title: KCCB3_6

city: Kyoto

first: Budiman

last: Kharma

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

description:
EC, G2
Gene expression data from human endometrioid endometrial cancer tissue, grade 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip U133 Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneArray Scanner System 3000.

data_processing: The data were analyzed using Affymetrix Expression Console 1.1 with default analysis settings and global scaling as normalization method using RMA Express.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Human endometrial cancer cell lines, SPAC-1L (a SPEC cell line), was maintained in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum and penicillin–streptomycin.

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

treatment_protocol: STAT1-specific short interfering RNAs (siRNA; FlexiTube siRNA QIAGEN catalogue no. SI02662884) and negative control siRNA (AllStars Negative Control siRNA; QIAGEN) were transfected into SPAC1L cells using HiPerFect Transfection Reagent as previously described. Briefly, 105 cells per well were seeded in 24-well plate, and incubated for 48 hours. The medium was aspirated and the cells were gently washed with RPMI1640 followed by transfection with the siRNA.

tag: tissue

value: endometrial cancer tissue


title: KCCB3_7

status: Public on Mar 20 2014

type: RNA

country: Japan

description:
EC, serous
Gene expression data from human serous papillary endometrial cancer tissue

label: biotin

molecule: total RNA

organism: Homo sapiens


title: Tsetse_fly_midgut-Infected_3days-sample9

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 3 days after infected blood meal, sample 9

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was added to 250 ml of 2x Agilent hybridization buffer and hybridized to Agilent Sodalis glossinidius custom Oligo Microarrays (earray Design ID = 041518; earray Slide Layout = IS-15744-8-V1) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09GE1_107_Sep09 and Grid: 041518_D_F_20120607) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

organism: Sodalis glossinidius

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 5µg RNA using the Chipshot Direct labeling and Clean-Up System kit (Promega) according to the manufacturer's instructions

extract_protocol: Total RNA was extracted from fly midgut by TRIzol (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Flies were exposed to Trypanosoma brucei gambiense infected mices.

tag: status

value: Infected

tag: timepoint

value: 3 days after infected blood meal

tag: treated with

value: infected blood meal

tag: source gender

value: female fly

tag: source tissue

value: Tsetse fly midgut


title: Tsetse_fly_midgut-Infected_3days-sample8

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 3 days after infected blood meal, sample 8


title: KCCB3_2

description:
EC, G1
Gene expression data from human endometrioid endometrial cancer tissue, grade 1


title: KCCB3_3

source_name: human endometrioid endometrial cancer tissue, grade 1


title: C3H MSC 001

type: genomic

city: Los Angeles

first: Shiyu

last: Liu

address: 2250 Alcazar Street, CSA103

country: USA

institute: CCMB

description: MeDIP-Sequencing Service

hyb_protocol: Corresponding IP (experimental) and Input (control) samples were co-hybridized to a 385K array using the approproate protocol, according to the NimbleGen Guide. The proximal regions of gene promoters and additional CpG islands were covered by close-set 50 base oligonucleotides (approx. -1,500 to + 800 bp around TSS).

scan_protocol: The two-color (IP-Cy5/Input-Cy3) arrays were scanned applying the Nimblescan 2.4 software.

data_processing: Raw data was extracted from Nimblescan files and computed to scaled and centered log2-Cy5/Cy3 values for each oligonucleotide probe, coverted into graphic data set (.gff files with SignalMap software). All steps from labelling to data processing have been performed as a service of NimbleGen, according to NimbleGen Arrays User’s Guide for Epigenetic Arrays.

molecule: genomic DNA

organism: Mus musculus

source_name: MeDIP DNA from bone marrow mesenchymal cells

label_protocol: 1 µg of whole-genome.amplified MeDIP DNA (IP) and genomic input DNA (Input) were labeled with Cy5 or Cy3 nonamers, respectively (via Klenow Fragment).

growth_protocol: The single suspension of bone marrow-derived all nucleated cells (ANCs) from femurs and tibias was seeded in 10 cm culture dishes. Colonies forming attached cells were passed once for further experimental use.

extract_protocol: Total DNA from cells at passage one was extracted using a DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The cells were cultured in normal conditions for passage one.

tag: sample type

value: normal control MSCs

tag: gender

value: Female

tag: age

value: 11 weeks

tag: strain

value: Bone marrow

tag: antibody

value: 5-methyl-cytosine (IP)

source_name: input DNA from bone marrow mesenchymal cells


title: Tsetse_fly_midgut-Infected_3days-sample7

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 3 days after infected blood meal, sample 7


title: LPR MSC 001

description: MeDIP-Sequencing Service

value: recipient MSCs from untreated

value: MRL/lpr


title: Tsetse_fly_midgut-Infected_3days-sample6

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 3 days after infected blood meal, sample 6


title: KCCB2_40


title: KCCB2_39


title: KCCB2_36

description:
EC, G3
Gene expression data from human endometrioid endometrial cancer tissue, grade 3


title: KCCB3_4

source_name: human endometrioid endometrial cancer tissue, grade 3


title: KCCB3_1


title: KCCB3_8

source_name: human endometrioid endometrial cancer tissue, grade 2


title: KCCB2_33


title: KCCB2_37


title: KCCB2_31

source_name: human serous papillary endometrial cancer tissue


title: KCCB2_29


title: KCCB2_30


title: KCCB2_27


title: KCCB2_26


title: KCCB2_28


title: KCCB2_25


title: Mother [POF1-9]

city: Madinah AlMunawara

first: Sulman

last: Basit

address: Qurban

department: Center for Genetics and Inherited Diseases

country: Saudi Arabia

institute: Taibah University

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

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

data_processing:
The array image was acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: Perepheral Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from lymphocytes obtained from perepheral blood  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: cell type

value: Lymphocytes

tag: disease state

value: female


title: Father [POF1-8]

value: male


title: Unaffected male [POF1-7]


title: phleom in winter, biological rep2

city: Beiijing

last: Chao

state: Beijing

address: Beijing Haidian Distric Qinghua East Road 35

department: College of Bioscience and Biotechnology

country: China

institute: Beijing Forestry University

description: Gene expression data from five-year old poplar phleom in winter

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

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

data_processing: The data were analyzed with Microarray Suite version5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus tomentosa

source_name: poplar phleom in winter-2

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

growth_protocol: Five–year-old populus tomentosa 741 strains in field were harvested as plant material in this research from Hebei, China

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

treatment_protocol: Samples collected were immediately frozen in liquid nitrogen and then stored in -80℃ until use.

value: phleom

tag: collection time

value: winter

value: five-year old


title: KCCB2_20

value: endometrial cancer tissue


title: KCCB2_17


title: phleom in winter, biological rep3

source_name: poplar phleom in winter-3


title: KCCB2_19


title: KCCB2_15


title: KCCB2_24


title: phleom in winter, biological rep1

source_name: poplar phleom in winter-1


title: KCCB2_23


title: Unaffected female [POF1-5]


title: KCCB2_18


title: KCCB2_16


title: KCCB2_22


title: phloem in summer, biological rep3

description: Gene expression data from five-year old poplar phleom in summer

source_name: poplar phloem in summer-3

value: summer


title: phleom in fall,biological rep1

description: Gene expression data from five-year old poplar phleom in fall

source_name: poplar phleom in fall-1

value: fall


title: phleom in fall,biological rep2

source_name: poplar phleom in fall-2


title: Unaffected female [POF1-4]


title: KCCB2_14


title: Affected female [POF1-2]

value: Premature ovarian insufficiency (POI)


title: BMMC mir-155 KO replicate1

city: Manchester

first: Silvia

last: Bulfone-Paus

address: Grafton Street

department: Faculty of Human and Medical Sciences

country: United Kingdom

institute: University of Manchester

description: Gene expression data from mir-155 KO BMMC

hyb_protocol: 5 µg of labeled ssDNA were mixed with the hybridization cokctail. Later,  samples were heated for 5 min at 99 Grad ºC and  then cooled down for 2 Min at 45 Grad ºC and  80 µl were loaded onto the Affymetrix Genechip® Mouse Gene 1.0 ST array. Chips were then set in the Affymetrix hybridization  oven at 45 ºC overnight.

scan_protocol: Scanning of chips was performed using the Gene Chip Scanner 7G from Affymetrix.

data_processing: Cel files were normalized using the Robust Multichip Average expression summary. Normalized data was analyzed using the Multi experiment Viewer (MeV) software version 4.8.1 applying the significance analysis of microarrays (SAM) and choosing a log2 fold change greater than 2

source_name: Bone marrow derived mast cells differentiatiated for 5 weeks of in vitro culture

label_protocol: cRNA was labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA LabelingReagent that is covalently linked to biotin followingt the instructions of the producer for the GeneChip® WT Terminal Labeling and Controls Kit

growth_protocol: Bone marrow cells were cultured for 5 weeks with recombinant murine IL-3 (0.5 ng/ml) SCF (1ng/ml) until differentiation into bone marrow derived mast cells  (BMMC)

extract_protocol: Total RNA from WT and miR-155-/- BMMCs was isolated using the RNeasy Mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Three independent cultures of bone marrow-derived mast cells (BMMC) from each WT and miR-155 ko mice were sensitized overnight  with 0.2 µg/ml anti-DNP IgE and stimulated with 20 ng/ml DNP-HSA for 1 hr.

tag: mouse strain

value: Bone marrow derived mast cells (BMMC)

tag: genotype/variation

value: mir-155 KO


title: BMMC mir-155 KO replicate2


title: KCCB2_13


title: phloem in summer, biological rep1

source_name: poplar phloem in summer-1


title: phloem in summer, biological rep2

source_name: poplar phloem in summer-2


title: BMMC mir-155 KO replicate3


title: BMMC WT replicate2

description: Gene expression data from WT BMMC

value: wild type


title: Affected female [POF1-1]


title: phloem in spring, biological rep3

description: Gene expression data from five-year old poplar phleom in spring

source_name: poplar phloem in spring-3

value: spring


title: Affected female [POF1-3]


title: KCCB2_9

source_name: human endometrioid endometrial cancer tissue, grade 1


title: phloem in spring, biological rep2

source_name: poplar phloem in spring-2


title: BMMC WT replicate3

description: Gene expression data from WT BMMC


title: BMMC WT replicate1

description: Gene expression data from WT BMMC


title: KCCB2_11


title: KCCB2_12


title: KCCB2_8


title: phloem in spring, biological rep1

source_name: poplar phloem in spring-1


title: Tr1_rep5

city: Munich

first: Thomas

last: Korn

address: Ismaninger Str. 22

department: Neurology

country: Germany

institute: TU Munich, Klinikum rechts der Isar

description: Gene expression data Tr1

hyb_protocol: 5µg cDNA were hybridized to Affymetrix Mouse Gene 1.0 ST arrays (Hybridization, Wash and Stain Kit Affymetrix)

scan_protocol: Affymetrix scanner 3000 7g.

data_processing:
affymetrix-algorithm-name = rma-gene-default (v.1.0)
program-name = Affymetrix Expression Console (v.1.3.1.187)

source_name: in vitro differentiated murine Th cell subset; Tr1

label_protocol: cDNA synthesis was performed using the AmbionR WT expression kit. Single-stranded cDNA was fragmented and labelled with biotin allonamide triphosphate using the GeneChipR WT terminal labelling kit.

