title: HCV+cirrhosis with HCC 12

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 32

status: Public on Sep 11 2009

type: RNA

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

country: USA

institute: Ohio State University

description: Gene expression using RMA method

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

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

data_processing: The RMA method in the R affy package was used to obtain probe set expression summaries.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver tissue

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

growth_protocol: Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Liver tissue samples were collected in liquid nitrogen or RNA later solution (Ambion, Inc, Austin, TX), and stored at -80°C until use.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).

treatment_protocol: Five mm frozen section slides were made and stained with H&E for Pathologist evaluation to determine tumor content. After Pathologist evaluation, normal/necrotic tissue was macrodissected. Twenty 20 mm sections were performed in a 15 ml tube with 10 ml of Trizol.

tag: disease state

value: HCV + cirrhosis without HCC

tag: tissue

value: liver


title: HEK293-NC_PolII

type: genomic

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

hyb_protocol: Hybridization to custom made tiling arrays was performed by Nimblegen (Roche) using standard protocols (see http://www.nimblegen.com/).

scan_protocol: Scanning was performed by Nimblegen (Roche) using standard protocols (see http://www.nimblegen.com/).

data_processing: Signal intensity data was extracted from the scanned images of each array using NimbleScan TM, Nimblegen's data extraction software. For each probe, a scaled log2-ratio was calculated. This is the ratio of the input signals for the experimental and test samples that where co-hybridized to the array. Scaling was performed by subtracting the bi-weight mean for the log2-ratio values for all probes on the array from each log2-ratio value.

molecule: genomic DNA

source_name: Chromatin immunoprecipiated DNA using PolII antibody, from HEK293 cell-line expressing yellow fluorescent protein

label_protocol: The immunoprecipitated material was amplified using WGA2 and WGA1 GenomePlex Whole Genome Amplification Kits (Sigma) according to manufacturers protocol. Sample labeling was performed by Nimblegen (Roche) using standard protocols (see http://www.nimblegen.com/).

extract_protocol:
DAY I
Crosslinking:
1.	Add 1/10th volume of crosslinking mix directly to the plate containing growth medium giving a final concentraion of 1% of FA and rotate gently for 10 minutes at room temperature.
2.	Quench the crosslinking reaction by the addition of 1/10th volume of 1.25M glycine giving 125 mM final concentration. Remove the medium from the plate. Aspirate medium. Wash cells twice with 10 ml ice cold PBS.
3.	Scrape cells from one dish with about 2-3 X 1 ml of ice cold PBS and move the cells into 15 ml conical Falcon tube. I usually combine cells from 4 plates into one Falcon tube.
4.	Pellet cells for 10 minutes at 1000 rpm at 4ºC.
Preparation of chromatin: (you can skip if you use Histone antibodies).
1.	Resuspend cell pellet (about 4x107 HEK293 cells from 4x10 cm dishes) in 1 ml of (Nuclear/Chromatin preparation) NCP Buffer I + protease inhibitors. Spin 2000 g 5 min at 4°C.
2.	Discard supernatant. Wash nuclei (the pellet) with resuspending (use pipet again) with 1 ml of NCP II + protease inhibitors. Spin 2000 g 5 min at 4°C.
Lysis and sonication:
1.	Resuspend in 600 µl of Lysis Buffer + protease inhibitors.
