to replicate previous work showing that both natural maternal odor and learned artificial maternal odor can rescue depressive-like behavior in the social behavior test and the FST.

tag: tx

value: Control

value: Bilateral Amygdala


title: pre-meiotic [S2_11_62_2]


title: pre-meiotic [S2_24_88_4]


title: pre-meiotic [S2_11_61_4]


title: pre-meiotic [S2_11_61_2]


title: pre-meiotic [S2_11_62_1]


title: pre-meiotic [S2_18_75_2]


title: pre-meiotic [S2_15_70_5]


title: pre-meiotic [S2_11_61_6]


title: pre-meiotic [S2_12_63_2]


title: pre-meiotic [S2_18_76_6]


title: pre-meiotic [S2_15_69_3]


title: pre-meiotic [S2_15_69_6]


title: pre-meiotic [S2_11_61_3]


title: pre-meiotic [S2_11_62_3]


title: pre-meiotic [S2_18_75_4]


title: pre-meiotic [S2_15_70_1]


title: pre-meiotic [S2_15_70_2]


title: pre-meiotic [S2_15_69_4]


title: pre-meiotic [S2_12_64_2]


title: pre-meiotic [S2_18_75_3]


title: pre-meiotic [ S2_21_81_2]


title: mock transfection BioRep1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Total RNA isolated 24 hours after mock transfection (lipofectamine 2000 alone)

hyb_protocol: Standard Illumina TotalPrep RNA Amplification Kit protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized using Illumina BeadStudio

organism: Homo sapiens

source_name: HeLa cells_mock_transfection

growth_protocol: DMEM supplemented with 10% FBS

extract_protocol: Total RNA was isolated with TRIzol

treatment_protocol: mature miR-503, miR-103, miR-494 duplex, siGFP, or mock transfection (lipofectamine 2000 alone) was transfected with lipofectamine 2000 at a concentration of 100nM in the well

tag: cell line

value: HeLa


title: miR-494 BioRep1

description: Total RNA isolated 24 hours after transfection of miR-494 mature duplexes

source_name: HeLa cells_miR-494_mature_duplex

label_protocol: Standard Illumina TotalPrep RNA Amplification Kit protocol


title: pre-meiotic [S2_15_69_2]


title: miR-103 BioRep1

description: Total RNA isolated 24 hours after transfection of miR-103 mature duplexes

source_name: HeLa cells_miR-103_mature_duplex


title: mock transfection BioRep2


title: siGFP BioRep1

description: Total RNA isolated 24 hours after transfection of siGFP mature duplexes

source_name: HeLa cells_siRNA_GFP


title: pre-meiotic [S2_21_81_3]


title: pre-meiotic [S2_15_69_5]


title: siGFP BioRep2


title: NCI-H716_YAP1.2

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: treatment

value: YAP mutant vector


title: miR-494 BioRep2


title: pre-meiotic [S2_15_70_6]


title: pre-meiotic [S2_12_64_4]


title: NCI-H716_YAP1.3


title: pre-meiotic [S2_12_64_3]


title: NCI-H716_Control.1


title: pre-meiotic [S2_18_76_5]


title: miR-503 BioRep1

description: Total RNA isolated 24 hours after transfection of miR-503 mature duplexes

source_name: HeLa cells_miR-503_mature_duplex


title: NCI-H716_Control.2


title: NCI-H716_Control.3


title: NCI-H716_YAP1.1


title: pre-meiotic [S2_18_75_1]


title: pre-meiotic [S2_11_62_4]


title: NCI-H716_Mock.1

value: control vector


title: pre-meiotic [S2_18_76_3]


title: pre-meiotic [S2_15_69_7]


title: NCI-H716_Mock.2


title: NCI-H716_Mock.3


title: miR-103 BioRep2


title: pre-meiotic [S2_21_81_4]


title: pre-meiotic [S2_21_81_1]


title: pre-meiotic [S2_18_76_4]


title: Gastr WT1 rep2

city: Los Angeles

first: Lily

last: Chao

state: CA

address: 4650 Sunset Blvd

institute: CHLA

description: Sample 7

hyb_protocol: per Illumina standard protocol

scan_protocol: per Illumina standard protocol

data_processing: per Illumina standard protocol

source_name: mouse

label_protocol: per Illumina standard protocol

growth_protocol: RNA samples prepared from mice fasted overnight

extract_protocol: Standard Trizol protocol

value: skeletal muscle

tag: genotype

value: wild type


title: Gastr TG1 rep2

description: Sample 10

value: Nur77 overexpression


title: pre-meiotic [S2_15_70_4]


title: pre-meiotic [S2_11_61_1]


title: Gastr TG2 rep2

description: Sample 11


title: miR-503 BioRep2


title: Gastr TG3 rep1

description: Sample 6


title: Gastr WT2 rep2

description: Sample 8


title: Gastr TG2 rep1

description: Sample 5


title: pre-meiotic [S2_18_76_2]


title: pre-meiotic [S2_12_64_1]


title: Gastr WT3 rep1

description: Sample 3


title: pre-meiotic [S2_21_82_2]


title: Gastr TG3 rep2

description: Sample 12


title: Gastr WT3 rep2

description: Sample 9


title: pre-meiotic [S2_21_82_1]


title: pre-meiotic [S2_12_63_1]


title: pre-meiotic [S2_12_63_3]


title: pre-meiotic [S2_12_64_5]


title: pre-meiotic [S2_15_70_3]


title: pre-meiotic [S2_12_63_4]


title: pre-meiotic [S2_21_81_5]


title: Gastr WT1 rep1

description: Sample 1


title: pre-meiotic [S2_11_61_5]


title: GATA1s A

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

state: OH

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

description:
Replicate 1
SAMPLE 3

hyb_protocol: Standard illumina hybridization protocol

data_processing: Data were quantile normalized and background was subtracted with IlluminaGUI

label: biotin

label_protocol: Standard Illumina protocol

growth_protocol: G1ME cells were cultured in 1% TPO supernatant (v/v)

extract_protocol: RNeasy column (Qiagen)

treatment_protocol: Retroviral supernatant was added to the cells at 1e6 cells per ml, and the culture was centrifuged at 3200rpm for 90min. The cells were incuabted in the virus for an additional 4h, and then the virus was removed.  The cells were crosslinked 48h later.

value: Mutant:derived from Gata1-null ES cells

tag: cell type

value: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential

tag: media

value: Cells grown in TPO supernatant (10% v/v)

tag: retrovirus

value: Sorted GFP-postive cells


title: pre-meiotic [S2_18_76_1]

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)

value: offspring of 3 Gy whole-body acute irradiated paternal and non-exposed maternal


title: post-meiotic [S1_29_57_2]

value: post meiotic

value: spleen


title: BS149_MITF-RFP-HA_rep1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v3.01) 'affy' package using the rma() function

source_name: BS149-glioblastoma cells, 24 h transient overexpression

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Cells were cultured in DMEM medium containing 10% Fetal Bovine Serum (FBS), 100 mg/L penicillin and 100 mg/L streptomycin.

extract_protocol: Total RNA was extracted with an RNeasy Mini kit and QIAshredder columns (both Qiagen).

tag: tumor stage

value: Type IV glioblastoma


title: BS149_RFP-HA_rep2


title: Gastr TG1 rep1

description: Sample 4


title: GATA1s B

description:
Replicate 2
SAMPLE 7


title: BS149_MITF-RFP-HA_rep3


title: Gastr WT2 rep1

description: Sample 2


title: post-meiotic [S1_12_23_5]

value: C57BL6/J (male) and CBA/Ca (female)

value: reference; equal mixture of paternal and maternal DNA


title: BS149_TEN1-ICD-GFP-His_rep3

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.14) 'affy' package using the rma() function


title: pre-meiotic [S2_21_81_6]

value: pre meiotic


title: post-meiotic [S1_24_48_3]


title: GATA1s C

description:
Replicate 3
SAMPLE 11


title: BS149_MITF-RFP-HA_rep2


title: post-meiotic [S1_28_56_2]


title: post-meiotic [S1_24_48_4]


title: BS149_RFP-HA_rep1


title: BS149_TEN1-ICD-GFP-His_rep2


title: post-meiotic [S1_11_21_2]


title: BS149_GFP-His_rep1


title: CFU-PreB colonies Hspa9+/-, biological replicate 2

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description:
Sample name: Het_2
Gene-level RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) at the Genome Technology Access Center (Washington University in St. Louis)

scan_protocol: Samples were scanned at the Genome Technology Access Center (Washington University in St. Louis)

data_processing: RMA-summarized gene-level expression values computed using Affymetrix Expression Console.

source_name: CFU-PreB colonies Hspa9+/-

label_protocol: Nugen Encore Biotin kit protocol

growth_protocol: CFU-PreB colonies grown in M3630 media (Stem Cell Technologies) were collected on Day 7.

extract_protocol: B220+ cells were sorted directly into TRIzol LS (Life Technologies) and RNA was extracted using standard protocols. cDNA was prepared using the PicoSL Ovation system (NuGen). Samples were hybridized to Mouse Gene 1.0 ST arrays.