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: strain background

value: sorted naive Th cells (CD4+ CD44- Foxp3-)

tag: differentiated with

value: 100 ng/ml IL-27 plus 0.5 ng/ml TGF-β

tag: th cell subtype


title: Tr1_rep4

description: Gene expression data Tr1


title: root in winter, biological rep3

description: Gene expression data from five-year old poplar root in winter

source_name: poplar root in winter-3

tag: tissue

value: root


title: root in winter, biological rep2

source_name: poplar root in winter-2


title: KCCB2_7


title: Tr1_rep2

description: Gene expression data Tr1


title: root in winter, biological rep1

source_name: poplar root in winter-1


title: WAT, HFD_Rep2

city: Tokyo

first: Yoshitaka

last: Taketomi

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

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

description: gene expression profile in white adipose tissues after high fat diet feeding in mice

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: white adipose tissue, high fat diet, replicate2

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: C57BL/6 mice were housed in climate-controlled (23 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard LFD (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was extracted from white adipose tissues derived from mice and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice (8-wk-old, female) were placed on a HFD (High fat diet 32; CLEA Japan) or LFD for 18 weeks.

value: white adipose tissue

tag: diet

value: high fat diet


title: root in fall, biological rep3

description: Gene expression data from five-year old poplar root in fall

source_name: poplar root in fall-3


title: KCCB2_5

source_name: human serous papillary endometrial cancer tissue


title: WAT, LFD_Rep2

description: gene expression profile in white adipose tissues after low fat diet feeding in mice

source_name: white adipose tissue, low fat diet, replicate2

value: low fat diet


title: root in fall, biological rep2

source_name: poplar root in fall-2


title: Tr1_rep1

description: Gene expression data Tr1


title: KCCB2_1

description:
EC, G2
Gene expression data from human endometrioid endometrial cancer tissue, grade 2


title: KCCB2_4

source_name: human endometrioid endometrial cancer tissue, grade 2


title: WAT, HFD_Rep1

source_name: white adipose tissue, high fat diet, replicate1


title: KCCB1_34


title: root in summer, biological rep3

description: Gene expression data from five-year old poplar root in summer

source_name: poplar root in summer-3


title: Th17_rep4

description: Gene expression data Th17

source_name: in vitro differentiated murine Th cell subset; Th17

value: 50 ng/ml IL-6 plus 0.5 ng/ml TGF-β


title: Th17_rep3

description: Gene expression data Th17


title: WAT, LFD_Rep1

source_name: white adipose tissue, low fat diet, replicate1


title: Th17_rep5

description: Gene expression data Th17


title: KCCB1_31

source_name: human endometrioid endometrial cancer tissue, grade 3


title: root in summer, biological rep2

source_name: poplar root in summer-2


title: root in summer, biological rep1

source_name: poplar root in summer-1


title: KCCB1_29

description:
EC, serous
Gene expression data from human serous papillary endometrial cancer tissue


title: root in spring,biological rep3

description: Gene expression data from five-year old poplar root in spring

source_name: poplar root in spring-3


title: BM LSK GFP4, biological rep 2

city: New York

first: Jiajing

last: Qiu

state: NY

address: 1468 Madison Ave, ANBG bldg 24-10

department: Hematology/Oncology Department of Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP4b

hyb_protocol: 20ul 1ug/ul fragmented cRNA was hybridized to Affymetrix Mouse 430 2.0 3' gene expression array

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Both raw image (.dat) and probe cell intensity data (.cel) were generated with the Affymetrix Gene Chip Operating Softwae (GCOS)
Probe level expression values were extracted by RMA.  The software for RMA calculation is Bioconductor affy package. RMA normalization was done via RACE website (Remote Analysis computation for gene Expression data) at http://race.unil.ch (Psarros, M., Heber, S., Sick, M., Thoppae, G., Harshman, K., and Sick, B. (2005). RACE: Remote Analysis Computation for gene Expression data. Nucleic Acids Res 33, W638-643.)

source_name: Mouse bone marrow Lin-Sca+cKit+ cells at GFP retaining level 4

label_protocol: biotin labeled cRNA was synthesized with Enzo BioArray High Yield RNA transcript labeling kit T7 (Enzo Life Science) and fragmentd following the namufacturer's protocol for Affymatrix GeneChip Target Preparation

growth_protocol: Doxycyclin was administrated at 1mg/ml in the drinking water to 6-8 weeks old hCD34 x H2BGFP double transgenic mice for 12 weeks before bone marrow was harvested

extract_protocol: Trizol extracted total RNA from freshly sorted cells was purified with Rneasy Micro Kit (Qiaagen) and amplified with SuperScriptTM RNA Amplification System (Invitrogen)

treatment_protocol: Lineage- Sca+ ckit+ bone marrow cells at GFP levels 0, 1, 2, 3, 4 were isolated by FACS

value: C57BL/6 background (Backcrossed to this background for at least 10 generation)

value: hCD34 x H2BGFP double transgenic

value: bone marrow

tag: cell phenotype

value: Lineage-Sca+ckit+

tag: rank of gfp retaining level

tag: gfp label

value: Chromatin dynamically labeled by GFP tagged Histone 2B

tag: pulse/chase tet-off system

value: GFP expression stopped upon Dox treatment that last 12 weeks

tag: label dilution

value: During chase period newly synthesized endogenous H2B dilutes H2B-GFP by one-half with each round of cell division


title: BM LSK GFP4, biological rep 4

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP4d

tag: strain


title: Th17_rep2

description: Gene expression data Th17


title: KCCB1_28

value: endometrial cancer tissue


title: KCCB1_30


title: Th17_rep1

description: Gene expression data Th17


title: BM LSK GFP4, biological rep 3

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP4c


title: root in spring,biological rep2

source_name: poplar root in spring-2

tag: age

value: five-year old


title: Th0_rep4

description: Gene expression data Th0

source_name: Th cell subset; Th0

tag: cell type

value: none (no exogenous cytokines)


title: Th0_rep5

description: Gene expression data Th0

value: sorted naive Th cells (CD4+ CD44- Foxp3-)


title: root in spring,biological rep1

source_name: poplar root in spring-1

value: spring


title: bud in winter, biological rep3

description: Gene expression data from five-year old poplar bud in winter

source_name: poplar bud in winter-3

value: bud

value: winter


title: Th0_rep3

description: Gene expression data Th0


title: BM LSK GFP4, biological rep 1

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP4a


title: BM LSK GFP3, biological rep 1

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP3a

source_name: Mouse bone marrow Lin-Sca+cKit+ cells at GFP retaining level 3


title: KCCB1_23


title: BM LSK GFP3, biological rep 2

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP3b


title: KCCB1_24

description:
EC, G1
Gene expression data from human endometrioid endometrial cancer tissue, grade 1


title: KCCB1_26

source_name: human serous papillary endometrial cancer tissue


title: bud in winter, biological rep2

source_name: poplar bud in winter-2


title: BM LSK GFP2, biological rep 3

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP2c

source_name: Mouse bone marrow Lin-Sca+cKit+ cells at GFP retaining level 2


title: Th0_rep2

description: Gene expression data Th0


title: bud in winter, biological rep1

source_name: poplar bud in winter-1


title: bud in fall, biological rep3

description: Gene expression data from five-year old poplar bud in fall

source_name: poplar bud in fall-3

value: fall


title: KCCB1_22

description:
EC, G3
Gene expression data from human endometrioid endometrial cancer tissue, grade 3


title: Th0_rep1

description: Gene expression data Th0


title: BM LSK GFP2, biological rep 1

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP2a


title: BM LSK GFP2, biological rep 2

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP2b


title: MSC 21 Sparse day 3

city: La Jolla

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

description: 15000 cells seeded and collected 3 days after seeded

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization. Probeset Summarization: Median Polish.

source_name: Sparse MSC day 3

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

growth_protocol: Mesenchymal cells were extacted from mouse bone marow and grown in Stem Cell media (Stem Cells Tech.).

extract_protocol: TRI reagent total RNA extraction according to manufacturer's protocol.

treatment_protocol: Independent cell samples were grown at the indicated confluence levels and RNA was collected.