2.	Incubate for 10 min at RT, put back on ice.
3.	Sonicate lysate to shear DNA to lengths between 200 and 1000 base pairs. Be sure to keep the samples ice cold. I use 8-10 x 10 sec at cycle 7 using power 70 % and at least 50 sec pauses
4.	Dilute the sonicated suspension 2 x with IP buffer. Centrifuge samples for 2x10 minutes at 11,000 g at 4°C.
5.	Optional: Take 50 µl of supernatant, dilute 3 x with IP buffer and incubate on 65ºC over night. Next day you can use this sample to control efficiency of sonication.
6.	Move the rest of the sup (about 1100  µl) into a 15 ml Falcon tube and dilute 5 x with IP buffer (the final SDS conts should be 0.1 %, the total vol will be about 6 ml)
Preclearing and IP:
7.	To reduce nonspecific background, pre-clear the sonicated and diluted cell lysate with adding 100-150 µl (20ul 50% slurry per IP) of protein G beads slurry pre-absorbed with 100µg/ml BSA and 500µg/ml sheared salmon sperm DNA (see suppl. protocol) Incubate at least two hours at 4°C.
8.	Pellet agarose by brief centrifugation (1min @ 1000rpm) and collect the supernatant fraction.
9.	Add the immunoprecipitating antibody (the amount will vary per antibody, I use 4 µg) to the 1 - 1.5 ml supernatant fraction (you can do 4-6 IP-s from 6 ml of lysate) and incubate overnight at 4ºC with rotation. For a control, use the same amount of IgG or non-specific antibody for immunoprecipitation.
10.	For a negative control, you can include a sample where you have instead of cell lysate 1 - 1.5 ml of IP buffer:Lysis 9:1
DAY II
Collection of the antibody/protein complexes:
1.	Carry the lysates over to the tubes containing 40 µl of 50%slurry and pre-absorbed Protein G Agarose Slurry and incubate additional two hours at 4ºC with rotation.  Be sure you have the same amount of beads in each tube.
2.	Pellet agarose by gentle centrifugation (5000 rpm for 1min). Carefully remove the supernatant that contains unbound, non-specific DNA.
3.	Store 250 µl of supernatants for your input fractions
Washings:
Wash the protein G sepharose/ antibody/ protein complex for 3-5 minutes on a rotating platform with each of the buffers listed in the order as given below:
1.	Low Salt Immune Complex Wash Buffer, WB I (3 X 1 ml)
2.	High Salt Immune Complex Wash Buffer, WB II (1 to 2 X 1 ml)
3.	LiCl Immune Complex Wash Buffer, WB III (1 X 1 ml)
4.	TE (2 X 1 ml)
Note: Washing conditions may differ slightly depending upon antibody affinity for antigen. More washes will give a lower background
Elution:
1.	Elute the histone complex from the antibody by adding 100 µl of elution buffer to the pelleted protein G sepharose/antibody/protein complex. I place the tubes on vortexer and mix at medium setting for 15 min.
2.	Spin down agarose, and carefully transfer the supernatant fraction (eluate) to another tube and repeat elution 2 X 75 µl of elution buffer and combine eluates (total volume=approximately 250 µl).
Reversing the cross-links:
4.	Add 10 µl 5M NaCl to the combined eluates (250 µl) and reverse protein/histone-DNA cross-links by heating at 65ºC for 4 hours to overnight. Reverse the cross-links of your input fractions as well.
DAY III
DNA purification:
A) Phenol/Chlorophorm protocol
1. Add 5  µl of 5M NaCl to each sample and to inputs to bring the final NaCl conts 0.25-0.3M and precipitate the DNA with 2.5 vol EtOH (375 µl)
2. Dissolve the pellets in 100ul TE and add
- 25 µl 5X Prot K buffer
- 1.5 µl Prot K (stock 10mg/ml)
3. incubate for 2 hours at 45ºC.
4. Add 75 µl of TE and extract with 200 µl of phenol or phenol/chlorophorm and 150 µl of chlorophorm
5. Precipitate with adding 1/10 vol of NaOAc, 2.5 vol of EtOH. To IP fractions add glycogen.
6. Resuspend in 50 µl TE