treatment_protocol: not applicable

value: B220+ cells from preB colonies

tag: genotype/variation


title: post-meiotic [S1_12_24_3]


title: post-meiotic [S1_15_29_1]


title: BS149_RFP-HA_rep3


title: post-meiotic [S1_29_58_2]


title: post-meiotic [S1_14_28_3]


title: CFU-PreB colonies Hspa9+/-, biological replicate 4

description:
Sample name: Het_4
Gene-level RMA expression value derived from Expression Console software


title: BS149_GFP-His_rep2


title: post-meiotic [S1_30_60_1]


title: post-meiotic [S1_29_58_1]


title: CFU-PreB colonies Hspa9+/-, biological replicate 3

description:
Sample name: Het_3
Gene-level RMA expression value derived from Expression Console software


title: BS149_GFP-His_rep3


title: CFU-PreB colonies Wildtype littermate, biological replicate 4

description:
Sample name: WT_4
Gene-level RMA expression value derived from Expression Console software

source_name: CFU-PreB colonies Wildtype littermate


title: post-meiotic [S1_12_23_6]


title: post-meiotic [S1_30_60_3]


title: post-meiotic [S1_27_54_3]


title: CFU-PreB colonies Hspa9+/-, biological replicate 5

description:
Sample name: Het_5
Gene-level RMA expression value derived from Expression Console software


title: CFU-PreB colonies Hspa9+/-, biological replicate 1

description:
Sample name: Het_1
Gene-level RMA expression value derived from Expression Console software


title: post-meiotic [S1_11_21_3]


title: CFU-PreB colonies Wildtype littermate, biological replicate 5

description:
Sample name: WT_5
Gene-level RMA expression value derived from Expression Console software


title: post-meiotic [S1_28_56_1]


title: CFU-PreB colonies Wildtype littermate, biological replicate 3

description:
Sample name: WT_3
Gene-level RMA expression value derived from Expression Console software


title: post-meiotic [S1_28_56_3]


title: post-meiotic [S1_29_57_3]


title: CFU-PreB colonies Wildtype littermate, biological replicate 2

description:
Sample name: WT_2
Gene-level RMA expression value derived from Expression Console software


title: post-meiotic [S1_30_60_2]


title: post-meiotic [S1_29_57_1]


title: post-meiotic [S1_29_58_3]


title: post-meiotic [S1_23_46_1]


title: post-meiotic [S1_23_46_2]


title: Renal cortical dendritic cells, biological rep2 (BALB/c)

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

country: Germany

institute: German Cancer Research Center

description: Gene expression data from renal cortical dendritic cells under homeostatic conditions (BALB/c)

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with R/Bioncoductor, using RMA (oligo package) as normalization method with default settings. Control probes and probes without gene symbol were removed.

source_name: Renal cortical dendritic cells (homeostatic kidney, BALB/c)

label_protocol: cDNA was fragmented and biotin-labeled using Nugen Encore Biotin Module (Nugen Technologies Inc.).

growth_protocol: Dendritic cells for microarray analysis were freshly isolated from mouse kidneys and directly subjected to RNA isolation.

extract_protocol: Total RNA was isolated from FACS-sorted cells using RNeasy Micro Kit (Qiagen) and amplified using Nugen Ovation One-Direct System (Nugen Technologies Inc.).

treatment_protocol: Healthy and transplanted kidneys were digested in RPMI medium, Collagenase IA- and DNase I- enriched. The cell suspensions obtained were stained with specific fluorochrome-conjugated antibodies. Renal dendritic cells were isolated from cortex and medulla of homeostatic (healthy) kidneys through fluorescence-activated cell sorting, according the their expression of surface markers CD45, CD11c and MHCII. Likewise, donor and host dendritic cells from cortex and medulla of renal allografts (3 days post-transplantation) were independently isolated due to their expression of respectively CD45.2 and CD45.1, as well as CD11c and MHCII.

tag: mouseid

tag: site

value: cortex

tag: condition

value: homeostasis

value: BALB/c


title: Host medullary dendritic cells, biological rep2

description: Gene expression data from host dendritic cells in renal medulla during allograft rejection

source_name: Host dendritic cells from medulla of renal allograft (3 days post-transplantation)

value: medulla

value: allograft host


title: CFU-PreB colonies Wildtype littermate, biological replicate 1

description:
Sample name: WT_1
Gene-level RMA expression value derived from Expression Console software


title: Renal medullary dendritic cells, biological rep2 (BALB/c)

description: Gene expression data from renal medullary dendritic cells under homeostatic conditions (BALB/c)

source_name: Renal medullary dendritic cells (homeostatic kidney, BALB/c)


title: post-meiotic [S1_16_32_1]

description: NimbleGen high resolution mouse aCGH data

tag: strain background

tag: sample group


title: post-meiotic [S1_23_46_4]

tag: exposed status of the sperm (that gave rise to the offspring)

tag: tissue


title: Renal cortical dendritic cells, biological rep3 (BALB/c)

tag: strain


title: Host medullary dendritic cells, biological rep1


title: post-meiotic [S1_24_48_8]

tag: sample type


title: post-meiotic [S1_16_32_2]


title: Renal medullary dendritic cells, biological rep4 (BALB/c)


title: Renal medullary dendritic cells, biological rep3 (BALB/c)


title: post-meiotic [S1_20_39_1]


title: Renal cortical dendritic cells, biological rep1 (BALB/c)


title: Renal cortical dendritic cells, biological rep4 (BALB/c)


title: Renal medullary dendritic cells, biological rep1 (BALB/c)


title: post-meiotic [S1_21_41_2]


title: Host medullary dendritic cells, biological rep3


title: post-meiotic [S1_21_42_1]


title: post-meiotic [S1_16_32_3]


title: Host cortical dendritic cells, biological rep3

description: Gene expression data from host dendritic cells in renal cortex during allograft rejection

source_name: Host dendritic cells from cortex of renal allograft (3 days post-transplantation)


title: Host cortical dendritic cells, biological rep2


title: post-meiotic [S1_24_48_5]


title: Host cortical dendritic cells, biological rep1


title: post-meiotic [S1_24_48_7]


title: post-meiotic [S1_24_48_6]


title: post-meiotic [S1_27_54_2]


title: post-meiotic [S1_21_41_3]


title: Donor cortical dendritic cells, biological rep2

description: Gene expression data from donor dendritic cells in renal cortex during allograft rejection

source_name: Donor dendritic cells from cortex of renal allograft (3 days post-transplantation)

value: allograft donor


title: post-meiotic [S1_27_54_1]


title: Donor medullary dendritic cells, biological rep2

description: Gene expression data from donor dendritic cells in renal medulla during allograft rejection

source_name: Donor dendritic cells from medulla of renal allograft (3 days post-transplantation)


title: Donor cortical dendritic cells, biological rep3


title: post-meiotic [S1_21_42_2]

source_name: spleen_DNA from maternal and paternal


title: post-meiotic [S1_21_41_1]


title: post-meiotic [S1_20_39_2]


title: post-meiotic [S1_21_42_3]


title: post-meiotic [S1_24_48_2]


title: Donor medullary dendritic cells, biological rep3


title: post-meiotic [S1_21_41_4]


title: post-meiotic [S1_23_46_3]


title: post-meiotic [S1_24_48_1]


title: Renal medullary dendritic cells, biological rep4 (C57BL/6)

description: Gene expression data from renal medullary dendritic cells under homeostatic conditions (C57BL/6)

source_name: Renal medullary dendritic cells (homeostatic kidney, C57BL/6)


title: Donor cortical dendritic cells, biological rep1


title: Donor medullary dendritic cells, biological rep1


title: Renal cortical dendritic cells, biological rep3 (C57BL/6)

description: Gene expression data from renal cortical dendritic cells under homeostatic conditions (C57BL/6)

source_name: Renal cortical dendritic cells (homeostatic kidney, C57BL/6)


title: BS149_TEN1-ICD-GFP-His_rep1

tag: cell line


title: Renal medullary dendritic cells, biological rep3 (C57BL/6)


title: post-meiotic [S1_12_24_1]


title: SVC_HFD_Day7_rep1

city: Seoul

first: Jae Bum

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: Short-term HFD

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: Stromal vascular fraction_HFD_Day7

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Seven-week-old male C57BL/6J mice were obtained from The Jackson Laboratory and were housed in colony cages in 12-h light/12-h dark cycles.

extract_protocol: Epididymal adipopse tissues were chopped and incubated in collagenase buffer. After centrifugation, adipocytes in the supernatant and pelleted stromal vascular cell (SVC) fraction were collected for RNA extraction.

treatment_protocol: Mice were fed normal chow diet (NCD) until they were subjected to 60% HFD for the indicated time periods.

value: Epididymal adipose tissue

tag: treatment

value: high fat diet

tag: time

value: 7 d


title: Renal medullary dendritic cells, biological rep1 (C57BL/6)


title: post-meiotic [S1_15_29_2]

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)

value: offspring of 3 Gy whole-body acute irradiated paternal and non-exposed maternal


title: post-meiotic [S1_12_23_4]

value: post meiotic

value: spleen


title: Renal cortical dendritic cells, biological rep4 (C57BL/6)


title: Renal cortical dendritic cells, biological rep1 (C57BL/6)


title: post-meiotic [S1_11_21_1]

value: C57BL6/J (male) and CBA/Ca (female)


title: post-meiotic [S1_11_21_4]

value: reference; equal mixture of paternal and maternal DNA


title: post-meiotic [S1_13_25_1]


title: post-meiotic [S1_12_23_3]


title: Renal cortical dendritic cells, biological rep2 (C57BL/6)


title: SVC_HFD_Day3_rep3

description: Short-term HFD

source_name: Stromal vascular fraction_HFD_Day3

value: 3 d


title: SVC_NCD_Day0_rep2

description: Short-term HFD

source_name: Stromal vascular fraction_NCD_Day0

value: normal chow

value: 0 d


title: post-meiotic [S1_13_25_2]


title: SVC_NCD_Day0_rep3

description: Short-term HFD


title: AD_HFD_Day7_rep2

description: Short-term HFD

source_name: Adipocyte fraction_HFD_Day7


title: post-meiotic [S1_14_28_1]


title: Renal medullary dendritic cells, biological rep2 (C57BL/6)

value: homeostasis


title: SVC_HFD_Day7_rep2

description: Short-term HFD


title: AD_HFD_Day7_rep3

description: Short-term HFD


title: SVC_HFD_Day3_rep1

description: Short-term HFD


title: post-meiotic [S1_15_30_5]


title: SVC_HFD_Day7_rep3

description: Short-term HFD


title: post-meiotic [S1_30_60_4]


title: post-meiotic [S1_13_25_3]


title: AD_HFD_Day3_rep2

description: Short-term HFD

source_name: Adipocyte fraction_HFD_Day3


title: FK506 4h, biological rep2

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

hyb_protocol: Fragmented samples were hybridized according to Affymetrix guidelines for 17hr in 45°C on GeneChip Mouse Gene 1.0 ST Array; The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The mouse gene chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: The samples were normalized using RMA algorithm in affy package in R v.2.15.2/Bioconductor

source_name: curdlan +FK506 4h

label_protocol: Single-stranded DNA were prepared according to the Ambion WT Expression Kit from 100ng of total RNA. 5.5ug of ssDNA were fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: Murine dendritic cells (D1) were cultured as previously described  (Granucci et al., 2001; Winzler et al., 1997)

extract_protocol: Total RNA was isolated by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol, Invitrogen) followed by Qiagen RNeasy clean-up procedure.