value: mesenchymal stem cell (MSC)

tag: confluence

value: Sparse


title: KCCB1_19

description:
EC, G2
Gene expression data from human endometrioid endometrial cancer tissue, grade 2


title: BM LSK GFP1, biological rep 2

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP1b

source_name: Mouse bone marrow Lin-Sca+cKit+ cells at GFP retaining level 1

value: C57BL/6 background (Backcrossed to this background for at least 10 generation)


title: bud in fall, biological rep1

source_name: poplar bud in fall-1

tag: collection time


title: KCCB1_17

source_name: human endometrioid endometrial cancer tissue, grade 2


title: KCCB1_18

source_name: human endometrioid endometrial cancer tissue, grade 1


title: bud in fall, biological rep2

source_name: poplar bud in fall-2


title: MSC 21 Sparse day 2

description: 15000 cells seeded and collected 2 days after seeded

source_name: Sparse MSC day 2


title: MSC 21 Sparse day 1

description: 15000 cells seeded and collected 1 day after seeded

source_name: Sparse MSC day 1


title: BM LSK GFP1, biological rep 1

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP1a

value: hCD34 x H2BGFP double transgenic


title: bud in summer,biological rep2

description: Gene expression data from five-year old poplar bud in summer

source_name: poplar bud in summer-2

value: summer


title: bud in summer,biological rep3

source_name: poplar bud in summer-3


title: bud in summer,biological rep1

source_name: poplar bud in summer-1


title: MSC 21 Dense day 2

description: 2.5 million cells seeded and collected 2 days after seeded

source_name: Dense MSC day 2

value: Dense


title: KCCB1_16

source_name: human endometrioid endometrial cancer tissue, grade 3


title: BM LSK GFP1, biological rep 3

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP1c

value: bone marrow

value: Lineage-Sca+ckit+

value: Chromatin dynamically labeled by GFP tagged Histone 2B


title: MSC 21 Dense day 3

description: 2.5 million cells seeded and collected 3 days after seeded

source_name: Dense MSC day 3


title: bud in spring,biological rep3

description: Gene expression data from five-year old poplar bud in spring

source_name: poplar bud in spring-3


title: KCCB1_12

description:
EC, G1
Gene expression data from human endometrioid endometrial cancer tissue, grade 1

value: endometrial cancer tissue


title: BM LSK GFP0, biological rep 1

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP0a

source_name: Mouse bone marrow Lin-Sca+cKit+ cells at GFP retaining level 0

value: GFP expression stopped upon Dox treatment that last 12 weeks

value: During chase period newly synthesized endogenous H2B dilutes H2B-GFP by one-half with each round of cell division


title: Tr1_rep3

description: Gene expression data Tr1

source_name: in vitro differentiated murine Th cell subset; Tr1

value: sorted naive Th cells (CD4+ CD44- Foxp3-)

value: 100 ng/ml IL-27 plus 0.5 ng/ml TGF-β


title: KCCB1_13


title: KCCB1_11

description:
EC, serous
Gene expression data from human serous papillary endometrial cancer tissue


title: MSC 21 Dense day 1

description: 2.5 million cells seeded and collected 1 day after seeded

source_name: Dense MSC day 1


title: KCCB1_8

description:
EC, G3
Gene expression data from human endometrioid endometrial cancer tissue, grade 3


title: Clone 4L.1.4 sample 2

description: MSC tertiary clone, derived from MSC21

source_name: MSC clone

treatment_protocol: Independent cell samples were grown to confluence and RNA was collected.

tag: culture

value: clone


title: KCCB1_9

source_name: human serous papillary endometrial cancer tissue


title: Clone 4L.1.4 sample 1

description: MSC tertiary clone, derived from MSC21


title: bud in spring,biological rep2

source_name: poplar bud in spring-2

value: bud

value: spring

value: five-year old


title: BM LSK GFP0, biological rep 2

description:
amplified RNA
The level of GFP indicates how many times cells have divided
GFP0b

tag: genotype/variation


title: bud in spring,biological rep1

source_name: poplar bud in spring-1


title: xylem in winter, biological rep3

description: Gene expression data from five-year old poplar xylem in winter

source_name: poplar xylem in winter-3

value: xylem

value: winter


title: Clone 4L.1.4 sample 3

description: MSC tertiary clone, derived from MSC21

value: mesenchymal stem cell (MSC)


title: xylem in winter, biological rep1

source_name: poplar xylem in winter-1


title: KCCB1_10


title: xylem in fall,biological rep3

description: Gene expression data from five-year old poplar xylem in fall

source_name: poplar xylem in fall-3

value: fall


title: xylem in winter, biological rep2

source_name: poplar xylem in winter-2


title: KCCB1_6


title: MSC21 sample 3

description: MSC population derived from mouse bone marrow

source_name: MSC population

value: population


title: xylem in fall,biological rep1

source_name: poplar xylem in fall-1


title: C42B_181_DHT_DOX 2

first: Gillian

last: Little

state: CA

address: 2250 Alcazar Street

institute: University of Southern California

description: replicate 2

hyb_protocol: Hybridization was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

scan_protocol: Scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

data_processing: The data were normalised using quantile normalisation in genome studio

label: Biotin

source_name: C4-2B/181 Prostate cancer cells

label_protocol: Labeling was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol

growth_protocol: cells were grown in RPMI supplemented with 10% FBS, then in phenol red free RPMI supplemented with 5% charcoal stripped serum for 48h prior to treatment,

extract_protocol: Total RNA was isolated using Aurum Total RNA kit (Bio-Rad Laboratories, Inc., Hercules, CA) and reverse-transcribed using the qScript cDNA synthesis kit (Quanta Biosciences, Gaithersburg, MD)

treatment_protocol: DHT was 10mM, dox was 250ug/ml for 48h prior to harvesting.  Veh control was ethanol.

tag: cell line

tag: treatment

value: DHT DOX


title: KCCB1_2

source_name: human endometrioid endometrial cancer tissue, grade 1


title: xylem in summer,biological rep3

description: Gene expression data from five-year old poplar xylem in summer

source_name: poplar xylem in summer-3

value: summer


title: C42B_181_DHT 3

description: replicate 3

value: DHT


title: xylem in fall,biological rep2

source_name: poplar xylem in fall-2


title: KCCB1_7

value: endometrial cancer tissue


title: xylem in summer,biological rep2

source_name: poplar xylem in summer-2


title: MSC21 sample 1


title: KCCB1_5

description:
EC, G2
Gene expression data from human endometrioid endometrial cancer tissue, grade 2


title: KCCB1_3


title: xylem in summer,biological rep1

source_name: poplar xylem in summer-1


title: C42B_181_DHT 2

description: replicate 2


title: KCCB1_1

source_name: human endometrioid endometrial cancer tissue, grade 2


title: xylem in spring,biological rep1

description: Gene expression data from five-year old poplar xylem in spring

source_name: poplar xylem in spring-1


title: xylem in spring,biological rep2

source_name: poplar xylem in spring-2


title: C42B_181_DHT_DOX 1

description: replicate 1


title: C42B_181_DHT_DOX 3

description: replicate 3


title: SPAC-1L_10

description:
SPAC-1L, STAT1-siRNA+rIFN 250um, rep1
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA and human recombinant IFN gamma 250 uM

source_name: human serous papillary endometrial cancer cell treated by STAT1 siRNA and human rIFN-gamma 250uM

value: endometrial cancer cell


title: SPAC-1L_11

description:
SPAC-1L, STAT1-siRNA+rIFN 250um, rep2
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA and human recombinant IFN gamma 250 uM


title: C42B_181_DHT 1

description: replicate 1


title: SPAC-1L_12

description:
SPAC-1L, STAT1-siRNA+rIFN 250um, rep3
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA and human recombinant IFN gamma 250 uM


title: C42B_181_Et 3

description: replicate 3

value: ethanol


title: C42B_181_Dox 1

description: replicate 1

value: Dox


title: C42B_181_Dox 2

description: replicate 2


title: SPAC-1L_9

description:
SPAC-1L, rIFN 250uM, rep3
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by human recombinant IFN gamma 250 uM

source_name: human serous papillary endometrial cancer cell treated by human rIFN-gamma 250uM


title: C42B_181_Dox 3

description: replicate 3


title: SPAC-1L_7

description:
SPAC-1L, rIFN 250uM, rep1
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by human recombinant IFN gamma 250 uM


title: SPAC-1L_5

description:
SPAC-1L, STAT1-siRNA, rep2
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA

source_name: human serous papillary endometrial cancer cell treated by STAT1-siRNA


title: SPAC-1L_6

description:
SPAC-1L, STAT1-siRNA, rep3
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA


title: SPAC-1L_8

description:
SPAC-1L, rIFN 250uM, rep2
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by human recombinant IFN gamma 250 uM


title: C42B_181_Et 1

description: replicate 1


title: C42B_181_Et 2

description: replicate 2


title: ips_live

city: Cambridge

first: Sandy

last: Klemm

state: MA

address: 31 Ames St.

department: Biology

institute: MIT

description: iPSCs grown in 2i/serum

hyb_protocol: Affymetrix hybrdization and wash protocol (3.2.3.1515R AGCC Portal software); GeneChip Hybridization Oven 640; Affymetrix GeneChip Fluidics Station 450

scan_protocol: Affymetrix 7G scanner (3.2.3.1515R AGCC Portal software)

data_processing: Data were processed using the GCRMA and Affy Bioconductor packages

molecule: polyA RNA

label_protocol: NUGEN Ovation RNA Amplification System V2 followed with FL-Ovation cDNA Biotin Module V2

growth_protocol: 2i/serum mESC media

extract_protocol: Trizol LS

value: iPSCs

tag: sample type

value: live


title: Live_J1_NIH3T3

description: Live J1 and NIH-3T3 expression fold change

hyb_protocol: Two Color Microarray-Based Gene Expression Analysis (Agilent) with Robbins Scientific Hybridization Incubator (1040-60-1AG)

scan_protocol: Agilent Scan Control protocol executed on Agilent Technology DNA Microarray Scanner with Surescan High-Resolution Technology (Model # G2505C)

data_processing:
Agilent Feature Extraction Software (v10.5.1.1)
Normalized log2 ratio (Cy3/Cy5) representing NIH-3T3/J1 expression ratios are in Series supplementary file processed_data.txt

source_name: J1 mESCs

label_protocol: Low Input Quick Amp Labeling Kit (Agilent)

growth_protocol: Standard media for NIH-3T3 fibroblasts and 2i/serum media for J1 ES cells

extract_protocol: Total RNA extracted by Trizol following manufacturer's instructions

treatment_protocol: None except as indicated

value: embryonic stem cells

source_name: NIH-3T3 fibroblasts

value: fibroblasts


title: Hybridized_J1_NIH3T3

description: Hybridized J1 and NIH-3T3 expression fold change

source_name: Hybridized J1 mESCs

value: hybridized

source_name: Hybridized NIH-3T3 fibroblasts


title: ips_hybridized

description: iPSCs grown in 2i/serum


title: sox2_negative_b

description: Secondary MEFs following 32 days of Yamanaka factor expression, sox2 negative fraction

source_name: sox2- d32

label_protocol: NUGEN Ovation RNA Amplification System V2 or NUGEN Ovation Pico WTA System V2 followed with FL-Ovation cDNA Biotin Module V2

growth_protocol: Standard mESC media except where otherwise noted

extract_protocol: Trizol

value: secondary MEFs following 32 days of Yamanaka factor expression, sox2 negative fraction


title: sox2_negative_a


title: sox2_positive_a

description: Secondary MEFs following 32 days of Yamanaka factor expression, sox2 postive fraction

source_name: sox2+ d32

value: secondary MEFs following 32 days of Yamanaka factor expression, sox2 postive fraction


title: sox2_positive_b


title: SPAC-1L_3

description:
SPAC-1L, non-treated, rep3
Gene expression data from non treated human serous papillary endometrial cancer cell, SPAC-1L

source_name: human serous papillary endometrial cancer cell, no treatment

tag: tissue


title: d32_a

description: Secondary MEFs following 32 days of Yamanaka factor expression

value: secondary MEFs following 32 days of Yamanaka factor expression


title: d32_b


title: SPAC-1L_1

description:
SPAC-1L, non-treated, rep1
Gene expression data from non treated human serous papillary endometrial cancer cell, SPAC-1L


title: SPAC-1L_2

description:
SPAC-1L, non-treated, rep2
Gene expression data from non treated human serous papillary endometrial cancer cell, SPAC-1L


title: ips_2i_b

description: iPSCs grown in 2i/serum

value: grown in 2i/serum


title: ips_mef_b

description: iPSCs co-cultured with MEFs

source_name: iPS-MEF

value: co-cultured with MEFs


title: Saureus_LAC_Vehicle_3

status: Public on Mar 19 2014

city: Albuquerque

first: Brian

middle: Marshall

last: Gray

state: NM

address: 1 University of New Mexico

department: Pharmaceutical Sciences

institute: University of New Mexico

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of vehicle control.  This is the third of three samples.