B) Recover DNA using Qiagen PCR purification Kit. Final elution is in 50ul EB.
DAY IV
Q-PCR
Buffers and Reagents:
Crosslinking mix: 	11% Formaldehyde (FA)
			100mM NaCl
			0.5mM EGTA
			50mM HEPES, pH 8.0
			Prepeare freshly
NCP I: 10 mM EDTA
	0.5 mM EGTA
	10 mM Hepes pH 6.5
0.25% TritonX-100
	Protease Inhibitors – add freshly
NCP II: 1 mM EDTA
	 0.5 mM EGTA
	 10 mM Hepes pH 6.5
	 200 mM NaCl
	Protease Inhibitors – add freshly
Lysis Buffer:     10mM EDTA
 20 mM Tris-HCl, pH 8.1.
0.5 % NP-40
1% SDS
Protease Inhibitors – add freshly
IP Buffer:         2 mM EDTA
150 mM NaCl
20 mM Tris-HCl, pH 8.1,
1 % Triton X-100
Protease Inhibitors – add freshly
Low Salt Immune Complex Wash Buffer (WB I):  	2 mM EDTA
20 mM Tris-HCl, pH 8.1
150 mM NaCl
0.1% SDS
1%Triton X-100

High Salt Immune Complex Wash Buffer (WB II):     2 mM EDTA
20 mM Tris-HCl, pH 8.1
500 mM NaCl
0.1% SDS
1%Triton X-100
LiCl Immune Complex Wash Buffer: 1 mM EDTA,
10 mM Tris-HCl, pH 8.1
0.25 M LiCl,1% NP40,
1% deoxycholate
			0.5 % NP-40
TE Buffer: 	10mM Tris-HCl
		1mM EDTA,pH 8.0.
Elution buffer: 1%SDS,
		0.1M NaHCO3
		Prepeare freshly 10 ml (84mg NaHCO3/1ml 10%SDS/9 ml dH20)
5x Proteinase K buffer:	50mM TrisHCl pH 7.5
				25mM EDTA
				1.25% SDS
Supplementary Protocol:
To make pre-absorbed protein G sepharose beads:
1.	Take 60 µl 50% slurry per IP (20 for preclearing, 40 for IP) of protein G sepharose beads slurry per 4x107 cells from 4x10 cm dishes.
2.	Wash the protein G beads in a final volume of 5 ml of 9:1 IP Buffer : Lysis Buffer
3.	Pre-absorb the beads with 100µg/ml BSA and 500µg/ml salmon sperm DNA and rotate overnight at 4°C or 2 hours at RT.
      Note: salmon sperm DNA should be shared by heating 30 min at 99.5 °C).
4.	Before using the beads in pre-clearing or IP, remove the pre-absorption mix and wash the pre-absorbed beads twice in 9:1 IP Buffer : Lysis Buffer

tag: antibody

value: PolII

tag: cell line

value: HEK293 stably expressing yellow fluorescent protein

source_name: Input genomic DNA from HEK293 cell-line expressing yellow fluorescent protein

label_protocol: Input material was amplified using WGA2 and WGA1 GenomePlex Whole Genome Amplification Kits (Sigma) according to manufacturers protocol. Sample labeling was performed by Nimblegen (Roche) using standard protocols (see http://www.nimblegen.com/).

value: none (input genomic DNA)


title: HEK293-AIRE1_H3

source_name: Chromatin immunoprecipiated DNA using H3 antibody, from HEK293 cell-line expressing AIRE protein

value: HEK293 stably expressing AIRE protein

source_name: Input genomic DNA from HEK293 cell-line expressing AIRE protein


title: HCV+cirrhosis without HCC 30

description: Gene expression using RMA method


title: HEK293-AIRE1_H3K4me3

source_name: Chromatin immunoprecipiated DNA using H3K4me3 antibody, from HEK293 cell-line expressing AIRE protein


title: HEK293-AIRE1_H3K27me3

source_name: Chromatin immunoprecipiated DNA using H3K27me3 antibody, from HEK293 cell-line expressing AIRE protein


title: HCV+cirrhosis without HCC 31

description: Gene expression using RMA method


title: Heart_female_KO_pool12

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Mouse Genome arrays 430 2.0 were hybridized with 10 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA for liver and heart separately (Irizarry et al., 2003).

organism: Mus musculus

source_name: Heart

label_protocol: 1 micro-gramme of total RNA were amplified and labeled using Affymetrix eukaryotic taget preparation (one-cycle amplification, #701025 Rev.2)

extract_protocol: RNA was isolated and purified with RNA clean up purification kits (Qiagen), and DNase treated. All RNA quantities were assessed by NanoDrop®ND-1000 spectrophotometer and the quality of RNA was controlled on Aligent 2100 bioanalyzer chips.

treatment_protocol: Twenty-four wild-type  (12 males and 12 females) and 24 knock-out PPARalpha SV129 mice (12 males and 12 females) approximately 10 to 12 weeks of age were killed at ZT14 and their livers and hearts quickly removed, frozen on liquid nitrogen, and stored at –80°C.

tag: Pool of total RNA from 4 PPARalpha knock-out female hearts


title: HCV+cirrhosis without HCC 27

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 26

description: Gene expression using RMA method


title: HEK293-AIRE1_AcH3

source_name: Chromatin immunoprecipiated DNA using AcH3 antibody, from HEK293 cell-line expressing AIRE protein


title: HEK293-NC_H3K27me3

source_name: Chromatin immunoprecipiated DNA using H3K27me3 antibody, from HEK293 cell-line expressing yellow fluorescent protein


title: WT

city: Kiyotake, Miyazaki

first: Atsushi

last: Saito

address: Kihara, 5200

department: Anatomy

country: Japan

institute: Miyazaki university

hyb_protocol: Affymetrix standard procedure

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with Expression Console version 1.1 using Affymetrix RMA algorithm and quantile as normalization method.

source_name: primary cultured chondrocytes wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using Two cycle target labeling kit (Affymetrix)

growth_protocol: Primary cultured chondrocytes were prepared from E18.5 rib cartilage of WT and Bbf2h7-/- mice. Chondrocytes were isolated using 0.2% collagenase D (Roche) after adherent connective tissue was removed by 0.2% trypsin (Sigma) and collagenase pretreatment. Isolated chondrocytes were maintained in α-MEM (Gibco) supplemented with 10% FCS and 50 µg/mL ascorbic acid. Adenovirus vectors expressing the mouse p60 BBF2H7 (1-377 aa, BBF-N) was constructed with the AdenoX Expression system (Clontech), according to the manufacturer’s protocol. The cells were infected with adenoviruses 30 h before analysis.