treatment_protocol: D1 cells were treated with 10ug/ml curdlan for 2h and 4h, and curdlan+FK506 for 2h and 4h.

tag: cell type

value: splenic long term dendritic cells


title: post-meiotic [S1_15_30_2]


title: AD_HFD_Day3_rep1

description: Short-term HFD


title: AD_HFD_Day7_rep1

description: Short-term HFD


title: AD_NCD_Day 0_rep1

description: Short-term HFD

source_name: Adipocyte fraction_NCD_Day 0


title: post-meiotic [S1_15_29_3]


title: FK506 4h, biological rep3


title: post-meiotic [S1_15_30_1]


title: post-meiotic [S1_12_24_2]


title: post-meiotic [S1_15_30_6]


title: SVC_HFD_Day3_rep2

description: Short-term HFD


title: post-meiotic [S1_12_23_1]


title: SVC_NCD_Day0_rep1

description: Short-term HFD


title: post-meiotic [S1_12_23_2]


title: AD_HFD_Day3_rep3

description: Short-term HFD


title: post-meiotic [S1_15_30_4]


title: post-meiotic [S1_15_30_3]


title: post-meiotic [S1_13_25_4]


title: post-meiotic [S1_14_28_2]


title: FK506 4h, biological rep1


title: Control [C_1_1_4]

value: offspring of parents with sham -ir


title: FK506 2h, biological rep2

source_name: curdlan +FK506 2h


title: Control [C_1_1_5]


title: Control [C_1_1_1]


title: AD_NCD_Day 0_rep2

description: Short-term HFD


title: Control [C_1_1_3]


title: Control [C_1_1_6]


title: Control [C_6_12_5]


title: Control [C_1_2_4]


title: Control [C_3_6_7]


title: Control [C_3_5_3]


title: Control [C_6_12_4]


title: FK506 2h, biological rep1


title: Curdlan 2h, biological rep3

source_name: curdlan 2h


title: Control [C_1_2_2]


title: FK506 2h, biological rep3


title: Control [C_10_19_5]


title: Curdlan 4h, biological rep3

source_name: curdlan 4h


title: Control [C_4_7_4]


title: Control [C_2_3_1]


title: Control [C_6_12_2]


title: Control [C_3_5_6]


title: Curdlan 2h, biological rep2


title: Control [C_5_10_1]


title: Curdlan 4h, biological rep1


title: Control [C_2_4_4]


title: Curdlan 4h, biological rep2


title: D1 NT, biological rep2

source_name: D1 nontreated


title: Control [C_10_20_5]


title: Curdlan 2h, biological rep1


title: Control [C_1_2_7]


title: D1 NT, biological rep1


title: D1 NT, biological rep3


title: AD_NCD_Day 0_rep3

description: Short-term HFD


title: CHP134, CPX treated 90m, polysomal RNA, bio.rep #3 (90 min)

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: Polysomal RNA sample extracted from CHP134 cells treated with 5 µM CPX for 90 minutes.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: The scanned TIFF images were analyzed numerically and the background corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 3

growth_protocol: CHP134 cells were purchased from ECACC (Cat. No. 06122002). The cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium 1640 medium supplemented with 10% fetal bovine serum (FBS) and 2 mM glutamine at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol: To extract polysomal RNA, the following procedure was applied. CHP134 cells were incubated with 100 μg/ml cycloheximide for 4 minutes, rinsed with phosphate buffer saline and lysed directly in cell-culture vessels [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1 % Triton X-100, 1 % sodium deoxycholate, 100 μg/ml cycloheximide, 0.2 U/μl RNase inhibitor, 1 mM DTT]. The lysate was collected with a cell scraper, pipetted into a microcentrifuge tube and after 5 minutes incubation on ice centrifuged for 10 min at 12000 g at 4 °C. The supernatant was transferred into a new microcentrifuge tube and stored at –80 °C. The lysates were fractionated by ultracentrifugation (Sorvall rotor, 100 min at 180000 g) through 15–50 % linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2.  Polysomal fractions were collected monitoring the absorbance at 254 nm. Polysomal RNA was isolated after proteinase K treatment, phenol–chloroform extraction and isopropanol precipitation and finally resuspended in 50 μl of water. RNA quality was assessed using the Agilent 2100 Bioanalyzer platform.

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with 5 µM CPX for 90 minutes.

tag: disease

value: neuroblastoma

tag: compound

value: CPX

tag: rna fraction

value: polysomal RNA

tag: biological replicate


title: Control [C_5_9_4]


title: Control [C_3_6_4]


title: Control [C_2_3_3]


title: CHP134, CPX treated 90m, polysomal RNA, bio.rep #2 (90 min)

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 2


title: Control [C_9_18_5]


title: Control [C_1_2_5]


title: Control [C_9_18_3]


title: Control [C_4_7_6]


title: CHP134, CPX treated 90m, total RNA, bio.rep #3 (90 min)

description: Total RNA sample extracted from CHP134 cells treated with 5 µM CPX for 90 minutes.

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 3

extract_protocol: Total RNA was extracted using RNeasy Plus Mini kit (Qiagen) following the instructions of the supplier and eluted in 50 μl of water.

value: total RNA


title: Control [C_2_3_4]

source_name: spleen_DNA from maternal and paternal


title: CHP134, untreated, total RNA, bio.rep #3 (90 min)

description: Total RNA sample extracted from untreated CHP134 cells.

source_name: CHP134 cells, untreated, total RNA, biological replicate 3

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with vehicle for 90 minutes.

value: vehicle


title: CHP134, untreated, polysomal RNA, bio.rep #2 (90 min)

description: Polysomal RNA sample extracted from untreated CHP134 cells.

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 2


title: Control [C_9_17_1]

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)


title: CHP134, CPX treated 90m, polysomal RNA, bio.rep #1 (90 min)

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 1


title: CHP134, untreated, total RNA, bio.rep #2 (90 min)

source_name: CHP134 cells, untreated, total RNA, biological replicate 2


title: Control [C_1_2_3]


title: Control [C_5_9_3]


title: CHP134, untreated, polysomal RNA, bio.rep #3 (90 min)

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 3


title: CHP134, CPX treated 90m, total RNA, bio.rep #2 (90 min)

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 2


title: Control [C_3_6_6]


title: CHP134, untreated, polysomal RNA, bio.rep #1 (90 min)

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 1


title: Control [C_2_3_2]


title: Control [C_10_19_7]


title: CHP134, untreated, total RNA, bio.rep #1 (90 min)

source_name: CHP134 cells, untreated, total RNA, biological replicate 1


title: CHP134, CPX treated 90m, total RNA, bio.rep #1 (90 min)

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 1


title: Control [C_5_10_5]


title: Control [C_9_18_4]


title: Control [C_9_18_6]


title: Control [C_5_9_2]


title: Control [C_5_10_4]


title: Control [C_6_12_3]


title: Control [C_9_18_2]


title: Control [C_8_16_2]


title: Control [C_9_17_4]


title: Control [C_5_10_3]


title: Control [C_6_12_1]


title: Control [C_5_9_5]


title: Control [C_1_1_2]


title: Control [C_9_17_2]


title: Control [C_8_16_3]


title: Control [C_8_15_2]


title: Control [C_4_7_5]


title: Control [C_5_9_1]


title: Control [C_8_16_4]


title: Control [C_9_18_1]


title: Control [C_9_17_3]


title: Control [C_8_16_1]


title: Control [C_8_15_1]


title: Control [C_5_10_2]


title: Control [C_4_7_7]


title: Control [C_3_5_8]


title: Control [C_2_4_1]


title: Control [C_2_3_6]


title: OAS_T11

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2, The complete_data.txt contains unmethylated and methylated signal intensities (along with average beta and pval).

label: Cy3, Cy5

source_name: Breast tumour

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: disease state

value: Tumor sample

value: fresh frozen tissue

tag: cancer subtype

value: Basal-like


title: Control [C_3_5_4]

value: spleen

value: C57BL6/J (male) and CBA/Ca (female)


title: Control [C_1_2_1]

value: reference; equal mixture of paternal and maternal DNA


title: Control [C_2_3_7]


title: Control [C_2_4_6]


title: Control [C_4_7_1]


title: OAS_N7

source_name: Normal breast tissue

value: Morphologically normal tissue


title: Control [C_2_4_3]


title: OAS_N9


title: OAS_T109

value: TNP


title: OAS_T40


title: OAS_N66


title: Control [C_3_6_2]


title: Control [C_10_20_4]


title: Control [C_2_4_2]


title: Control [C_3_5_2]


title: Control [C_3_5_5]


title: OAS_N8


title: OAS_N40


title: Control [C_4_7_3]


title: OAS_N50


title: OAS_N13


title: Control [C_3_5_1]


title: OAS_N110


title: OAS_N4


title: Control [C_4_7_2]


title: OAS_N6


title: OAS_T81


title: Control [C_3_6_8]


title: OAS_N3


title: OAS_N19A


title: OAS_N2


title: Control [C_3_6_1]


title: Control [C_2_4_5]


title: OAS_N116


title: Control [C_3_5_7]


title: OAS_N5


title: OAS_N1


title: Control [C_3_6_5]


title: OAS_T122


title: Control [C_3_6_3]


title: OAS_N18


title: Control [C_10_20_2]


title: Control [C_10_20_3]


title: Control [C_2_3_5]


title: OAS_T88

value: LumA


title: Control [C_10_19_4]


title: Homo_N3-1

city: Beijing

first: Weitao

last: Man

address: Fuxing Hospital affiliated to Capital Medical University,Beijing,China

country: China

description: Gene expression data from glioblastoma tissue.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array, 1 ug of cRNA were hybridized for 16 hr at 48℃ on Affymetrix GeneChip miRNA  Array were washed and stained in the affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with  Affymetrix ExpressionConsole-1_4_0 (EC 5.0) using Robust Multichip Average (RMA) as normalization method.

source_name: Adjacent normal brain tissue

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

growth_protocol: A totle of  3 GBM tissues and the matched adjacent normal brain tissues were obtained from patients who underwent primary surgical treatment according to clinical protocols.