hyb_protocol: Hybridication was performed by AmbryGen (Aliso Viejo, CA, USA) following the NimbleGen-Roche standard protocol.  See http://www.nimblegen.com/downloads/support/05434505001_NG_Expression_UGuide_v6p0.pdf

scan_protocol: Scanning was performed by AmbryGen (Aliso Viejo, CA, USA) following the standard NimbleGen-Roche protocol.  See http://www.nimblegen.com/downloads/support/05434505001_NG_Expression_UGuide_v6p0.pdf

data_processing: The raw data (.pair files) were subjected to quantile normalization and background correction by AmbryGen as implemented in the NimbleScan software package.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: Staphylococcus aureus USA300 LAC with vehicle

label_protocol: Labeling was performed by AmbryGen (Aliso Viejo, CA, USA) following the NimbleGen-Roche standard protocol (Nimblegen-Roche, Madison, WI, USA).  See http://www.nimblegen.com/downloads/support/05434505001_NG_Expression_UGuide_v6p0.pdf

growth_protocol:
Staphylococcus aureus USA300 LAC was grown from early-log phase freezedown for 5 hours in trypticase soy broth at 37 °Cwith 0.05% DMSO.
Staphylococcus aureus USA300 LAC was grown from early-log phase freezedown for 5 hours in trypticase soy broth at 37 °Cwith 0.05% DMSO, with 12 uM benzbromarone.

extract_protocol: Total RNA was harvested using the RNEasy Mini Kit and RNAProtect reagent and DNA was removed via on-column DNAse digestion with the RNAse-free DNAse set (all from Qiagen Inc., Valencia, CA, USA).  RNA concentration and quality was determined by spectrophotometry on a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

value: Vehicle control


title: SPAC-1L_4

description:
SPAC-1L, STAT1-siRNA, rep1
Gene expression data from human serous papillary endometrial cancer cell, SPAC-1L, treated by STAT1-siRNA


title: Saureus_LAC_BBM_3

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of benzbromarone.  This is the third of three samples.

source_name: Staphylococcus aureus USA300 LAC with benzbromarone

value: benzbromarone


title: Saureus_LAC_BBM_2

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of benzbromarone.  This is the second of three samples.


title: DMM.C

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all arrays.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

organism: Mycobacterium tuberculosis H37Rv

source_name: Antifolate treated sample

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: M. tuberculosis strain H37Rv cultures were grown in 7H9+GAT.

extract_protocol: Total RNA was extracted TRIzol chloroform:isopropanol phase separation using phaselock gels to separate the aqueous phase.  Samples were isolated by immobilization on Qiagen RNeasy columns as per manufacturer's instructions.  On- and off-column DNase treatments were performed to minimuze genomic or plasmid nucleic acid contamination of the final sample.

treatment_protocol: To investigate the impact of antifolate treatment, cultures were supplemented with either no drug, 30 uM WR99210, 20uM DEM, or 10 uM DMM.  Samples for microarray were harvested after 24 hours of exposure.

value: Treated with 10 uM dimethylmethotrexate for 24 hours


title: ips_2i_a

description: iPSCs grown in 2i/serum


title: WR.C

value: Treated with 30 uM WR9910 for 24 hours


title: ips_mef_a

description: iPSCs co-cultured with MEFs


title: Saureus_LAC_BBM_1

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of benzbromarone.  This is the first of three samples.


title: WR.B


title: WR.A


title: Pool control (Western diet)

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

description: Gene expression data from liver  male mice on a semipurified Western diet for 11 weeks

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome MOE430A 2.0.

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: liver_control diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA

growth_protocol: Two-month-old male mice with a C57BL/6J genetic background were fed with semipurified Western diet and 0.01% oleanolic acid to provide a dose of 10 mg/kg/day for 11 weeks

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit.

treatment_protocol: Liver were removed, washed to remove blood, frozen in liquid nitrogen and stored at -70C.

tag: strain background

value: apolipoprotein E-deficient

value: 2 months

tag: gender

value: male

tag: fed with

value: Western control diet

value: liver


title: Pool Oleanolic acid

description: Gene expression data from liver apolipoprotein E-deficient male mice on a Western diet  containing 0.01% oleanolic acid to provide a dose of 10 mg/kg/day for 11 weeks

source_name: liver_Oleanolic diet

value: Western diet containing 0.01% oleanolic acid to provide a dose of 10 mg/kg/day for 11 wks


title: Saureus_LAC_Vehicle_1

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of vehicle control.  This is the first of three samples.


title: DEM.C

value: Treated with 20 uM diethylmethotrexate for 24 hours


title: DEM.B


title: DMM.B


title: AR0865_06: WT CLP

city: Suita

first: Takafumi

last: Yokota

state: Osaka

address: 2-2 Yamadaoka

department: Hematology & Oncology

institute: Osaka University

description: CLP sorted from wild-type bone marrow

hyb_protocol: 2.0 ug of Cy3-labelled cDNA in a reaction volume of 25 ul containing 1x Agilent blocking agent following the manufacturers instructions.   25 ul of 2x Agilent hybridization buffer was added to the mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent)  and for 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CLP from wild-type bone marrow

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 6.1ng Total RNA using the Ovation® Pico WTA System V2 (NuGEN) according to the manufacturer's instructions, followed by DNA Clean & Concentrator-25 purification (Zymo Research).    Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Rneasy Micro Kit(50) (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Freshly isolated lympho-hematopoietic progenitor cells from bone marrow

value: bone marrow

value: CLP

value: Wild Type


title: AR0865_08: SFRP5 CLP

description: CLP sorted fromSFRP5-TG bone marrow

source_name: CLP from SFRP5-TG bone marrow


title: AR0865_05: WT LSK

description: LSK sorted from wild-type bone marrow

source_name: LSK cells from wild-type bone marrow

value: LSK


title: AR0865_07: SFRP5 LSK

description: LSK sorted from SFRP5-TG bone marrow

source_name: LSK cells from SFRP5-TG bone marrow


title: MSC21 sample 2

description: MSC population derived from mouse bone marrow

source_name: MSC population

value: mesenchymal stem cell (MSC)

value: population


title: DMM.A


title: NoDrug.B

source_name: Untreated (control)

value: Untreated control


title: NoDrug.A


title: DEM.A


title: Saureus_LAC_Vehicle_2

description: This sample is Staphylococcus aureus USA300 LAC grown to log phase in the presence of vehicle control.  This is the second of three samples.

value: Vehicle control


title: NoDrug.C


title: i2PS cells rep2

first: Kostas

last: Kostarelos

address: AV Hill Building, Upper Brook St

department: Faculty of Medical and Human Sciences

description: i2PS replicate 2

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Scanning was performed on Illumina Bead reader

data_processing: Data was normalised using quantile normalisation in Illumina GenomeStudio software. Data was expressed as the logarithm of the average signal intensity of the three replicates of each sample. Corrected p values were obtained with Bonferroni correction. E14TG2A was used as the reference group throughout the experiment.

source_name: i2PS cells

label_protocol: RNA labelling was performed using the Ambion Total Prep-TM 96 kit and according to the manufacturer specifications.

growth_protocol: i2PS and E14 cells were grown initially on mouse embryonic fibroblast feeder layers under standard mouse embryonic stem cell culture conditions (i.e. DMEM/LIF). Cells were then plated on gelatin coated culture vessels and passaged (3 times) until no fibroblasts remained.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quantity and quality were assessed with Nanodrop and Agilent Bioanalyser.

value: BALB/c

value: Liver

tag: origin

value: Hepactocytes reprogrammed to pluripotency in vivo


title: SAHA at 6hrs, biological rep2

city: Boston

first: Panagiotis

last: Konstantinopoulos

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) were carried out using standard protocols.

data_processing: Raw gene expression data (Affymetrix .CEL files) were imported in BRB-ArrayTools Version: 4.2.0 - Beta_2 (Biometrics Research Branch, National Cancer Institute) and were processed and normalized using GC Robust Multi-Array (RMA) analysis.

source_name: SKOV3 cells treated with 1µM SAHA for 6 hrs

growth_protocol: The epithelial ovarian cancer cell line SKOV-3 was obtained by ATCC (American Type Culture Collection, Manassas, VA) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer's instructions.

treatment_protocol: SKOV-3 ovarian cancer cells were treated with 1µM SAHA or vehicle-control (0.01% DMSO) for 6 or 24 hours.

value: SAHA

tag: time

value: 6 h


title: SAHA at 24hrs, biological rep1

scan_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) were carried out using standard protocols.

source_name: SKOV3 cells treated with 1µM SAHA for 24 hrs


title: i2PS cells rep3

description: i2PS replicate 3


title: E14TG2A cells rep1

description: E14 replicate 1

source_name: E14TG2A cells

value: Inner cell mass of blastocyst

value: Cell line purchased from ATCC


title: i2PS cells rep1

description: i2PS replicate 1


title: SAHA at 24hrs, biological rep2

label_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) were carried out using standard protocols.