extract_protocol: Experimental sample RNAs were isolated using RNeasy (QIAGEN).

treatment_protocol: Bbf2h7-/- mice were generated using a targeting vector containing a neomycin resistant gene. The Bbf2h7 targeting vector was electroporated into embryonic stem (ES) cells derived from 129/Sv (D3). Homologous recombination was identified by genomic PCR and Southern blotting. Germ-line transmission of the mutant allele was achieved using C57BL/6 mice.

tag: cell type

value: primary cultured chondrocytes


title: Heart_female_KO_pool11


title: HEK293-AIRE1_AIRE

source_name: Chromatin immunoprecipiated DNA using AIRE antibody, from HEK293 cell-line expressing AIRE protein

value: AIRE


title: HCV+cirrhosis without HCC 29

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 28

description: Gene expression using RMA method


title: HEK293-NC_H3K4me3

source_name: Chromatin immunoprecipiated DNA using H3K4me3 antibody, from HEK293 cell-line expressing yellow fluorescent protein


title: HEK293-AIRED312A

description: Human Embryonic Kidney 293 cell-lines stably expressing Auto Immune REgulator protein with the D312A mutation under the human cytomegalovirus immediate-early (CMV) promoter.

hyb_protocol: 1500ng of labelled cRNA was hybridized overnight according to Illumina's protocol.

scan_protocol: Beadscan.

data_processing: The data was processed using BeadStudio 3.1.3.0 by background substraction and RankInvariant normalization.

label: biotin - Streptavadin Cy3

source_name: HEK293 cells expressing AIRED312A protein

label_protocol: Labelled cRNA was prepared using Illumina TotalPrep RNA Amplification Kit (Ambion) starting with 250ng total RNA and overnight incubation according to manufactures protocol. The quality of the labeled cRNA was controlled using 2100 Bioanalyzer (Agilent).

extract_protocol: The was extracted with Trizol reagent (Invitrogen), treated 2x30 min with Turbo DNAse (Ambion) and purified with QIAquick PCR Purification Kit (Qiagen). The quality of the RNA was controlled using 2100 Bioanalyzer (Agilent).

value: Human Embryonic Kidney 293 (HEK293)


title: HEK293-NC_H3

source_name: Chromatin immunoprecipiated DNA using H3 antibody, from HEK293 cell-line expressing yellow fluorescent protein


title: Heart_female_KO_pool10


title: HCV+cirrhosis without HCC 25

description: Gene expression using RMA method


title: Heart_female_WT_pool9

tag: Pool of total RNA from 4 wild-type female hearts


title: HCV+cirrhosis without HCC 20

description: Gene expression using RMA method


title: HEK293-NC_AIRE

source_name: Chromatin immunoprecipiated DNA using AIRE antibody, from HEK293 cell-line expressing yellow fluorescent protein


title: HCV+cirrhosis without HCC 17

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 23

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 24

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 21

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 22

description: Gene expression using RMA method


title: HEK293-NC

description: A reference HEK293 cell-line stably expressing yellow fluorescent protein under the human cytomegalovirus immediate-early promoter

source_name: HEK293 cells expressing yellow fluorescent protein


title: HCV+cirrhosis without HCC 19

description: Gene expression using RMA method

source_name: liver tissue


title: HCV+cirrhosis without HCC 18

description: Gene expression using RMA method


title: Heart_male_KO_pool6

tag: Pool of total RNA from 4 PPARalpha knock-out male hearts


title: HEK293-AIRE1

description: One of the analyzed Human Embryonic Kidney 293 cell-lines stably expressing Auto Immune REgulator protein under the human cytomegalovirus immediate-early (CMV) promoter.

source_name: HEK293 cells expressing AIRE protein


title: HCV+cirrhosis without HCC 16

description: Gene expression using RMA method


title: HCV+cirrhosis with HCC 10

description: Gene expression using RMA method

value: HCV + cirrhosis with HCC


title: HCV+cirrhosis with HCC 8

description: Gene expression using RMA method


title: SACHI_transfected_with_NIK_analysed_at_3_5_08

city: Bethesda

first: Oleg

middle: Konstantin

last: Glebov

state: MD

address: 8901 Wisconsin Ave., Bldg. 8, Rm. 5101

department: Genetics

institute: NCI

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 17 hr at 45C on Affymetrix HGU133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe set summarization, convolution background subtraction and quantile normalization were done using Robust Microarray Average method.

source_name: Multiple Myeloma Cell Line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual).

growth_protocol: Cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum (Hyclone) and penicillin/streptomycin (Invitrogen).