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

treatment_protocol: The tissues were obtained from the operation room and were snap-frozen immediately, stored at -80℃.

tag: individual

value: patient 3

value: Adjacent normal brain tissue

tag: gender

value: male

tag: age(years)


title: Control [C_10_19_6]

tag: strain background

tag: sample group

value: offspring of parents with sham -ir


title: Homo_G2-1

institute: Fuxing Hospital affiliated to Capital Medical University

source_name: Glioblastoma tissue

value: patient 2

tag: tissue

value: Glioblastoma tissue


title: Control [C_4_7_8]

tag: strain

tag: sample type


title: OAS_T123


title: Homo_N1-1

value: patient 1


title: Homo_G3-1


title: Control [C_1_2_6]

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)


title: Homo_G1-1


title: Homo_N2-1


title: Control [C_10_19_1]


title: OAS_T89

value: Tumor sample


title: Control [C_10_19_2]


title: OAS_T68

value: fresh frozen tissue


title: Control [C_10_19_3]


title: OAS_T66


title: OAS_T62


title: OAS_T27


title: OAS_T47


title: Shh-cre:Ezh2-flox/flox mutant 4

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
M4
Gene expression data from E14.5 Ezh2 epithelial knock-out lungs (using Shh-cre driver).

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

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

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

source_name: E14.5 mouse lungs from Shh-cre:Ezh2-flox/flox mutant

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

growth_protocol: Embryonic gestation to E14.5.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Mini Kit.

treatment_protocol: Lungs dissected out into RNAlater (Invitrogen), stored at 4C overnight, then removed from RNAlater and snap-frozen in liquid nitrogen, and stored at -80C until RNA extraction.

tag: strain/background

value: mixed C57BL/6 x 129S6

tag: genotype/variation

tag: age

value: embryonic day 14.5

value: lung


title: Shh-cre:Ezh2-flox/flox mutant 3

description:
M3
Gene expression data from E14.5 Ezh2 epithelial knock-out lungs (using Shh-cre driver).


title: Shh-cre:Ezh2-flox/flox mutant 2

description:
M2
Gene expression data from E14.5 Ezh2 epithelial knock-out lungs (using Shh-cre driver).


title: OAS_T39

value: LumB


title: OAS_T116


title: OAS_T13


title: OAS_T14


title: Shh-cre:Ezh2-flox/flox mutant 1

description:
M1
Gene expression data from E14.5 Ezh2 epithelial knock-out lungs (using Shh-cre driver).


title: OAS_T111


title: OAS_T107


title: Control [C_10_20_1]

value: spleen

value: C57BL6/J (male) and CBA/Ca (female)

value: reference; equal mixture of paternal and maternal DNA


title: OAS_T58


title: Shh-cre control 4

description:
C4
Gene expression data from E14.5 Shh-cre control lungs.

source_name: E14.5 mouse lungs from Shh-cre control

value: Shh-cre


title: OAS_T52

value: LumA


title: OAS_T37


title: Shh-cre control 3

description:
C3
Gene expression data from E14.5 Shh-cre control lungs.


title: Shh-cre control 2

description:
C2
Gene expression data from E14.5 Shh-cre control lungs.


title: OAS_T8

value: Basal-like


title: OAS_T55


title: Shh-cre control 1

description:
C1
Gene expression data from E14.5 Shh-cre control lungs.


title: OAS_T90


title: OAS_T30


title: OAS_T6


title: OAS_T108


title: Hemophilia A without inhibitors biological rep6

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama I Rd. Chulapat I Bldg. Room 1312 Wangmai Pathumwan

department: Clinical Chemistry

country: Thailand

institute: Chulalongkorn University

description: Small ncRNA expression data from hemophilia A patients without inhibitors

hyb_protocol: Biotin-labeled RNA samples (500 ng/sample) were hybridized on GeneChip miRNA 3.0 microarrays (Affymetrix), each of which contains 19,724 probe sets covering over 5,600 human miRNAs, pre-miRNAs, snoRNAs, and scaRNAs, whose sequence information is based on the miRBase database version 17 http://www.mirbase.org/.  After hybridization, the hybridization cocktail was extracted from each microarray and all microarrays were automatically washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: The microarrays were scanned using GeneChip Scanner 3000 7G (Affymetrix). All washing, staining, and scanning steps were controlled by the Affymetrix Command Console software according to the manufacturer’s instruction for GeneChip miRNA 3.0 microarrays.

data_processing: The Expression Console software (Affymetrix) was then used to evaluate the success of the labeling protocol and array processing. Partek Genomics Suite software was used to analyze the intensities for the probe elements across the microarray and to identify significantly differentially expressed ncRNAs. The data normalization procedures for Affymetrix miRNA microarrays include RNA background correction, quantile normalization, log(base 2) transformation of intensity data, and probe set summarization using Median Polish method. Analysis of variance was then used for identifying significantly differentially expressed ncRNAs in HA according to the Partek Genomics Suite workflow recommended by Affymetrix.

source_name: Hemophilia A patients without inhibitors

label_protocol: All RNA samples were poly (A)-tailed and biotin-labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA, USA). After labeling, the enzyme linked oligosorbent assays (ELOSA) were performed to confirm that the biotin labeling processes were successful.

extract_protocol: Total RNA was isolated and purified from whole blood using the RiboPure Blood Kit (Life Technologies) according to the manufacturer’s protocol with modifications to enhance the enrichment of low molecular weight RNAs. Briefly, whole blood in the RNAlater Solution was centrifuged and the pellet mixed with 800 µl Lysis Solution (Life Technologies). A total of 10 µl acetic acid was added to the lysates and total RNA was extracted by adding 500 µl acid-phenol chloroform. Following centrifugation, the aqueous (upper) phase was carefully transferred to a 15 ml RNase-free tube and total RNA was then precipitated by adding 2.7 ml of 100% ethanol. RNA was purified using a RNA Filter Cartridge (Life Technologies). Purified RNA on the filter was then eluted by adding 100 µl Elution Solution (Life Technologies) containing 0.1 mM EDTA. RNA concentration was measured using the NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and the purity of RNA was determined by the 260/280 ratio of higher than 1.8. All RNA samples were analyzed by a gel-on-chip analysis using Agilent Bioanalyzer to assess RNA integrity and the enrichment of low molecular weight RNAs.

value: Whole blood

value: Hemophilia A without inhibitors


title: OAS_T9


title: Hemophilia A without inhibitors biological rep5


title: OAS_T7


title: Hemophilia A without inhibitors biological rep4


title: OAS_T23


title: Hemophilia A without inhibitors biological rep3


title: Hemophilia A without inhibitors biological rep1


title: OAS_T4


title: OAS_T5


title: Hemophilia A with inhibitors biological rep2

description: Small ncRNA expression data from hemophilia A patients with inhibitors

source_name: Hemophilia A patients with inhibitors

value: Hemophilia A patients with inhibitors


title: OAS_T25


title: Ikzf1Neo+/- splenocytes non-treated

city: Nijmegen

first: Rene

last: Marke

state: Gelderland

address: Philipps van Leijdenslaan 15

department: Kindergeneeskunde

country: Netherlands

institute: Radboudumc

description:
3 pooled mice
102175-20.AVG_Signal

hyb_protocol: according to the Illumina Manual “Direct Hybridization Assay Guide

scan_protocol: Illumina iScan

data_processing:
Illumina GenomeStudio v2011.1 Gene Expression Software  Expression software
Log2 transformation and RMA normalized using Arraystar

label_protocol: Illumina Totalprep-96

growth_protocol: RPMI containing Glutamax supplemented with 10% FBS, 1% P/S and 5 µg/mL LPS

extract_protocol: RNA was extracted with RNeasy Minikit (Qiagen), followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: untreated (normal RPMI) or Prednisolone treated for 16 hours.

tag: cell type

value: splenocytes

tag: treated ith

value: none (untreated control)


title: Hemophilia A with inhibitors biological rep3


title: Wildtype splenocytes+Prednisolone

description:
3 pooled mice
102175-23.AVG_Signal

value: wild type

value: Prednisolone for 16hr


title: Hemophilia A with inhibitors biological rep1


title: OAS_T17

value: Tumor sample

value: fresh frozen tissue


title: Ikzf1Neo+/- splenocytes+Prednisolone

description:
3 pooled mice
102175-24.AVG_Signal


title: Control biological rep4

description: Small ncRNA expression data from healthy individual

source_name: Healthy individual

value: healthy


title: Hemophilia A without inhibitors biological rep2


title: OAS_T24


title: Wildtype splenocytes non-treated

description:
3 pooled mice
102175-19.AVG_Signal


title: Homo_N3-2

description: Gene expression data from Adjacent normal brain tissue.