title: VEHICLE at 24hrs, biological rep1

source_name: SKOV3 cells treated with vehicle-control (0.01% DMSO) for 24 hrs

value: vehicle


title: VEHICLE at 24hrs, biological rep2


title: VEHICLE at 6hrs, biological rep1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: SKOV3 cells treated with vehicle-control (0.01% DMSO) for 6 hrs


title: SAHA at 6hrs, biological rep1


title: VEHICLE at 6hrs, biological rep2


title: E14TG2A cells rep2

description: E14 replicate 2


title: male EtOH (6033090025_E)

city: Maywood

first: Toni

middle: R

last: Pak

state: IL

address: 2160 S. First Ave

department: Cell and Molecular Physiology

institute: Loyola University Stritch School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI software

organism: Rattus norvegicus

source_name: hypothalamus

label_protocol: Standard Illumina biotinylation procedure

extract_protocol: Total RNA from PND 7 rat pup hypothalami (N = 6/treatment/sex) was isolated using RNeasy Plus Mini Kit (Qiagen, Inc.) according to manufacturer’s instructions and submitted to the Southern California Genotyping Consortium (SCGC) for microarray processing

value: Wistar

value: PND 7

tag: Sex

value: male

value: EtOH

value: hypothalamus


title: female EtOH (6033090025_G)

tag: strain

value: female


title: female EtOH (6033090025_L)

tag: age


title: male EtOH (6033090025_A)


title: male EtOH (6033090025_F)


title: female EtOH (6033090025_H)


title: female EtOH (6033090025_K)


title: female water (5665175044_J)

value: water


title: female water (5665175044_K)


title: male EtOH (6033090025_D)


title: female EtOH (6033090025_I)


title: female water (5665175044_I)


title: male EtOH (6033090025_C)


title: male EtOH (6033090025_B)


title: female EtOH (6033090025_J)


title: E14TG2A cells rep3

description: E14 replicate 3


title: female water (5665175044_L)


title: Btg1;Btg2 dKO_BM B220+ CD43- cells

city: Nijmegen

first: Blanca

last: Scheijen

address: Kapittelweg 29

country: Netherlands

institute: Radboudumc

description: Hardy fractions DEF

hyb_protocol: Standard Illumina direct hybridization protocol

scan_protocol: Standard Illumina direct hybridization scanning protocol

data_processing: The data were normalised using RMA normalisation with Arraystar

label_protocol: Biotinylated cRNA were prepared using the Illumina Ambion Total Prep-96 Kit

extract_protocol: BM was isolated from tibia and femur by flushing. The BM B220+ CD43+ and B220+ CD43- fraction were sorted by flow cytometry. RNA was extracted QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

tag: genotype

value: Btg1;Btg2 dKO


title: WT_BM B220+ CD43+ cells

description: Hardy fractions ABC

value: wild type


title: Btg1:Btg2 dKO_BM B220+ CD43+ cells

description: Hardy fractions ABC


title: WT_BM B220+ CD43- cells

description: Hardy fractions DEF


title: male water (5665175044_F)


title: male water (5665175044_E)


title: female water (5665175044_G)


title: Ets2 present in fibroblasts with the PyMT oncogene present in epithelial cells

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

description: Gene expression data from mammary fibroblasts with Ets2 and the PyMT oncogene present in epithelial cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Mouse Genome 430A 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression levels were estimated from GeneChip probe intensities using WEDGE++ algorithm (WPP), an enhanced integrated version of the published RMA, quantile-normalization and background-correction algorithms.

source_name: Fibroblasts isolated from mammary gland with Ets2 present in fibroblasts and the PyMT oncogene present in epithelial cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Fibroblasts were isolated from mammary gland tissue using a modified protocol for gravity separation.

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

treatment_protocol: Fibroblasts were grown in 10% FBS DMEM in a 37º incubator with 7% CO2.

value: FVB/N

value: 9 Weeks

value: Mammary Gland

value: Fibroblasts


title: shMll3-2;p53-/- HSCPC Rep2

city: Chengdu

first: Chong

last: Chen

state: Sichuan

address: 17 Renmin S. Road-No. 3

department: State Key Laboratory of Biotherapy

institute: Sichuan University

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse-ref8 v2 R3 Array. Slides were washed and stained in the Illumina instrument.

data_processing: The data were median centered using R

source_name: shMll3-2;p53-/- HSCPC

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

extract_protocol: Cells were lysed and RNA extracted with Trizol reagent in accordance with the prescribed protocol provided by the manufacturer. Quality control was performed with Agilent Bioanalyser and Nanodrop.

tag: transplanted with

tag: time point

value: 6 wks after transplant

value: sorted lin-ckit+ hematopoietic stem and progenitor cells (HSCPCs)


title: male water (5665175044_A)


title: female water (5665175044_H)


title: shMll3-2;p53-/- HSCPC Rep3


title: shRen;p53-/- HSCPC Rep3

source_name: shRen;p53-/- HSCPC


title: male water (5665175044_D)


title: shMll3-1;p53-/- HSCPC Rep2

source_name: shMll3-1;p53-/- HSCPC


title: Lung LVI 48h rep1

city: Singapore

first: Vincent

middle: Tak Kwong

last: Chow

state: Singapore

address: 5 Science Drive 2, BLK MD4 (NUS)

department: Microbiology

country: Singapore

institute: National University of Singapore (NUS)

description: replicate 1

hyb_protocol: 750 ng of biotinylated cRNA samples were hybridized onto single-channel MouseRef-8 v1.1 Expression Beadchip microarrays. The standard Illumina hybridization, washing and binding of fluoroscent dye Cy3 were used.

scan_protocol: All microarray slides were scanned using the Illumina BeadArray Reader with the scan factor of 0.7 and at the Cy3 channel-specific wavelength.

data_processing: Lumi package from Bioconductor was used to perform variance-stabilizing transformation and robust spline normalization.

source_name: Lung, LVI infection, 48 h

label_protocol: Biotinylated cRNAs were prepared using the Illumina Totalprep RNA Amplification kit (Illumina, San Diego, CA) according to manufacturer's protocol.

extract_protocol: For each sample, the lungs of three individual mice were pooled. Mortar and pestle were used to disrupt lung tissue in liquid nitrogen and total RNAs were extracted using Rneasy Plus Mini kit (Qiagen, Hilden, Germany). RNA purity was ensured by an OD260/OD280 ratio of >1.8. The integrity of the RNA was confirmed by electrophoresis in a 1.0% native agarose gel prepared using DEPC-treated 1´ TAE buffer.

treatment_protocol: Female BALB/c mice (7-8 weeks old) were anesthetized with Avertin via intra-peritoneal injection and inoculated intra-nasally with 35 ul each of egg allantoic fluid containing 1.4´105 TCID50/ml of influenza virus strain A/Aichi/2/68 (LVI), lung homogenate containing 2.9´106 TCID50/ml of mouse adapted influenza virus strain A/Aichi/2/68 (HVI), or uninfected lung homogenate as negative control. Mice were housed in individually ventilated cages maintained at 21°C with 12h light-dark cycles. The lungs of control mice and those infected with LVI and HVI were harvested at 12, 48 and 96 h post-infection.

value: BALB/c

value: 7-8 weeks old

value: lung

value: LVI infection

tag: time of sample collection

value: 48h post-infection


title: Neutrophils, MPI infection, 9 h post-infection_rep2

description: replicate 2

hyb_protocol: 600 ng of labeled cRNA was hybridized onto Agilent SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37°C.

scan_protocol: Slides were scanned using Agilent High Resolution Microarray Scanner (C-model).

data_processing: Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). GeneSpring GX 11.5 (Agilent) was utilized for 75th percentile normalization on log-transformed intensity data. Baseline transformation to median for each batch of data from each replicate was performed. Batch effect correction was also carried out to correct markers that showed consistent signals within batches but large variations between batches.

label_protocol: 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.

growth_protocol: MPRO cells were cultured in Iscove's modified Dulbecco's medium (IMDM) containing 4 mM L-glutamine, 3 g/l sodium bicarbonate, 10 ng/ml murine GM-CSF, and 20% heat-inactivated fetal bovine serum (FBS) at 37°C with 5% CO2. The culture medium was replenished in 1-2 days to obtain 5´105 cells per ml. MPRO neutrophils were obtained following induced differentiation of MPRO cells in the growth medium supplemented with 10 mM all-trans retinoic acid (ATRA) for 5 days.

extract_protocol: Total RNAs were extracted using the Rneasy Mini kit (Qiagen) according to the manufacturer's recommendations. The quantity and purity of total RNA were measured by the Nanodrop ND-100 spectrophotometer, while RNA integrity was verified by the Agilent 2100 Bioanalyzer.

treatment_protocol: MPRO neutrophils were incubated with either murine lung homogenate (mock infection), influenza virus strain A/Aichi/2/68 propagated in eggs (LVI; at MOI of 0.1), mouse adapted influenza virus strain A/Aichi/2/68 (HVI; at MOI of 0.1), or HVI propagated in MDCK cells (MPI; at MOI of 1) for 1 h at 37°C with 5% CO2. Cells were resuspended into 24-well plate at concentration 3´106 cells per well and collected either at 3 or 9 h post-infection.

value: neutrophil

value: MPRO

value: MPI infection

value: 9 h post-infection

tag: moi

tag: concentration (ng/ul)

tag: rin


title: male water (5665175044_C)

value: Wistar

value: PND 7

value: male

tag: treatment

value: water

tag: tissue

value: hypothalamus


title: shMll3-1;p53-/- HSCPC Rep1

tag: strain background


title: Ets2 null fibroblasts with no oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 deletion and no oncogene present in epithelial cells.

source_name: Fibroblasts isolated from mammary gland with Ets2 deletion in fibroblasts and no oncogene present in epithelial cells

value: FVB/N

value: 9 Weeks

value: Mammary Gland

value: Fibroblasts


title: male water (5665175044_B)


title: Ets2 present in fibroblasts with no oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 and no oncogene present in epithelial cells.

source_name: Fibroblasts isolated from mammary gland with Ets2 present in fibroblasts and no oncogene present in epithelial cells


title: Lung HVI 48h rep1

description: replicate 1

source_name: Lung, HVI infection, 48 h

value: BALB/c

tag: gender

value: female

value: 7-8 weeks old

value: HVI infection


title: Lung LVI 48h rep2

description: replicate 2

value: lung

value: LVI infection

value: 48h post-infection


title: Ets2 null fibroblasts with the PyMT oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 deletion and the PyMT oncogene present in epithelial cells.