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

treatment_protocol: Transductions were performed by spin infection in the presence of 8 ng/ml polybrene (Sigma) as described previously (Quong et al., 1999). After 24 h the virus-containing medium was replaced with selection medium containing 2 ng/ml puromycin. After cell growth was stable, the cells were used in the experiments described.

value: SACHI

tag: transfection

value: NIK

tag: date


title: SACHI_transfected_with_IKKB_analysed_at_3_5_08

value: IKKB


title: HEK293-NC_AcH3

source_name: Chromatin immunoprecipiated DNA using AcH3 antibody, from HEK293 cell-line expressing yellow fluorescent protein

source_name: Input genomic DNA from HEK293 cell-line expressing yellow fluorescent protein


title: SACHI_transfected_with_None_analysed_at_3_5_08


title: Heart_female_WT_pool7


title: Heart_male_WT_pool3

tag: Pool of total RNA from 4 wild-type male hearts


title: Heart_male_KO_pool4


title: HCV+cirrhosis with HCC 7

description: Gene expression using RMA method


title: HCV+cirrhosis with HCC 9

description: Gene expression using RMA method


title: Heart_male_KO_pool5


title: Heart_female_WT_pool8


title: SACHI_transfected_with_IKKB_analysed_at_2_28_08


title: HCV+cirrhosis without HCC 15

description: Gene expression using RMA method


title: HCV+cirrhosis with HCC 6

description: Gene expression using RMA method


title: Heart_male_WT_pool2


title: Heart_male_WT_pool1


title: HCV+cirrhosis without HCC 14

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 12

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 11

description: Gene expression using RMA method


title: SACHI_transfected_with_None_analysed_at_2_28_08


title: HCV+cirrhosis without HCC 13

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 9

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 10

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 5

description: Gene expression using RMA method


title: HCV+cirrhosis with HCC 5

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 4

description: Gene expression using RMA method


title: Liver_female_WT_pool8

source_name: Liver

tag: Pool of total RNA from 4 wild-type female livers


title: Liver_female_KO_pool12

tag: Pool of total RNA from 4 PPARalpha knock-out female livers


title: H929_transfected_with_NIK_analysed_at_1_24_08


title: HCV+cirrhosis without HCC 6

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 7

description: Gene expression using RMA method


title: SACHI_transfected_with_NIK_analysed_at_2_28_08


title: HCV+cirrhosis without HCC 8

description: Gene expression using RMA method


title: SACHI_transfected_with_None_analysed_at_1_30_08


title: SACHI_transfected_with_NIK_analysed_at_1_30_08


title: H929_transfected_with_IKKB_analysed_at_1_24_08


title: Liver_female_WT_pool9


title: Liver_female_WT_pool7


title: Liver_female_KO_pool11


title: Liver_female_KO_pool10


title: HEK293-AIRE2

description: Second of the analyzed Human Embryonic Kidney 293 cell-lines stably expressing Auto Immune REgulator protein under the human cytomegalovirus immediate-early (CMV) promoter.


title: H929_transfected_with_None_analysed_at_1_24_08


title: HCV+cirrhosis without HCC 3

description: Gene expression using RMA method


title: H929_transfected_with_IKKB_analysed_at_1_17_08


title: SACHI_transfected_with_IKKB_analysed_at_1_30_08


title: H929_transfected_with_IKKB_analysed_at_1_10_08


title: H929_transfected_with_None_analysed_at_1_17_08


title: Liver_male_KO_pool6

tag: Pool of total RNA from 4 PPARalpha knock-out male livers


title: HCV+cirrhosis with HCC 4

description: Gene expression using RMA method


title: HCV+cirrhosis without HCC 2

description: Gene expression using RMA method


title: Liver_male_KO_pool5


title: HCV+cirrhosis without HCC 1

description: Gene expression using RMA method


title: H929_transfected_with_NIK_analysed_at_1_17_08


title: Liver_male_WT_pool2

tag: Pool of total RNA from 4 wild-type male livers


title: H929_transfected_with_NIK_analysed_at_1_10_08


title: Liver_male_WT_pool3


title: Liver_male_KO_pool4


title: HCV+cirrhosis with HCC 2

description: Gene expression using RMA method


title: Liver_male_WT_pool1


title: Patient 27, biopsy; Control

status: Public on Sep 16 2009

city: Copenhagen

first: Morten

last: Hansen

address: Blegdamsvej 3B

department: Department of Cellular and Melocular Medicine

country: Denmark

institute: Faculty of Health Sciences

description: Gene expression data from human colonic mucosa

hyb_protocol: The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin (BSA) and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied. The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn (SAPE).

scan_protocol: Scanned with a GeneArray scanner at the excitation wavelength of 488 nm.

data_processing: Scaled and normalized using robust multi-array analysis (RMA) in the statistical software R.