value: patient 3

value: Adjacent normal brain tissue

value: male


title: Homo_G3-2

value: Glioblastoma tissue


title: Homo_N2-2

value: patient 2


title: Homo_G2-2


title: Control biological rep5


title: Homo_G1-2

value: patient 1


title: OAS_T18

value: Basal-like


title: Homo_N1-2


title: Control biological rep2

value: Whole blood


title: OAS_T1


title: OAS_T104


title: Fibros_3

city: Graz

first: Andreas

last: Reinisch

address: Auenbruggerplatz 38

department: Dept. of Internal Medicine, Division of Hematology, Stem Cell Research Unit

country: Austria

institute: Medical University of Graz

description: plastic adherent cells

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: Adult skin fibroblasts

extract_protocol: Genomic DNA was isolated from 5x10E6 cells using the Qiagen DNA Blood Mini Kit.

value: Adult skin fibroblasts

tag: passage


title: OAS_T105


title: Control biological rep1


title: CD71+ Erythroblasts_Hemozoin_d1

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

institute: NHSBT Oxford

hyb_protocol: Hybridization to GeneChip Human Genome U133_Plus_2.0 arrays (Affymetrix) was according to the manufacturer’s recommendations. Briefly, hybridisation was for 16 hours at 45 degrees C, rotating at 60rpm.

scan_protocol: Genechips were scanned using an Affymetrix GeneChip scanner following washing on a Fluidics Station 450.

data_processing:
Cell intensity calculation and scaling was performed using GeneChip Operating Software (GCOS) (Affymetrix) and data analysed by the Robust Multiarray Average (RMA) method of Irrizarry using the Bioconductor suite packages in R (www.bioconductor.org). Probes with low signal intensity in all samples were filtered out and the resulting probes analysed for differential expression in Excel (Microsoft). Expression data for genes of interest were hierarchically clustered by gene and by experiment using Average linkage and Pearson correlation with Genesis (Graz University of Technology)
Probes with low signal intensity in all samples were filtered out and the resulting probes analysed for differential expression in Excel (Microsoft). Expression data for genes of interest were hierarchically clustered by gene and by experiment using Average linkage and Pearson correlation with Genesis (Graz University of Technology)

source_name: CD71+ Pro-erythroblasts and normoblasts isolated at d6 and cultured for a further day in the presence of hemozoin

label_protocol: Biotinylated fragmented cRNA was synthesized from 100ng of pooled RNA using the 2-Cycle cDNA Synthesis and the 2-Cycle Target Labelling and Control Reagent kits (Affymetrix, Santa Clara, CA).

growth_protocol: PBMCs were isolated from a buffy coat (NHSBT, Bristol, UK) and early erythroblasts were expanded for one week in 10% conditioned medium (CM) from the bladder cancer cell line 5637, 10% non-heat inactivated FBS (SLI, Salisbury, UK) and 1mg/ml Cyclosporin A (Sandoz Pharmaceuticals, Surrey, UK) in a-modified MEM. Erythroid cells were washed twice before transfer into phase II medium comprising a-MEM with 1U/ml recombinant Epo (Ortho Biotech Janssen Cilag Ltd, Bucks, UK), 10ng/ml SCF (R&D Systems, Abingdon, UK), 0.3 mg/ml holo-transferrin (MP Biomedical, London, UK), 1mM dexamethasone (Faulding Pharmaceuticals plc, Warwickshire, UK), 3% non-heat inactivated FBS (SLI) and 1% deionized fraction V BSA.  Erythroid precursors differentiate into mature erythroblasts and hemoglobinized normoblasts over 14 days. On day 6 of this second phase the cultures are enriched for erythroid progenitors using magnetic bead isolations (Miltenyi Biotec). Briefly CD3+ cells were depleted by a LD column and CD71+ cells selected from the excluded fraction using an LS column. Eluted cells from the final step were >90% viable.

extract_protocol: Total RNA using 7.5 x10^5 cells per treatment was extracted using Trizol (Invitrogen, Paisley, UK) in accordance with the manufacturer’s instructions. An additional phenol-chloroform step was included. RNA integrity was evaluated using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only RNA with RIN>9 was processed further for microarray.

treatment_protocol: Purified erythroblasts were incubated in freshly  prepared Phase II medium with hemozoin or TNFa for 24 hours before harvesting for RNA extraction

tag: days cultured after cd71+ isolation at day 6

tag: media additions

value: Hemozoin

value: CD71+ Pro-erythroblasts and normoblasts


title: BM_MSC_1

description: plastic adherent cells

source_name: Mesenchymal stem and progenitor cells (MSPCs) from human bone marrow

label_protocol: Standard Infinium HD Methylation Assay protocol


title: cord_MSC_3

description: plastic adherent cells

source_name: Mesenchymal stem and progenitor cells (MSPCs) from human umbilical cord (UC)


title: BM_MSC_2

description: plastic adherent cells

value: Mesenchymal stem and progenitor cells (MSPCs)


title: cord_MSC_2

description: plastic adherent cells


title: control_1

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

institute: UCSC

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene expression 1.0 st Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: The data were analyzed with Partek Genomic Suite (v.6.5) using rma as probeset summarization algoritm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. Tot RNA was  purified using the RNAeasy mini purification kit (QIAGEN) according to the RNA cleanup protocol

tag: cell line

value: hepatocholangiocarcinoma


title: control_2


title: Fibros_2

description: plastic adherent cells


title: treated_2

tag: incubated with

value: sorafenib 2.5 mM under serum deprivation for 12 hrs


title: Control biological rep3

tag: disease state


title: CD71+ Erythroblasts_TNFa_d1

source_name: CD71+ Pro-erythroblasts and normoblasts isolated at d6 and cultured for a further day in the presence of TNFa

value: TNF-alpha


title: Fibros_1

description: plastic adherent cells


title: treated_1


title: control_3


title: cord_MSC_1

description: plastic adherent cells


title: treated_3


title: CD71+ Erythroblasts_d0

source_name: CD71+ Pro-erythroblasts and normoblasts isolated at d6 of the second phase culture indicated in Growth Protocol.


title: CD71+ Erythroblasts_Control_d1

source_name: CD71+ Pro-erythroblasts and normoblasts isolated at d6 and cultured for a further day in the absence of hemozoin or TNFa


title: Rice_Jamaica_root_rep_2

status: Public on Feb 03 2015

city: Shang Hai

first: Li

last: Song

address: FengLin Road

institute: SIPPE

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit, Affymetrix, P/N 900720 apparatus. Hybridization Oven 640: Affymetrix, 800139 (220V). Fluidics Station 450: Affymetrix, P/N 00-0079.

scan_protocol: GeneChip® Scanner 3000: Affymetrix, P/N 00-00212

data_processing: normalization of the microarray data using the MAS5.0 methods

organism: Oryza sativa

source_name: Jamaica root

label_protocol: One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493

extract_protocol: RNeasy mini kit, QIAGEN, P/N 74104

value: 7 days old

value: root

tag: cultivar

value: Jamaica


title: BM_MSC_3

description: plastic adherent cells


title: Rice_CJF1_root_rep_2

source_name: CJF1 root

value: F1 hybrid between C bao and Jamaica


title: Rice_CJF1_root_rep_1


title: AT_MSC_3

description: plastic adherent cells

source_name: Mesenchymal stem and progenitor cells (MSPCs) from human white adipose tissue (WAT)


title: Rice_Jamaica_root_rep_1


title: Rice_CJF1_leaf_rep_2

source_name: CJF1 leaf

value: 4 weeks old

value: leaf


title: AT_MSC_1

description: plastic adherent cells


title: Rice_C bao_leaf_rep_2

source_name: C bao leaf

value: C bao


title: Rice_Jamaica_leaf_rep_1

source_name: Jamaica leaf


title: AT_MSC_2

description: plastic adherent cells


title: P15 postnatal biological rep. 2

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

description: mRNA expression during parotid acini terminal differentiation

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Rat 230 2.0 Arrays according to the Nugene FL-Ovation cDNA Biotin Module V2 Labeling and Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)

data_processing: The data were normalized using the 'rma' function in the Bioconductor package 'affy', with the default settings.  Prior to analysis data were filtered according to the following: 1. Remove any probe not mapping to an Entrez ID 2. For two or more probes mapping to the SAME Entrez ID, keep only the one with the largest variability across the samples 3. Remove all probes with have variability across the samples below the 50th percentile (essentially filters out the probes whose variability is in the bottom half).

source_name: Rat postnatal day 15 (parotid acini total RNA)

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for NuGEN Ovation Pico WTA System V2 reagent Kit from 1.5ng and 4.5ng total RNA

extract_protocol: PICO Pure RNA isolation kit from Life Technologies was used per the manufacturers instructions

value: Sprauge Dawley


title: P25 postnatal biological rep. 2

source_name: Rat postnatal day 25 (parotid acini total RNA)


title: P20 postnatal biological rep. 3

source_name: Rat postnatal day 20 (parotid acini total RNA)


title: P20 postnatal biological rep. 1


title: Rice_C bao_root_rep_2

source_name: C bao root


title: Rice_Jamaica_leaf_rep_2


title: Rice_CJF1_leaf_rep_1


title: P25 postnatal biological rep. 1


title: P9 postnatal biological rep. 3

source_name: Rat postnatal day 9 (parotid acini total RNA)


title: P9 postnatal biological rep. 1


title: P2 postnatal biological rep. 3

source_name: Rat postnatal day 2 (parotid acini total RNA)


title: P1_sarcoma

city: Salt Lake City

first: Joshua

middle: D

last: Schiffman

state: Utah

address: 2000 Circle of Hope Dr

department: Pediatric Oncology/Hematology

institute: Huntsman Cancer Institute

hyb_protocol: Arrays were hybridized overnight, Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing: CEL files are combined by OncoScan Console software to generate OSCHP files which are analyzed by Nexus Express for Oncoscan software, using the TuScan algorithm

source_name: FFPE

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan.