source_name: Fibroblasts isolated from mammary gland with Ets2 deletion in fibroblasts and the PyMT oncogene present in epithelial cells


title: Neutrophils, HVI infection, 9 h post-infection_rep2

description: replicate 2

value: neutrophil

value: MPRO

value: 9 h post-infection


title: Neutrophils, LVI infection, 9 h post-infection_rep2

description: replicate 2


title: Lung HVI 48h rep2

description: replicate 2


title: Neutrophils, mock infection, 9 h post-infection_rep2

description: replicate 2

value: mock infection


title: shMll3-2;p53-/- HSCPC Rep1

value: 6 wks after transplant

value: sorted lin-ckit+ hematopoietic stem and progenitor cells (HSCPCs)


title: Neutrophils, LVI infection, 3 h post-infection_rep2

description: replicate 2

value: 3 h post-infection


title: Neutrophils, MPI infection, 3 h post-infection_rep2

description: replicate 2

value: MPI infection


title: Lung LH 48h rep2

description: replicate 2

source_name: Lung, mock infection, 48 h

value: LH infection


title: Lung HVI 12h rep2

description: replicate 2

source_name: Lung, HVI infection, 12 h

value: 12h post-infection


title: shRen;p53-/- HSCPC Rep2


title: Neutrophils, HVI infection, 3 h post-infection_rep2

description: replicate 2


title: Experiment3_si_YFP_2N (G1)

city: Portland

first: Ken

last: Kikuchi

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

hyb_protocol: Illumina MouseRef-8 v 2.0 protocol

scan_protocol: Illumina MouseRef-8 v 2.0 protocol

data_processing: Pre-processing of raw data in GenomeStudio, Quantile normalization with no background subtraction, differential expression analysis using GeneSifter software

source_name: Mouse alveolar rhabdomyosarcoma tumor culture

label_protocol: Ambion MessageAmp Premier

extract_protocol: Method of RNA isolation: Rnsasy Total RNA kit (Qiagen)

treatment_protocol: Cells were transfected by 10nM siYFP or control siRNA with 0.2% lipofectamine2000

tag: Stage

tag: tranfection

value: 10nM siYFP

tag: genotype/variation

value: Myf6Cre,Pax3:Foxo1a,p53 conditional aRMS mouse


title: Lung HVI 12h rep1

description: replicate 1

tag: strain

value: BALB/c

value: female

value: 7-8 weeks old


title: Experiment3_si_YFP_4N (G2/M)


title: shRen;p53-/- HSCPC Rep1


title: Lung LH 48h rep1

description: replicate 1

tag: age

value: lung


title: Lung LH 12h rep2

description: replicate 2

source_name: Lung, mock infection, 12 h


title: Experiment2_si_YFP_3N (S)

value: S


title: Neutrophils, MPI infection, 9 h post-infection_rep1

description: replicate 1

tag: cell type

value: neutrophil


title: Lung LVI 12h rep2

description: replicate 2

source_name: Lung, LVI infection, 12 h

value: LVI infection


title: Neutrophils, mock infection, 3 h post-infection_rep2

description: replicate 2

value: MPRO


title: Lung LVI 12h rep1

description: replicate 1


title: Neutrophils, LVI infection, 9 h post-infection_rep1

description: replicate 1

value: 9 h post-infection


title: Neutrophils, mock infection, 9 h post-infection_rep1

description: replicate 1

value: mock infection


title: Lung HVI 96h rep2

description: replicate 2

source_name: Lung, HVI infection, 96 h

value: HVI infection

value: 96h post-infection


title: Experiment3_si_control_4N (G2/M)

value: control siRNA


title: Experiment3_si_control_2N (G1)


title: Experiment2_si_YFP_2N (G1)


title: Lung LH 12h rep1

description: replicate 1

value: LH infection


title: Experiment2_si_YFP_4N (G2/M)


title: Lung HVI 96h rep1

description: replicate 1


title: Neutrophils, HVI infection, 9 h post-infection_rep1

description: replicate 1


title: Neutrophils, LVI infection, 3 h post-infection_rep1

description: replicate 1

value: 3 h post-infection


title: Neutrophils, HVI infection, 3 h post-infection_rep1

description: replicate 1


title: Aerobic glucose-limited chemostat_GRO41

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Hybridization, washing and scanning of Affymetrix chips were done according to manufacturers’ instructions. For each strain analysed, microarrays were run on three independent cultures.

data_processing: Processing of expression data (normalization, expression cut-off, etc.) was performed as described previously (Boer et al., J Biol Chem., 278:3265-74). The Significance Analysis of Microarrays (SAM, version 3.0) (Tusher et al., Proc Natl Acad Sci U S A., 98:5116-21) add-in to Microsoft Excel was used for comparison of replicate array experiments using a minimal fold change of two and false discovery rate of 1%. Overrepresentation of functional categories in sets of differentially expressed genes was analysed according to (Knijnenburg et al., BMC Genomics., 8:25).

label: Biotin-Streptavidin

organism: Saccharomyces cerevisiae

source_name: Glucose-limited chemostat culture -0.1H-1

label_protocol: Processing of total RNA was performed according to Affymetrix’s instructions. RNA target preparation for microarray expression analysis was carried out according the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, USA) using 200 ng of total RNA for both pure and mixed cultures. The protocol was carried out with minor modifications, i.e the Affymetrix polyA RNA controls were excluded from the aRNA amplification protocol and the IVT reactions were incubated for 16 h at 40°C. The quality of total RNA, cDNA, cRNA, and fragmented aRNA was checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

growth_protocol: Controlled batch and chemostat cultivation was carried out at 30°C in 2-L laboratory bioreactors (Applikon, Schiedam, The Netherlands) with working volumes of 1 L. Synthetic medium (Verduyn et al., Yeast, 8:501-17)supplemented with 7.5 g L-1 or 20 g L-1 glucose was used in aerobic and anaerobic cultures, respectively. In anaerobic bioreactor batch cultures, the medium contained 25 g L-1 glucose. Culture pH was maintained at 5.0 by automatic addition of 2 M KOH. In aerobic cultures, antifoam Pluronic PE 6100 (BASF, Ludwigshafen, Germany) was used. The antifoam was autoclaved (110 °C)separately from the other medium ingredients and added as a 15% (w/v) stock solution to give a final concentration of 0.15 g L-1. Aerobic bioreactors were sparged with 500 mL min-1 air and stirred at 800 rpm to ensure fully aerobic conditions. Anaerobic bioreactors were stirred at 800 rpm and sparged with 500 mL min-1 nitrogen (< 10 ppm oxygen). To minimize diffusion of oxygen, the bioreactors were equipped with Nonprene tubing and Viton O-rings and medium reservoirs were continuously flushed with nitrogen.  Anaerobic growth media were supplemented with the anaerobic growth factors ergosterol (10 mg L-1) and Tween 80 (420 mg L-1). In anaerobic cultures, antifoam C Emulsion (Sigma-Aldrich) was autoclaved separately (120 °C) as 20 % (w/v) solution and added to a final concentration of 0.2 g L-1.

extract_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Piper et al., J Biol Chem. 277:37001-8.).

tag: genotype background

value: CEN.PK113-5D (MATa MAL2-8C SUC2  ura3-52)

value: MATa ura3-52 aro8Δ::loxP-kanMX-loxP  pRS316 (CEN6-ARS4 URA3)

tag: carbon source

value: glucose


title: Neutrophils, mock infection, 3 h post-infection_rep1

description: replicate 1


title: Experiment2_si_control_4N (G2/M)

value: Myf6Cre,Pax3:Foxo1a,p53 conditional aRMS mouse


title: Lung LH 96h rep2

description: replicate 2

source_name: Lung, mock infection, 96 h

value: BALB/c

value: female

value: 7-8 weeks old


title: Lung LVI 96h rep2

description: replicate 2

source_name: Lung, LVI infection, 96 h

value: lung


title: Lung LVI 96h rep1

description: replicate 1

value: LVI infection


title: Experiment1_si_YFP_2N (G1)

value: 10nM siYFP


title: Experiment1_si_YFP_4N (G2/M)


title: Experiment2_si_control_3N (S)

value: S


title: Lung LH 96h rep1

description: replicate 1


title: Experiment1_si_control_3N (S)


title: Control, biological rep2

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

description: Gene expression data from isolated terminal end buds

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: terminal end buds from mice

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Littermates were raised in the same cages.

extract_protocol: Trizol extraction of total RNA followed by column purification (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Control (Ovol2flox/+ or Ovol2flox/+;K14-Cre, 2 mice/array) and conditional knockout (Ovol2flox/-;K14-Cre, 3 mice/array)

value: Terminal end bud (mammary gland)

value: 4.5 week old

tag: genotype


title: Experiment2_si_control_2N (G1)


title: Experiment1_si_YFP_3N (S)


title: Experiment1_si_control_2N (G1)


title: Ovol2 KO, biological rep1


title: Aerobic glucose-limited chemostat_BK6

scan_protocol: Hybridization, washing and scanning of Affymetrix chips were done according to manufacturers’ instructions. For each strain analysed, microarrays were run on three independent cultures.

treatment_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Piper et al., J Biol Chem. 277:37001-8.).

value: CEN.PK113-7D (MATa MAL2-8C SUC2 )

value: MATa MAL2-8C SUC2


title: Aerobic glucose-limited chemostat_BK9


title: Experiment1_si_control_4N (G2/M)

value: control siRNA


title: 06_CYP-treated mouse at 48H

status: Public on Mar 18 2014

city: Kyoto

first: Takeshi

last: Okinami

address: 54 Shogoin-Kawahara-Cho, Sakyo-ku

department: Department of Urology

institute: Kyoto University Graduate School of Medicine

description:
Gene expression data from the bladder of CYP-treated mouse
06_CYP150-48H-#13

hyb_protocol: Following fragmentation, cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affimetrix).

data_processing:
The data acquisition was performed with the Affymetrix GeneChip Command Console Software and the data were analyzed with GeneSpring GX Version 11.5.1 (Aglient technologies).
Summarization Algorithm ： RMA16, Confidence level ： All, Baseline Options ： Do not perform baseline transformation

source_name: Whole bladder 48 hours after CYP-treatment.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 4425209, Affymetrix).

growth_protocol: Mice were housed at a constant room temperature with a cycle of 12-hours light and 12-hours dark. Food and water were available ad libitum.

extract_protocol: Rneasy Mini kits extraction of total RNA was performed according to the manufacturer's protocols.

treatment_protocol: Mice were injected intraperitoneally with 150mg/kg body weight of CYP diluted in saline (CYP group) and mice were injected saline alone as controls (CTRL group). Treated mice were killed 48 hours after administaration and the whole bladders harvested.