source_name: Biopsy from human colonic mucosa

label_protocol: In accordance with the Affymetrix protocol and the two-cycle eukaryotic target labelling assay, double-stranded cDNA was synthesized from total RNA and an IVT reaction was subsequently performed to produce biotin-labelled cRNA from the cDNA.

extract_protocol: RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol

tag: Control


title: HCV+cirrhosis with HCC 3

description: Gene expression using RMA method


title: H929_transfected_with_None_analysed_at_1_10_08


title: Horse #4 Right Stifle

status: Public on Sep 10 2009

type: other

city: Lexington

first: Michael

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #4 right stifle articular cartilage 532
Source_name_ch2 = Horse #4 right stifle repair tissue 635
Source_name_ch1 = Horse #4 right stifle repair tissue 532
Source_name_ch2 = Horse #4 right stifle articular cartilage 635

hyb_protocol: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized 48 hours at 42C.

scan_protocol: DyeSaver2 was applied each slide with one dip.  Slides were scanned with a Molecular Devices GenePix Personal 4100A Scanner using GenePix Pro 5.0

data_processing: Data analyzed by planned linear contrast, followed by SAS-based one sample t-test.

label: AlexaFluor555, AlexaFluor647

molecule: other

organism: Equus caballus

source_name: Normal Articular Cartilage

label_protocol: Invitrogen Indirect PLUS Labeling

extract_protocol: Amplified RNA from total RNA

tag: Tissue

value: Grossly normal articular cartilage from right stifle of an adult Quarterhorse ("R9")

label: AlexaFluor647, AlexaFluor555

source_name: Articular Repair Tissue

value: Articular repair tissue from right stifle of an adult Quarterhorse ("R9")


title: Horse #4 Left Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #4 left stifle articular cartilage 532
Source_name_ch2 = Horse #4 left stifle repair tissue 635
Source_name_ch1 = Horse #4 left stifle repair tissue 532
Source_name_ch2 = Horse #4 left stifle articular cartilage 635

value: Grossly normal articular cartilage from left stifle of an adult Quarterhorse ("R9")

value: Articular repair tissue from left stifle of an adult Quarterhorse ("R9")


title: Horse #2 Right Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #2 right stifle articular cartilage 532
Source_name_ch2 = Horse #2 right stifle repair tissue 635
Source_name_ch1 = Horse #2 right stifle repair tissue 532
Source_name_ch2 = Horse #2 right stifle articular cartilage 635

value: Grossly normal articular cartilage from right stifle of an adult Quarterhorse ("R7")

value: Articular repair tissue from right stifle of an adult Quarterhorse ("R7")


title: Horse #3 Right Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #3 right stifle articular cartilage 532
Source_name_ch2 = Horse #3 right stifle repair tissue 635
Source_name_ch1 = Horse #3 right stifle repair tissue 532
Source_name_ch2 = Horse #3 right stifle articular cartilage 635

value: Grossly normal articular cartilage from right stifle of an adult Quarterhorse ("R8")

value: Articular repair tissue from right stifle of an adult Quarterhorse ("R8")


title: Horse #3 Left Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #3 left stifle articular cartilage 532
Source_name_ch2 = Horse #3 left stifle repair tissue 635
Source_name_ch1 = Horse #3 left stifle repair tissue 532
Source_name_ch2 = Horse #3 left stifle articular cartilage 635

value: Grossly normal articular cartilage from left stifle of an adult Quarterhorse ("R8")

value: Articular repair tissue from left stifle of an adult Quarterhorse ("R8")


title: Horse #1 Right Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #1 right stifle articular cartilage 532
Source_name_ch2 = Horse #1 right stifle repair tissue 635
Source_name_ch1 = Horse #1 right stifle repair tissue 532
Source_name_ch2 = Horse #1 right stifle articular cartilage 635

value: Grossly normal articular cartilage from right stifle of an adult Quarterhorse ("R5")

value: Articular repair tissue from right stifle of an adult Quarterhorse ("R5")


title: Horse #2 Left Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #2 left stifle articular cartilage 532
Source_name_ch2 = Horse #2 left stifle repair tissue 635
Source_name_ch1 = Horse #2 left stifle repair tissue 532
Source_name_ch2 = Horse #2 left stifle articular cartilage 635

value: Grossly normal articular cartilage from left stifle of an adult Quarterhorse ("R7")

value: Articular repair tissue from left stifle of an adult Quarterhorse ("R7")


title: CLL-2

city: Los Angeles

first: Sanjai

last: Sharma

state: CA

department: Hematology Oncology

institute: UCLA West LA VA Medical Center

description: untreated cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data anayzed with MAS 5.0 Afymetrix software.