extract_protocol: Genomic DNA was extracted from FFPE using the Ambion Recover All Total Nucleic Acid Isolation Kit. DNA quantity was assessed with a Qubit using the Quant-it DNA High Sensitivity kit from Invitrogen

tag: diagnosis

value: Li-Fraumeni Syndrome tumors

tag: tumor type

value: pleomorphic sarcoma


title: P20 postnatal biological rep. 2


title: P15 postnatal biological rep. 1


title: P15 postnatal biological rep. 3


title: P25 postnatal biological rep. 3


title: Lu-1995-B

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description:
Fast Froen
4474300106_F

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol

scan_protocol: Scanned using the Illumina Bead Array Reader

data_processing:
The microarray data was processedthrough BeadStudio software, version 3.1. (Illumina Inc.) and then normalized using faster cyclic loess function
nonnormalized data: raw expression in log2, no background correction and normalization

source_name: Lung

label_protocol: Biotinylated cDNA were prepared using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: RNA was extracted using the miRNeasy Mini kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser

tag: tumor

value: Normal


title: Rice_C bao_root_rep_1

tag: tissue


title: Lu-1995-A

description:
Fast Froen
4474300106_E

value: Tumor


title: Lu-2045-B

description:
Fast Froen
4474300106_D


title: P9 postnatal biological rep. 2

tag: strain


title: P5 postnatal biological rep. 1

source_name: Rat postnatal day 5 (parotid acini total RNA)


title: P5 postnatal biological rep. 3


title: Lu-1790-A

description:
Fast Froen
4474300102_E


title: P2 postnatal biological rep. 2


title: Lu-2172-B

description:
Fast Froen
4474300102_D


title: Lu-2172-A

description:
Fast Froen
4474300102_C


title: P0 postnatal biological rep. 1

source_name: Rat day of birth (parotid acini total RNA)


title: Lu-1321-C

description:
Fast Froen
4474300102_B


title: P5 postnatal biological rep. 2


title: E20 embryo biological rep. 3

source_name: Rat embryo day E20 (parotid acini total RNA)


title: P0 postnatal biological rep. 3


title: E20 embryo biological rep. 1


title: P0 postnatal biological rep. 2


title: Lu-1321-A

description:
Fast Froen
4474300102_A


title: E18 embryo biological rep. 3

source_name: Rat embryo day E18 (parotid acini total RNA)


title: Lu-1050-B

description:
Fast Froen
4474300096_H


title: Lu-2045-A

description:
Fast Froen
4474300106_C


title: P2 postnatal biological rep. 1


title: LU-2499 [4823821011_H]

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

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

data_processing: BeadStudio software v3.2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from lung tumor or adjacent normal tissues using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: F

tag: tumor or normal

value: N


title: LU-2172 [4823821011_K]


title: E18 embryo biological rep. 2

tag: age


title: Lu-1050-A

description:
Fast Froen
4474300096_G


title: LU-2172 [4823821011_I]

value: T


title: LU-2499 [4823821011_F]


title: LU-1995 [4823821010_I]

value: M


title: LU-2045 [4823821011_A]


title: LU-2045 [4823821011_C]


title: Lu-1222-C

description:
Fast Froen
4474300096_B


title: Rice_C bao_leaf_rep_1


title: Lu-1222-A

description:
Fast Froen
4474300096_A


title: Lu-1031-B

description:
Fast Froen
4474300094_B


title: LU-1790 [4823821006_K]


title: Lu-593-A

description:
Fast Froen
4474300058_A


title: LU-1995 [4823821010_K]


title: Lu-1031-A

description:
Fast Froen
4474300094_A


title: Lu-905-B

description:
Fast Froen
4474300058_C


title: Lu-593-B

description:
Fast Froen
4457315117_F


title: LU-1942 [4823821010_C]


title: E20 embryo biological rep. 2


title: Lu-2499-A

description:
Fast Froen
4457315113_G


title: Lu-2456-B

description:
Fast Froen
4457315113_F


title: Lu-2456-A

description:
Fast Froen
4457315113_B


title: LU-1740 [4823821006_H]


title: Lu-2499-B

description:
Fast Froen
4457315115_A


title: Lu-1660-B

description:
Fast Froen
4457315103_E


title: Lu-161-B

description:
Fast Froen
4457315103_D


title: Lu-1740-B

description:
Fast Froen
4457315105_B


title: Lu-1333-A

description:
Fast Froen
4457315101_D


title: LU-1405 [4823821004_K]


title: LU-1942 [4823821010_A]


title: LU-1479 [4823821005_A]


title: LU-1450 [4823821004_H]


title: LU-1660 [4823821005_K]


title: LU-1740 [4823821006_F]


title: LU-1479 [4823821005_C]


title: Lu-132-A

description:
Fast Froen
4457315101_B


title: Lu-106-B

description:
Fast Froen
4457315100_G


title: Lu-1790-B

description:
Fast Froen
4457315105_E


title: Lu-1333-C

description:
Fast Froen
4457315101_E


title: LU-1405 [4823821004_I]


title: LU-1450 [4823821004_F]


title: Lu-161-A

description:
Fast Froen
4457315097_H


title: Lu-132-B

description:
Fast Froen
4457315101_C


title: Lu-1479-B

description:
Fast Froen
4457315097_E


title: Lu-1450-B

description:
Fast Froen
4457315097_D


title: LU-1660 [4823821005_I]


title: LU-1222 [4823821003_H]


title: Lu-1405-B

description:
Fast Froen
4457315097_B


title: LU-1222 [4823821003_F]


title: Lu-1405-A

description:
Fast Froen
4457315096_C


title: Lu-1068-A

description:
Fast Froen
4457315092_F


title: Lu-1068-B

description:
Fast Froen
4457315096_B


title: LU-1333 [4823821004_A]


title: LU-1790 [4823821006_I]


title: Lu-106-A

description:
Fast Froen
4457315100_F


title: E18 embryo biological rep. 1


title: LU-1333 [4823821004_C]


title: Lu-1014-A

description:
Fast Froen
4457315092_A


title: Lu-1014-B

description:
Fast Froen
4457315092_B


title: Lu-824-B

description:
Fast Froen
4457315090_G


title: Lu-824-A

description:
Fast Froen
4457315090_F


title: Lu-1479-A

description:
Fast Froen
4457315097_A


title: Lu-1450-A

description:
Fast Froen
4457315096_G


title: LU-1096 [4823821002_H]


title: LU-1096 [4823821002_F]


title: Lu-789-B

description:
Fast Froen
4482545332_E


title: Lu-789-C

description:
Fast Froen
4482545332_F


title: Lu-905-A

description:
Fast Froen
4482545312_E


title: Lu-426-B

description:
Fast Froen
4482545271_F


title: LU-1321 [4823821003_C]


title: Lu-426-A

description:
Fast Froen
4482545271_E


title: LU-1321 [4823821003_A]


title: Lu-1096-B

description:
Fast Froen
4474300108_H


title: Lu-1660-A

description:
Fast Froen
4474300108_E


title: Lu-1096-A

description:
Fast Froen
4474300108_G


title: Lu-1740-A

description:
Fast Froen
4474300108_A


title: Lu-1942-A

description:
Fast Froen
4482545378_C


title: Lu-1942-B

description:
Fast Froen
4482545378_D


title: LU-1068 [4823821001_H]


title: LU-1014 [4821682056_C]


title: LU-1050 [4823821001_I]


title: LU-1068 [4823821001_F]


title: LU-1031 [4821682056_F]


title: LU-824 [4821682049_H]


title: LU-789 [4821682049_A]


title: LU-824 [4821682049_F]


title: LU-1031 [4821682056_H]


title: LU-1050 [4823821001_K]


title: LU-905 [4821682055_C]


title: LU-593 [4821682048_A]


title: LU-1014 [4821682056_A]


title: LU-905 [4821682055_A]


title: TNE_090305

city: Pula

first: Ignazio

middle: Stefano

last: Piras

address: Loc. Piscinamanna

description: TRAMP mice affected by mouse prostate intraepithelial neoplasia

hyb_protocol: 5.5 μg of fragmented and labeled cDNA target was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array at 45°C for 17 h on a GeneChip Hybridization Oven 640 (Affymetrix)

scan_protocol: Hybridized arrays were washed and stained on a gene Chip Fluidics Station 450 and finally scanned on a Gene Chip Scanner 3000 7G (Affymetrix), generating an intensity file (*.CEL) for each array

data_processing: Normalization with RMA algorithm followed by non specific filtering, performed removing: 1) non annotated and duplicated probes 2) low variance probes using interquartile function (IQR) (Bourgon et al., PNAS 2010, 107;9546-9551)

source_name: Prostatic Cancer Stem Cells

label_protocol: cDNA was fragmented and end-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: TPIN-SC and TNE-SC were cultured as previously described (Mazzoleni et al., 2013; Stem Cells Transl Med 2:678-689) in serum-free DMEM F12 (Lonza, Switzerland) containing EGF and FGF2

extract_protocol: RNeasy Micro and Mini kit (Qiagen, Chatsworth, CA, USA)

tag: mouse model

value: transgenic adenocarcinoma of the mouse prostate (TRAMP) model

tag: cell type

value: cancer stem-like cells obtained for prostates of mice affected by neuroendocrine tumors


title: PEYER'S PATCHES_WT_LYSODC_1

city: MARSEILLE

first: Hugues

last: Lelouard

address: Centre d’Immunologie de Marseille-Luminy  Parc Scientifique & Technologique de Luminy, 163 avenue de luminy

country: France

institute: CIML

description: Cell phenotype: CD11cHiMHCIIHiCD172a+CD11bHiBst2+CD8-CD4-

hyb_protocol: Following fragmentation and end-labelling, cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm and raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) 3.2.

data_processing: The data were extracted with the Affymetrix software Expression Console 1.1. using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: LYSODC FROM PEYER'S PATCHES OF C57BL/6 WT MICE

label_protocol: Biotinylated double strand cDNA targets were prepared, starting from 5 to 17 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit according to manufacturer recommendations.