value: Balbc/A

value: Five-week-old

tag: agent

value: CYP

value: whole bladder


title: Ovol2 KO, biological rep2


title: Neutrophils, MPI infection, 3 h post-infection_rep1

description: replicate 1

value: neutrophil

value: MPRO

value: MPI infection

tag: time of sample collection

value: 3 h post-infection

tag: moi


title: Aerobic glucose-limited chemostat_GRO42

value: CEN.PK113-5D (MATa MAL2-8C SUC2  ura3-52)

value: MATa ura3-52 aro8Δ::loxP-kanMX-loxP  pRS316 (CEN6-ARS4 URA3)

value: glucose


title: Control, biological rep1

value: female


title: 05_CYP-treated mouse at 48H

description:
Gene expression data from the bladder of CYP-treated mouse
05_CYP150-48H-#12


title: 01_CTRL mouse at 48H

description:
Gene expression data from the bladder of CTRL mouse
01_CYP0-48H-#21

source_name: Whole bladder 48 hours after sham treatment.

value: control


title: 02_CTRL mouse at 48H

description:
Gene expression data from the bladder of CTRL mouse
02_CYP0-48H-#22


title: 04_CYP-treated mouse at 48H

description:
Gene expression data from the bladder of CYP-treated mouse
04_CYP150-48H-#11


title: 03_CTRL mouse at 48H

description:
Gene expression data from the bladder of CTRL mouse
03_CYP0-48H-#23


title: Embryo at E10.5, rathke's pouch 2

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression of the rathke's pouch at E10.5

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed in Genespring v 7.3.1. A standard workflow for microarray analysis included removal of probesets that did not map uniquely to the mm9 ENSEMBL genome and the identification of genes, transcripts, and probesets whose RMA- measured expression level was at least 6.2 in at least one sample

source_name: embryo_E10.5_rathke's pouch

label_protocol: Biotynilated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Embryos were collected from CD1 outbred mice with the day of vaignal plug designated E0.5.  Embryos were flash frozen, cryostat section were made a processed.  Laser capture microdissection was carried out with an Arcturus Veritas.

extract_protocol: RNA was purified using the ZR RNA MicroPrep kit (Zymo). Nugen RiboSpia Ovation Pico WTA System V2 was used for aplification.

tag: embryonic stage

value: rathke's pouch


title: Embryo at E10.5, rathke's pouch 4


title: Embryo at E10.5, rathke's pouch 5


title: Embryo at E10.5, olfactory pit 3

description: Gene expression of the olfactory pit at E10.5

source_name: embryo_E10.5_olfactory pit

value: olfactory pit


title: Embryo at E10.5, rathke's pouch 1


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 4

description: Gene expression of the neuroepithelium underlying lateral nasal prominence at E10.5

source_name: embryo_E10.5_neuroepithelium underlying lateral nasal prominence


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 7

description: Gene expression of the neuroepithelium underlying medial nasal prominence at E10.5

source_name: embryo_E10.5_neuroepithelium underlying medial nasal prominence


title: Embryo at E10.5, olfactory pit 4


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 8

value: neuroepithelium underlying medial nasal prominence


title: Embryo at E10.5, olfactory pit 2


title: Embryo at E10.5, rathke's pouch 3


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 6


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 5


title: Embryo at E10.5, medial nasal prominence 1

description: Gene expression of the medial nasal prominence at E10.5

source_name: embryo_E10.5_medial nasal prominence

value: medial nasal prominence


title: Embryo at E10.5, maxillary arch 5

description: Gene expression of the maxillary arch  at E10.5

source_name: embryo_E10.5_maxillary arch

value: maxillary arch


title: Embryo at E10.5, maxillary arch epidermal ectoderm 2

description: Gene expression of the maxillary arch epidermal ectoderm  at E10.5

source_name: embryo_E10.5_maxillary arch epidermal ectoderm

value: maxillary arch epidermal ectoderm


title: Embryo at E10.5, maxillary arch epidermal ectoderm 4


title: Embryo at E10.5, maxillary arch epidermal ectoderm 1


title: Embryo at E10.5, maxillary arch 4


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 3


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 1


title: Embryo at E10.5, olfactory pit 1


title: Embryo at E10.5, medial nasal prominence 2


title: Embryo at E10.5, neuroepithelium underlying lateral nasal prominence 2


title: Embryo at E10.5, maxillary arch 2


title: Embryo at E10.5, medial nasal prominence 3


title: Embryo at E10.5, maxillary arch epidermal ectoderm 3


title: Embryo at E10.5, medial nasal prominence 4


title: Embryo at E10.5, mandibular arch epidermal ectoderm 3

description: Gene expression of the mandibular arch epidermal ectoderm at E10.5

source_name: embryo_E10.5_mandibular arch epidermal ectoderm

value: mandibular arch epidermal ectoderm


title: Embryo at E10.5, lateral nasal eminence 1

description: Gene expression of the lateral nasal eminence at E10.5

source_name: embryo_E10.5_lateral nasal eminence

value: lateral nasal eminence


title: Embryo at E10.5, lateral nasal eminence 2


title: Embryo at E10.5, control neuroepithelium not flanking facial emincences 1

description: Gene expression of the control neuroepithelium not flanking facial emincences at E10.5

source_name: embryo_E10.5_control neuroepithelium not flanking facial emincences


title: Embryo at E10.5, mandibular arch epidermal ectoderm 2


title: Embryo at E9.5, otic vesicle 5

description: Gene expression of the otic vesicle at E9.5

source_name: embryo_E9.5_otic vesicle

value: otic vesicle


title: Embryo at E10.5, control neuroepithelium not flanking facial emincences 3


title: Embryo at E10.5, maxillary arch 1


title: Embryo at E10.5, mandibular arch 3

description: Gene expression of the mandibular arch at E10.5

source_name: embryo_E10.5_mandibular arch

value: mandibular arch


title: Embryo at E10.5, central neuroepithelium at midline 4

description: Gene expression of the central neuroepithelium at midline at E10.5

value: central neuroepithelium at midline


title: Embryo at E10.5, mandibular arch epidermal ectoderm 1


title: Embryo at E10.5, mandibular arch epidermal ectoderm 4


title: Embryo at E10.5, control neuroepithelium not flanking facial emincences 4


title: Embryo at E10.5, lateral nasal eminence 3


title: Embryo at E10.5, control neuroepithelium not flanking facial emincences 2


title: Embryo at E10.5, lateral nasal eminence 4


title: Embryo at E10.5, maxillary arch 3


title: Embryo at E10.5, central neuroepithelium at midline 1


title: Embryo at E9.5, otic vesicle 3


title: Embryo at E10.5, central neuroepithelium at midline 2


title: Embryo at E9.5, otic vesicle 6


title: Embryo at E9.5, otic vesicle 1


title: Embryo at E9.5, otic vesicle 4


title: Embryo at E10.5, central neuroepithelium at midline 3


title: Embryo at E9.5, otic vesicle 2


title: Embryo at E10.5, mandibular arch 4


title: Embryo at E10.5, mandibular arch 1


title: ee-Pul_over_ee-Mal

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: Scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Log transformations were not performed during the data processing and analysis steps.

organism: Streptococcus suis P1/7

source_name: S. suis grown to early exponential phase in CM medium supplemented with pullulan

label_protocol: RNA (1 μg) from S. suis samples was labeled using the Cyanine 5 (Cy5) labeling reaction (indirect labeling of synthesized cDNA with the CyScribe Post-Labeling and Purification kit; Amersham Biosciences, Buckinghamshire, United Kingdom).

growth_protocol: S. suis was grown in Todd-Hewitt broth (THB) (Difco) at 37°C under 5% CO2 for 18 hr. A complex medium (CM) comprising of 10 g/l proteose peptone, 5 g/l trypticase peptone, 5 g/l yeast extract, 2.5 g/l KCl, 1 mM Urea, and 1 mM Arginine, pH 7.0 was used to assess growth on different carbon sources by supplementation with different carbohydrates (glucose-Glu, pullulan-Pul, maltotriose-Mal) at final concentrations of 1% (w/v)

extract_protocol: For RNA extraction, S. suis S10 was grown to exponential and early stationary phase as indicated in Figure 5.2. Ten ml of culture was collected and centrifugated for each timepoint. The pellet was immediately frozen in liquid nitrogen and stored over night at 4°C in 1.5 ml RNAlater (Ambion). To isolate RNA, 1.5 ml RLT lysis buffer (Qiagen) was added to the pellet dissolved in RNAlater, incubated at 15 min at r.t. and centrifuged (13000 g for 30 min). The cells were dissolved in 600 µl RA1 reagent (Macherey-Nagel) plus {beta}-mercaptoethanol and lysed using a FastPrep-24 (MP. Biomedicals, Solon, OH) for 6.0 m/sec at 20 sec. Total RNA was purified using NucleoSpin RNA II (Macherey-Nagel).

treatment_protocol: RNA was extracted during early and late exponential growth phase.