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen column for RNA isolation

value: B cell

tag: disease state

value: chronic lymphocytic leukemia


title: CLL-5

description: untreated cells


title: CLL-4

description: untreated cells


title: KO

city: Miyazaki

first: Kazunori

last: Imaizumi

address: 5200 Kihara, Kiyotake

institute: Division of Molecular and Cellular Biology, Department of Anatomy, Faculty of Medicine, University of Miyazaki

description: Gene expression data from OASIS KO calvaria

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

source_name: OASIS KO calvaria

label_protocol: Labeling was performed byMIYAZAKI Prefectural Industrial Support Foundation.

growth_protocol: These experiments were performed with the consent of the Animal Care and Use Committees of Miyazaki University and Osaka University.

extract_protocol: Experimental sample RNAs from calvaria at  postnatal 4 days were isolated using RNeasy (QIAGEN).

treatment_protocol: OASIS-/- mice were generated using a targeting vector containing a neomycin resistant gene. The OASIS targeting vector was electroporated into embryonic stem (ES) cells derived from 129/Sv (D3).

tag: tissue

value: KO calvaria


title: Normal B cells-2

description: untreated cells

source_name: Normal B cells-2

value: normal


title: HCV+cirrhosis with HCC 1

description: Gene expression using RMA method

value: HCV + cirrhosis with HCC

value: liver


title: Horse #1 Left Stifle

description:
This "sample" represents an average of two dye swap slides.  The actual channel assignments were as follows:
Source_name_ch1 = Horse #1 left stifle articular cartilage 532
Source_name_ch2 = Horse #1 left stifle repair tissue 635
Source_name_ch1 = Horse #1 left stifle repair tissue 532
Source_name_ch2 = Horse #1 left stifle articular cartilage 635

value: Grossly normal articular cartilage from left stifle of an adult Quarterhorse ("R5")

value: Articular repair tissue from left stifle of an adult Quarterhorse ("R5")


title: BM-MSC culture osteogenic induction for 7 days rep 1

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

country: Germany

institute: Charité

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 7 days.
BM-MSC of a male 67-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 7 day for osteogenic differentiation.

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

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

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database SiPaGene (www.bioretis.de).

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 7 days from normal donor 1

label_protocol: 2µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix).

growth_protocol: Human BM cells obtained from iliac crest aspirates were amplified by cultivation in alpha-MEM with 10 % fetal calf serum (FCS), 1 ng/mL fibroblast growth factor 2 (FGF2), 20 µmol/L L-glutamine and 100 units/mL penicillin G.

extract_protocol: RNA was collected using the RNeasy mini kit (Qiagen).

treatment_protocol: After expansion for 1 passage, cells were stimulated with 10E-7 M dexamethasone for osteogenic induction for 1, 3 and 7 days.

tag: gender

value: male

tag: age

value: 67 years

tag: treatment

value: dexamethasone

tag: treatment time

value: 7 days


title: CLL-3

description: untreated cells

tag: cell type


title: ORMES-9 rep. 1

city: Rehovot

first: Amos

last: Tanay

address: The Weizmann Insititute

department: Computer Science and Applied Math

country: Israel

institute: The Weizmann Institute

description: ORMES-9 rep. 1

hyb_protocol: Standard NimbleGen protocols were used.

scan_protocol: Standard NimbleGen protocols were used.

data_processing: MeDIP data was normalized as described (Gal-Yam, Egger et al. 2008), with the exception of subtraction of M.SssI data, which was omitted since the main application of the data was the analysis of DMRs. Briefly, raw channel intensities were quantile normalized and then combined into a detailed model that expresses the correlation between probe's CpG content, probe's G+C content and array binding ratio. binding ratios were corrected using data on MeDIP of DNA that was treated with M.SssI to full methylation.

organism: Macaca mulatta

label_protocol: Standard NimbleGen protocols were used.

growth_protocol: Skin fibroblasts were established as described previously (Mitalipov, Yeoman et al. 2002).  Briefly, tissue biopsy samples were washed in 0.5 mM EDTA in Ca2+ and Mg2+ free Dulbecco PBS (Invitrogen, Carlsbad, CA) and minced into pieces before incubation in Dulbecco Modified Eagle’s Medium (DMEM, Invitrogen) containing 1 mg/ml collagenase IV (Invitrogen) at 37°C in 5% CO2 for 20 min.  Tissue pieces were then vortexed, washed and seeded into 75 cm3 cell culture flasks (Corning, Acton, MA) containing DMEM supplemented with 100 IU/ml penicillin, 100 µg/ml streptomycin (Invitrogen), 10% FBS and cultured at 37°C in 5% CO2.