extract_protocol: Extraction of total RNA was perform using the Qiagen micro RNAeasy Plus Kit following the manufacturer's instructions

tag: genotype

value: wildtype

value: FEMALE

value: PEYER'S PATCH

value: 6 TO 8 WEEKS OLD


title: PEYER'S PATCHES_WT_LYSODC_3


title: LU-426 [4811409059_H]


title: LU-789 [4821682049_C]


title: LU-593 [4821682048_C]


title: LU-2456 [4811409058_I]


title: female CA1_clone_blastocyst_TSA treated_rep4

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description:
Gene expression in cloned blastocyst
CAI_F_4

hyb_protocol: 1.65ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and transformed by default setting.
Normalized data expressed in log2 scale. Raw signal intensities were normalized by default setting of GeneSpring12.5.

source_name: adult CA1 clone blastocyst_female_TSA treated

label_protocol: 5.0 ug of amplified RNA was labelled with Cianine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In vitro fertilized (IVF) or cloned embryos were cultured in potassium modified simplex optimization medium (KSOM) at 37.5 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) from single blastocysts and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).

treatment_protocol: The reconstructed oocytes were transferred into a droplet of KSOM and incubated at 37 °C under 5% CO2 in humidified air for 1–3 h. They were activated by incubation for 1 h in Ca2+-free KSOM containing 2.5 mMSr2+, 5 µg/mL CB, and 50 nM trichostatin A (TSA). After activation, they were cultured in KSOM containing 5 µg/mL CB and 50 nM TSA for 5 h. Then the SCNT-derived embryos were transferred to KSOM containing 50 nM TSA and cultured for an additional 2 h. After TSA treatment, SCNT-derived embryos were transferred to KSOM and incubated at 37 °C under 5% CO2 in humidified air. After 96 h in culture, the cloned embryos reached to blastocyst stage were subjected to microarray gene analyses.

tag: strain background

value: female

tag: donor cell

value: CA1 pyramidal cell

tag: Stage

value: blastocyst


title: PEYER'S PATCHES_WT_LYSOMAC_3

description: Cell phenotype: CD11cHiMHCIILoCD172a+CD11b+Bst2+CD8-CD4+

source_name: LYSOMAC FROM PEYER'S PATCHES OF C57BL/6 WT MICE


title: PEYER'S PATCHES_WT_CD11B+ cDC_3

description: Cell phenotype: CD11cHiMHCIIHiCD172a+CD11b+Bst2-CD8-CD4-

source_name: CD11B+ CONVENTIONAL DENDRITIC CELLS FROM PEYER'S PATCHES OF C57BL/6 WT MICE


title: PEYER'S PATCHES_WT_CD11B+ cDC_1


title: PEYER'S PATCHES_WT_LYSOMAC_1


title: PEYER'S PATCHES_WT_LYSODC_2


title: TNE_070116


title: TNE_080925


title: TPIN_110324

value: cancer stem-like cells obtained from prostates of 10-11 week old


title: LU-2456 [4811409058_K]


title: PEYER'S PATCHES_WT_LYSOMAC_2


title: female CA1_clone_blastocyst_TSA treated_rep2

description:
Gene expression in cloned blastocyst
CAI_F_2


title: TPIN_071112


title: TPIN_101028


title: PEYER'S PATCHES_WT_CD11B+ cDC_2


title: LU-106 [4811409058_A]


title: female CA1_clone_blastocyst_TSA treated_rep3

description:
Gene expression in cloned blastocyst
CAI_F_3


title: IVF_control_blastocyst_female_rep1

description:
Gene expression in blastocyst
IVF_F_1

source_name: IVF control blastocyst_female

value: IVF


title: LU-132 [4811409042_K]


title: female CA1_clone_blastocyst_TSA treated_rep1

description:
Gene expression in cloned blastocyst
CAI_F_1


title: LU-426 [4811409059_F]


title: cumulus_clone_blastocyst_TSA treated_rep1

description:
Gene expression in cloned blastocyst
CC_1

source_name: adult cumulus clone blastocyst_TSA treated

value: cumulus cell


title: cumulus_clone_blastocyst_TSA treated_rep3

description:
Gene expression in cloned blastocyst
CC_3


title: [S774-187 NW-LPN Cy3]-[S614-187 NW-MPN Cy5]

city: Urbana

first: Sonia

middle: Josefina

last: Moisá

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois

description: Sample were total RNA from bovine skeletal muscle tissue (Longissimus dorsi)

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 30 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Longissimus dorsi

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Aberdeen Angus × Simmental steers were early or normal weaned.

extract_protocol: A sample of Longissimus dorsi muscle was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

treatment_protocol: Aberdeen Angus × Simmental steers used in this study came from cow that received a low and a high plane of nutrition during the last 90 days before calving. Offsprings from these cows were selected to be early or normal weaned.

tag: breed

value: Angus × Simmental

value: Skeletal muscle

tag: weaning

value: Normal weaning

tag: maternal plane of nutrition

value: Low Plane Nutrition

tag: age (days)

tag: skeletal muscle tissue

value: Medium Plane Nutrition


title: LU-132 [4811409042_I]

value: F

value: T


title: IVF_control_blastocyst_female_rep3

description:
Gene expression in blastocyst
IVF_F_3


title: [S517-354 NW-LPN Cy3]-[S697-354 EW-MPN Cy5]

value: Early weaning


title: [S614-354 NW-MPN Cy3]-[S713-354 EW-LPN Cy5]


title: cumulus_clone_blastocyst_TSA treated_rep2

description:
Gene expression in cloned blastocyst
CC_2


title: [S634-354 EW-MPN Cy3]-[S541-354 NW-MPN Cy5]


title: [S835-354 EW-LPN Cy3]-[S774-354 NW-LPN Cy5]


title: LU-106 [4811409058_C]

value: M

value: N


title: [S604-354 NW-MPN Cy3]-[S731-354 NW-LPN Cy5]


title: female Purkinje_clone_blastocyst_TSA treated_rep3

description:
Gene expression in cloned blastocyst
Pur_F_3

source_name: adult Purkinje clone blastocyst_female_TSA treated

value: Purkinje cell


title: IVF_control_blastocyst_female_rep2

description:
Gene expression in blastocyst
IVF_F_2

value: female


title: female Purkinje_clone_blastocyst_TSA treated_rep4

description:
Gene expression in cloned blastocyst
Pur_F_4


title: LU-161 [4811409042_F]


title: female Purkinje_clone_blastocyst_TSA treated_rep1

description:
Gene expression in cloned blastocyst
Pur_F_1


title: [S476-187 NW-MPN Cy3]-[S476-354 NW-MPN Cy5]


title: [S731-78 NW-LPN Cy3]-[S399-187 NW-LPN Cy5]


title: male CA1_clone_blastocyst_TSA treated_rep4

description:
CAI_M_4
Gene expression in cloned blastocyst

source_name: adult CA1 clone blastocyst_male_TSA treated

value: male

value: CA1 pyramidal cell


title: [S674-354 EW-LPN Cy3]-[S572-354 EW-MPN Cy5]


title: female Purkinje_clone_blastocyst_TSA treated_rep2

description:
Gene expression in cloned blastocyst
Pur_F_2

value: blastocyst


title: male CA1_clone_blastocyst_TSA treated_rep3

description:
CAI_M_3
Gene expression in cloned blastocyst


title: male CA1_clone_blastocyst_TSA treated_rep1

description:
CAI_M_1
Gene expression in cloned blastocyst


title: Sertoli_clone_blastocyst_TSA treated_rep1

description:
SC_1
Gene expression in cloned blastocyst

source_name: neonatal Sertoli clone blastocyst_TSA treated

value: neonatal Sertoli cell


title: [S762-354 NW-LPN Cy3]-[S762-187 NW-LPN Cy5]


title: Sertoli_clone_blastocyst_TSA treated_rep2

description:
SC_2
Gene expression in cloned blastocyst


title: male CA1_clone_blastocyst_TSA treated_rep2

description:
CAI_M_2
Gene expression in cloned blastocyst


title: IVF_control_blastocyst_male_rep5

description:
IVF_M_5
Gene expression in blastocyst

source_name: IVF control blastocyst_male

value: IVF


title: Sertoli_clone_blastocyst_TSA treated_rep4

description:
SC_4
Gene expression in cloned blastocyst


title: Sertoli_clone_blastocyst_TSA treated_rep3

description:
SC_3
Gene expression in cloned blastocyst


title: LU-161 [4811409042_H]

source_name: Lung


title: IVF_control_blastocyst_male_rep4

description:
IVF_M_4
Gene expression in blastocyst


title: [S463-354 NW-MPN Cy3]-[S541-78 NW-LPN Cy5]

value: Angus × Simmental


title: [S731-187 NW-LPN Cy3]-[S674-187 EW-LPN Cy5]

value: Skeletal muscle


title: [S541-187 NW-MPN Cy3]-[S835-187 EW-LPN Cy5]

value: Normal weaning


title: [S586-354 EW-MPN Cy3]-[S634-187 EW-MPN Cy5]


title: [S463-78 NW-LPN Cy3]-[S463-187 NW-MPN Cy5]

value: Low Plane Nutrition


title: [S660-187 EW-LPN Cy3]-[S572-187 EW-MPN Cy5]

value: Medium Plane Nutrition


title: [S697-187 EW-MPN Cy3]-[S604-187 NW-MPN Cy5]


title: male Purkinje_clone_blastocyst_TSA treated_rep3

description:
Pur_M_3
Gene expression in cloned blastocyst

source_name: adult Purkinje clone blastocyst_male_TSA treated


title: [S697-78 EW-MPN Cy3]-[S614-78 NW-MPN Cy5]


title: [S713-187 EW-LPN Cy3]-[S660-354 EW-LPN Cy5]