tag: condition

value: CM medium supplemented with pullulan

tag: timepoint

value: early exponential phase

source_name: S. suis grown to early exponential phase in CM medium supplemented with maltose

value: CM medium supplemented with maltose


title: le-Pul_over_ee-Pul

source_name: S. suis grown to late exponential phase in CM medium supplemented with pullulan

value: late exponential phase


title: ee-Mal_over_le-Mal#2

source_name: S. suis grown to late exponential phase in CM medium supplemented with maltose


title: le-Glu_over_ee-Glu#2

source_name: S. suis grown to late exponential phase in CM medium supplemented with glucose

value: CM medium supplemented with glucose

source_name: S. suis grown to early exponential phase in CM medium supplemented with glucose


title: Embryo at E9.5, maxillary arch 4

description: Gene expression of the maxillary arch at E9.5

source_name: embryo_E9.5_maxillary arch

tag: tissue


title: ee-Glu_over_ee-THB

source_name: S. suis grown to early exponential phase in THB

value: THB


title: le-Mal_over_le-Glu#2


title: Embryo at E10.5, mandibular arch 2


title: ee-THB_over_le-THB

source_name: S. suis grown to late exponential phase in THB


title: Embryo at E9.5, neuroepithelium 2

description: Gene expression of the neuroepithelium at E9.5

value: neuroepithelium


title: ee-Mal_over_le-Mal#1


title: Embryo at E9.5, neuroepithelium 4


title: Embryo at E9.5, maxillary arch 2


title: ee-Glu_over_ee-Mal


title: ee-Mal_over_le-THB


title: Embryo at E9.5, neuroepithelium 3


title: Embryo at E9.5, neuroepithelium 5


title: Embryo at E9.5, maxillary arch 1


title: Embryo at E9.5, neuroepithelium 1


title: le-THB_over_le_Pul


title: Embryo at E9.5, maxillary arch 3


title: Embryo at E9.5, mandibular arch 5

description: Gene expression of the mandibular arch at E9.5

source_name: embryo_E9.5_mandibular arch


title: le-Mal_over_le-Glu#1


title: Embryo at E9.5, mandibular arch 3


title: Embryo at E9.5, mandibular arch 6


title: Embryo at E9.5, maxillary arch 5


title: ee-THB_over_ee-Glu


title: temporary ponds family 3 Sävar-Tärnögern JB003-4300D

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

hyb_protocol: Prepare a MAGEX slide by hydration in WB2 buffer (1xSSC, 0.1% SDS) at ambient temperature followed by incubation in PB1 buffer (5xSSC, 0.2% BSA, 0.2% SDS) for 45 minutes at 48°C. Rinse the slide with water followed by immersion in isopropanol at ambient temperature and centrifuge dry. Place a Lifterslip CS/3 (Erie Scientific Company) over each array region on the slide. Combine the Cy labeled sample (5.5ul of 15 pmol/ul Cy3 label) and reference (1 ul of 2 pmol/ul Cy5 label) cDNA and briefly denature at 95°C for 3 min followed by immediate incubation on ice. Prepare a 33 ul hybridization mix containing 5xSSC, 25% deionized formamide, 0.02% BSA, 1ug A45 oligonucleotide, 0.1% SDS, 5% Dextran, and 6.5 ul of the combined Cy3-labeled sample and Cy5-labeled reference cDNA. Briefly warm the hybridization solution at 37°C and then place onto the MAGEX array and incubate the prepared slide in a Hybex incubator at 42°C for 18 hrs. Hybridized slides were washed once with WB1 buffer (1xSSC, 0.1% SDS) at 48°C for 5 min; twice with WB2 buffer (0.1x SSC, 0.1% SDS) at 48°C for 10 min; and once with WB3 (0.01x SSC, 0.1% SDS) at 48°C for 10 min. Dry the slides by centrifugation at 200 x g and store in a desiccator prior to data collection.

scan_protocol: Scanning was done on a Packard Bioscience Scan Array Express Micro array scanner with the Cy3 PMT gain at 80% and Cy5 PMT gain at 70%. Laser strength was set at 90% for both channels. MAGEX 2008 microarray slides were scanned at 5 um resolution with an X=0 mm, Y=11.73 mm, W=22 mm, and H=52.38mm.

data_processing: Data was aquired from raw scanned MAGEX 2008 array images using ImaGene v9.0.

organism: Rana temporaria

source_name: liver, decreasing water

label_protocol: Amplified cDNA (500 ng) was random labeled with 2 ul of 1 mM Cy3-dCTP (GE Healthcare) using the DecaLabel DNA Labeling Kit (Fermentas Canada).

growth_protocol: Rana temporaria eggs were collected from six islands within the Gulf of Bothnia, northern Sweden. For each island, samples of 20–50 eggs were taken from a maximum of 10 clutches and transported to the laboratory. Each clutch was assumed to represent one female, as female R. temporaria lay only one egg clump per season. Eggs from each female were kept in separate containers filled with aged tap water. The eggs were stored in thermo-constant laboratory conditions and kept cool (4 °C) until all eggs were collected. When all eggs were collected, the temperature of the laboratory was set to 22 °C for the remainder of the experiment. A light : dark cycle of 18 h : 6 h was employed. The tadpoles were fed ad libitum every fourth day on a mixture (1 : 2) of finely ground fish food and rabbit chow. The food mass was 15 mg per tadpole at the beginning of the experiment, increased to 30 mg at day 9, 45 mg at day 13, 60 mg at day 17, and 75 mg from day 21 and to the end of the experiment. Water was replaced every fourth day, prior to feeding.

extract_protocol: Total RNA was extracted from RNAlater (Life Technologies) preserved liver tissue using TRIzol (Life Technologies) and a Retsch MM301 mixer mill with a 3mm tungsten carbide bead and 1 ug used to prepare amplified cDNA using the SMARTer cDNA synthesis kit (Clontech Laboratories). SMARTer cDNA samples were purified using the GeneJET PCR Purification Kit (Fermentas Canada).

treatment_protocol: Tadpoles originating from each island were raised to Gosner stage 23 (active swimming) (Gosner, 1960) and then one set was reared in constant water while a second set was reared under reduced water conditions. Four tadpoles from each female (two allocated to each treatment) were randomly chosen and placed into individual plastic containers (9.5 cm × 9.5 cm, height 10 cm). The containers were filled with 750 mL of tap water, previously aged and aerated together with dried deciduous leaves. The leaves were removed when the water was transferred to the experimental containers. The tadpoles were subjected to one of two treatments, either constant water level (C) or simulated pool drying (D). In the simulated drying treatment the initial water volume of 750 mL was lowered by 33% every fourth day, starting at day 5 and continued until day 25, after which the water volume in the D treatment was kept constant at 66 mL. The water temperature did not differ between the two treatments. The experiment was terminated at Gosner stage 37 (front legs visible), after which tadpoles were weighed. Liver samples were obtained from individuals in all groups at a fixed time point 14 days post commencement of water adjustment and when animals had reached Gosner stage 37.

tag: island of origin

value: Sävar-Tärnögern

tag: family

value: liver

tag: treatment

value: decreasing water

tag: developmental stage

value: Gosner Stage 37


title: le-THB_over_ee-THB


title: temporary ponds family 5 Sävar-Tärnögern JB003-4198D


title: temporary ponds family 4 Sävar-Tärnögern JB003-4160D


title: temporary ponds family 2 Sävar-Tärnögern JB003-4200U


title: temporary ponds family 7 Sävar-Tärnögern JB003-4301D


title: temporary ponds family 9 Sävar-Tärnögern JB003-4230U


title: temporary ponds family 4 Ålgrundet JB003-4166U

value: Ålgrundet


title: temporary ponds family 8 Ålgrundet JB003-4195U


title: temporary ponds family 2 Ålgrundet JB003-4193U


title: temporary ponds family 5 Ålgrundet JB003-4299U


title: Embryo at E9.5, epidermal ectoderm 5

description: Gene expression of the epidermal ectoderm at E9.5

source_name: embryo_E9.5_epidermal ectoderm

tag: strain

value: epidermal ectoderm


title: Embryo at E9.5, mandibular arch 1


title: le-Glu_over_ee-Glu#1


title: Embryo at E9.5, epidermal ectoderm 7


title: Embryo at E9.5, epidermal ectoderm 2


title: Embryo at E9.5, epidermal ectoderm 4


title: Embryo at E9.5, epidermal ectoderm 6


title: le-Glu_over_le-THB


title: Embryo at E9.5, mandibular arch 2


title: Embryo at E9.5, epidermal ectoderm 3


title: Embryo at E9.5, epidermal ectoderm 1


title: Embryo at E9.5, cranial mesenchyme 5

description: Gene expression of the cranial mesenchyme at E9.5

source_name: embryo_E9.5_cranial mesenchyme

value: cranial mesenchyme


title: Embryo at E9.5, cranial mesenchyme 4


title: temporary ponds family 6 Ålgrundet JB003-4163D


title: Embryo at E9.5, cranial mesenchyme 6


title: temporary ponds family 1 Ålgrundet JB003-4160U


title: permanent ponds family 4 Stora Fjäderägg JB003-4299D

value: Stora Fjäderägg


title: Embryo at E9.5, mandibular arch 4

value: mandibular arch


title: permanent ponds family 5 Stora Fjäderägg JB003-4203D


title: permanent ponds family 6 Stora Fjäderägg JB003-4166D


title: permanent ponds family 8 Öster Hällskär JB003-4229D

value: Öster Hällskär


title: permanent ponds family 5 Öster Hällskär JB003-4302D


title: permanent ponds family 10 Stora Fjäderägg JB003-4161D


title: permanent ponds family 9 Stora Fjäderägg JB003-4192U


title: permanent ponds family 10 Öster Hällskär JB003-4193D


title: Embryo at E9.5, cranial mesenchyme 2


title: permanent ponds family 6 Öster Hällskär JB003-4161U


title: permanent ponds family 2 Öster Hällskär JB003-4165D


title: permanent ponds family 9 Öster Hällskär JB003-4203U


title: Embryo at E8.5, non-floor plate neural epithelium 5

description: Gene expression of the non-floor plate neural epithelium at E8.5

source_name: embryo_E8.5_non-floor plate neural epithelium

value: non-floor plate neural epithelium


title: Embryo at E8.5, non-floor plate neural epithelium 2


title: Embryo at E9.5, cranial mesenchyme 1


title: Embryo at E8.5, non-floor plate neural epithelium 1


title: Embryo at E8.5, mesenchyme 2

description: Gene expression of the mesenchyme at E8.5

value: mesenchyme


title: Embryo at E8.5, mesenchyme 5


title: Embryo at E9.5, cranial mesenchyme 3


title: Embryo at E8.5, mesenchyme 3


title: Embryo at E8.5, non-floor plate neural epithelium 3


title: Embryo at E8.5, non-floor plate neural epithelium 4


title: Embryo at E8.5, floor plate neural epithelium 4

description: Gene expression of the floor plate neural epithelium at E8.5

source_name: embryo_E8.5_floor plate neural epithelium

value: floor plate neural epithelium


title: Embryo at E8.5, floor plate neural epithelium 3


title: temporary ponds family 4 Sävar-Tärnögern JB003-4302U

source_name: liver, constant water

value: constant water


title: temporary ponds family 6 Sävar-Tärnögern JB003-4301U


title: Embryo at E8.5, mesenchyme 4


title: Embryo at E8.5, floor plate neural epithelium 2


title: Embryo at E8.5, mesenchyme 1


title: temporary ponds family 10 Sävar-Tärnögern JB003-4231U


title: temporary ponds family 9 Sävar-Tärnögern JB003-4225U


title: temporary ponds family 2 Sävar-Tärnögern JB003-4321U


title: temporary ponds family 1 Sävar-Tärnögern JB003-4165U


title: temporary ponds family 8 Ålgrundet JB003-4227D


title: temporary ponds family 6 Ålgrundet JB003-4225D