title: [S476-78 NW-MPN Cy3]-[S774-78 NW-LPN Cy5]


title: [S399-354 NW-LPN Cy3]-[S399-78 NW-LPN Cy5]


title: IVF_control_blastocyst_male_rep7

description:
IVF_M_7
Gene expression in blastocyst


title: IVF_control_blastocyst_male_rep2

description:
IVF_M_2
Gene expression in blastocyst


title: [S762-78 NW-LPN Cy3]-[S586-78 EW-MPN Cy5]


title: male Purkinje_clone_blastocyst_TSA treated_rep1

description:
Pur_M_1
Gene expression in cloned blastocyst


title: [S586-187 EW-MPN Cy3]-[S517-187 NW-LPN Cy5]


title: IVF_control_blastocyst_male_rep1

description:
IVF_M_1
Gene expression in blastocyst


title: [S517-78 NW-LPN Cy3]-[S835-78 EW-LPN Cy5]


title: male Purkinje_clone_blastocyst_TSA treated_rep4

description:
Pur_M_4
Gene expression in cloned blastocyst


title: male Purkinje_clone_blastocyst_TSA treated_rep2

description:
Pur_M_2
Gene expression in cloned blastocyst


title: [S634-78 EW-MPN Cy3]-[S713-78 EW-LPN Cy5]

description: Sample were total RNA from bovine skeletal muscle tissue (Longissimus dorsi)


title: [S674-78 EW-LPN Cy3]-[S604-78 NW-MPN Cy5]


title: [S503-354 EW-MPN Cy3]-[S503-78 EW-MPN Cy5]


title: [S572-78 EW-MPN Cy3]-[S503-187 EW-MPN Cy5]


title: Cyanothece sp. ATCC 51142_time_41.75_biorep2_techrep3

city: East Lansing

first: Sandeep

middle: B.

last: Gaudana

state: MI

address: 612 Wilson Road

institute: Michigan State University

description: Bilogical replicate 2 of 2, technical replicate 3 of 3, sampled at 41.75 h into constant light cultivation

hyb_protocol: 300ng of each labeled sample to be co-hybridized was fragmented and hybridized on custom array:  Agilent Custom GE, 8x15K Microarray - AMADID 018970.

scan_protocol: Agilent Technologies Scanner G2505C was used

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Crocosphaera subtropica ATCC 51142

source_name: Cyanothece sp. ATCC 51142_time_41.75

label_protocol: 1ug of total RNA was labeled using Kreatech ULS labeling system each sample was labeled with Cy5 a pool of the samples was used as a control - this was labeled with Cy3

growth_protocol: Axenic cultures of Cyanothece 51142 were cultivated in ASP2 medium without nitrate in air-sparged and stirred bioreactor with external illumination of 230 µmol photons.

extract_protocol: Samples were drawn to extract RNA for microarray analysis such that the product of volume and OD730nm was 50.0.  Total RNA was extracted from the samples using TRI reagent (Sigma–Aldrich).

treatment_protocol: The culture was entrained under light/dark cycles (12 h /12 h) (LD) for 4 days and then released into continuous light (LL)

tag: sample

tag: time in constant light (hours)

source_name: Cyanothece sp. ATCC 51142

value: Pool 1-18

tag: time point

value: Control:equimolar pool of all samples


title: Cyanothece sp. ATCC 51142_time_36.415_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 3, sampled at 36.415 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_36.415


title: Primary human monocytes from patient with gram-negative sepsis #1

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was handled and normalized in BASE (https://casa4.bmc.lu.se/onk/). All data was mean background corrected followed by quantile normalization. Array control probes were removed.

source_name: Primary human monocytes

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

extract_protocol: Total RNA was extracted with TRIZOL. Quality control was performed with Agilent 2100 Bioanalyser.

value: primary monocyte

tag: disease state

value: Gram negative sepsis


title: Cyanothece sp. ATCC 51142_time_36.415_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 3, sampled at 36.415 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_36.415_biorep2_techrep3

description: Bilogical replicate 2 of 2, technical replicate 3 of 3, sampled at 36.415 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_Control_pool_techrep2

description: Control: equimolar pool of RNA from all 9 time points and their biological replicates, so a total of 18 samples

source_name: Cyanothece sp. ATCC 51142_time_Control

value: Control


title: Cyanothece sp. ATCC 51142_time_41.75_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 3, sampled at41.75 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_31.125_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 3, sampled at 31.125 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_31.125


title: Primary human monocytes from patient with tuberculosis #1

value: Tuberculosis


title: Cyanothece sp. ATCC 51142_time_38.08_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 2, sampled at 38.08 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_38.08


title: Primary human monocytes from patient with gram-negative sepsis #3


title: [S579-78 EW-LPN Cy3]-[S579-187 EW-LPN Cy5]

tag: tissue

value: Early weaning


title: Cyanothece sp. ATCC 51142_time_34.96_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 2, sampled at 34.96 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_34.96


title: Cyanothece sp. ATCC 51142_time_34.96_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 2, sampled at 34.96 h into constant light cultivation


title: Primary human monocytes from patient with metastatic breast cancer #4

value: Metastatic breast cancer


title: Cyanothece sp. ATCC 51142_time_38.08_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 2, sampled at 38.08 h into constant light cultivation


title: Primary human monocytes from healthy control #1

value: Healthy control


title: Primary human monocytes from healthy control #3


title: Cyanothece sp. ATCC 51142_time_27.83_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 2, sampled at 27.83 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_27.83


title: Cyanothece sp. ATCC 51142_time_31.125_biorep2_techrep3

description: Bilogical replicate 2 of 2, technical replicate 3 of 3, sampled at 31.125 h into constant light cultivation


title: Primary human monocytes from patient with tuberculosis #3


title: Primary human monocytes from patient with tuberculosis #2


title: Primary human monocytes from patient with metastatic breast cancer #3


title: [S579-354 EW-LPN Cy3]-[S660-78 EW-LPN Cy5]


title: Primary human monocytes from patient with gram-negative sepsis #2


title: IVF_control_blastocyst_male_rep3

description:
IVF_M_3
Gene expression in blastocyst

tag: strain

tag: gender

value: male

value: blastocyst


title: Primary human monocytes from healthy control #2

tag: cell type


title: Cyanothece sp. ATCC 51142_time_31.125_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 3, sampled at 31.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_24.54_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 2, sampled at 24.54 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_24.54


title: Primary human monocytes from patient with metastatic breast cancer #2


title: Cyanothece sp. ATCC 51142_time_24.54_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 2, sampled at 24.54 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_27.83_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 2, sampled at 27.83 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_25.915_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 3, sampled at 25.915 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_25.915


title: Cyanothece sp. ATCC 51142_time_25.915_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 3, sampled at 25.915 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_25.915_biorep2_techrep3

description: Bilogical replicate 2 of 2, technical replicate 3 of 3, sampled at 25.915 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_21.125_biorep2_techrep3

description: Bilogical replicate 2 of 2, technical replicate 3 of 3, sampled at 21.125 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_21.125


title: Cyanothece sp. ATCC 51142_time_21.125_biorep2_techrep2

description: Bilogical replicate 2 of 2, technical replicate 2 of 3, sampled at 21.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_21.125_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 3, sampled at 21.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_36.415_biorep1_techrep3

description: Bilogical replicate 1 of 2, technical replicate 3 of 3, sampled at 36.415 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_41.75_biorep1_techrep3

description: Bilogical replicate 1 of 2, technical replicate 3 of 3, sampled at 41.75 h into constant light cultivation


title: los1_URA3.7

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: BY4742 LOS1 Knockout

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2

organism: Saccharomyces cerevisiae

source_name: BY4742 LOS1 Knockout

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Yeast_2 Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

growth_protocol: Cultures were grown at 30°C overnight in a 96 well plate in YPD and then 2.5µl of the overnight culture was inoculated into 147.5µl of culture media in 100 well Bioscreen plates. Yeast growth rates were analyzed in the OD420-580 range in the Bioscreen C MBR machine (Growth Curves USA) as previously described using the Yeast Outgrowth Data Analyzer (YODA)

extract_protocol: Wild type and los1∆ cells were inoculated in 5ml YEPD overnight culture.  Three isolates of each strain were tested, with six cultures (duplicates) for wild type cells and three cultures for los1∆ cells.  Overnight cultures were then diluted to <0.05 OD600 in 50ml YEPD and shaken at 225 rpm at 30°C until exactly 0.5 OD600 was reached.    The entire cuture was then transferred to conical tubes and centrifuged at 4°C for 2 minutes at 3000g in a counter top centrifuge.  Supernatant was removed and resuspended in 1 ml ice cold Martin Lysis buffer (40mM KCl, 7.5 mM MgCl2, 1 mM DTT, 25 mM Tris-HCl pH7.5, 0.5 mg/ml heparin, 100µg/ml cycloheximide, in ddH2O).  Suspensions were transferred to microfuge tubes containing 0.4g glass beads (Sigma) and vortexed for 30 seconds, 8 times with 30 seconds on ice between vortex steps.  10µl of 20% triton X-100 and 10µl 20% Na deoxycholate  were added to each tube and vortexed for 15 seconds.  Lysate was cleared of debris by centrifugation at 17k g in a microcentrifuge at 4°C for 2 minutes.  Cleared lysate was then treated by the RNeasy Qiagen RNA prep following the manufacturer’s protocol.


title: los1_URA3.8

description: BY4742 LOS1 Knockout


title: Cyanothece sp. ATCC 51142_time_36.415_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 3, sampled at 36.415 h into constant light cultivation


title: los1_URA3.9

description: BY4742 LOS1 Knockout


title: BY4742_2pct_Glu.4

description: BY4742 Wild Type

source_name: BY4742 Wild Type


title: IVF_control_blastocyst_male_rep6

description:
IVF_M_6
Gene expression in blastocyst

source_name: IVF control blastocyst_male

value: IVF