extract_protocol: MeDIP was performed as previously described (Gal-Yam, Egger et al. 2008) with the following alterations: 10 µg of sonicated genomic DNA (300–1000 bp in length) was denatured, incubated O/N at 4°C with 10 µg of anti-methyl cytosine antibody (Diagenode, Belgium) in 1× IP buffer (100 mM Na-Phosphate pH 7.0,1.4 M NaCl ,0.5 % Triton X-100, Sigma, St. Louis, MO) , and subsequently with 40 µl of Dynabeads (M-280 Sheep anti-Mouse IgG – 6.7 × 108 beads/ml) (Invitrogen, Carlsbad, CA) for 2 h at 4°C. The beads were washed with IP buffer and incubated with digestion buffer (50 mM Tris pH 8.0,10 mM EDTA, 0.5 % SDS, Sigma, St. Louis, MO) and 5.6μl proteinase K (Roche ,Germany, 20 mg/ml stock) for 3 h at 500C and the DNA extracted by phenol chloroform and EtOH (Sigma, St. Louis, MO) precipitation. For array experiments the output from 3 MeDIP reactions was combined (total of 30 µg starting DNA) to constitute one replicate to eliminate the need for whole genome amplification. The sonicated DNA served as input. MeDIP arrays were done in biological triplicates.

treatment_protocol: The ORMES-22 and -9 (Oregon Rhesus Macaque Embryonic Stem) and CRES-2 (Cloned Rhesus Embryonic Stem) lines used in this study were produced in our laboratory (Mitalipov, Kuo et al. 2006; Byrne, Pedersen et al. 2007). The stem cells were grown at 37°C, 3% CO2, 5%O2 and 92% N2 on feeder cells consisting of mitotically inactivated mouse embryonic fibroblasts (mEF) in DMEM/F12 medium (Invitrogen, Grand Island, NY)   supplemented with 15% fetal bovine serum (FBS) (Hyclone, Logan UT), 0.1 mM b-mercaptoethanol (Sigma, St. Louis, MO), 1% nonessential amino acids (Invitrogen), 2 mM L-glutamine (Invitrogen), 4 ng/ml FGF2 (Sigma), with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

value: ES cells

tag: cell line


title: WT

description: Gene expression data from WT calvaria

source_name: WT calvaria

value: WT calvaria


title: CLL-1

description: untreated cells


title: CRES-2 rep. 3

description: CRES-2 rep. 3

value: ES cell-like

tag: genome/variation

value: somatic cell nuclear transformed


title: 30 h post-estradiol,biological rep3

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

hyb_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: The data were analyzed with Bioconductor package in R, justRMA() functionwas used for the normalization.

source_name: G1E ER4 cell, after estradiol induction, 30hr

growth_protocol: G1E-ER4 cells were cultured as described previously. Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997;17: 1642-1651.

extract_protocol: RNA from G1E-ER4 cells was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: G1E-ER4 cells growing in log phase were induced to differentiate for 0, 3, 7, 14, 21, or 30 hours with 20nM estradiol.

value: G1E ER4


title: 30 h post-estradiol,biological rep2

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual.


title: CRES-2 rep. 2

description: CRES-2 rep. 2


title: ORMES-9 rep. 3

description: ORMES-9 rep. 3


title: 21 h post-estradiol,biological rep3

scan_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual

source_name: G1E ER4 cell, after estradiol induction, 21hr


title: ORMES-22 rep. 3

description: ORMES-22 rep. 3


title: Normal B cells-1

description: untreated cells

source_name: Normal B cells-1

value: B cell


title: 30 h post-estradiol,biological rep1


title: CRES-2 rep. 1

description: CRES-2 rep. 1


title: ORMES-22 rep. 1

description: ORMES-22 rep. 1


title: Human fetal lung 53 dpc

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: human fetal lung 53 dpc

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 38 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.

label: Biotin

source_name: whole lung human fetus

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

tag: LabID

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H20029

tag: Sex

value: Unknown

tag: Race

tag: Disease Status

value: Control

tag: Post-Mortem Interval

value: <2 hrs

tag: microarray hybridization data 12/12/2006

tag: cross validation

value: test sample


title: ORMES-22 rep. 2

description: ORMES-22 rep. 2


title: Human fetal lung 82 dpc

description: human fetal lung 82 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H20022

value: training sample


title: Fibroblasts rep. 2

description: Fibroblasts rep. 2

value: Fibroblasts


title: 21 h post-estradiol,biological rep1


title: 21 h post-estradiol,biological rep2


title: 14 h post-estradiol,biological rep2

source_name: G1E ER4 cell, after estradiol induction, 14hr


title: Fibroblasts rep. 3

description: Fibroblasts rep. 3


title: Fibroblasts rep. 1

description: Fibroblasts rep. 1


title: Human fetal lung 91 dpc

description: human fetal lung 91 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19967

value: Male


title: Human fetal lung 117 dpc

description: human fetal lung 117 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19120

value: Female


title: 7 h post-estradiol,biological rep1

source_name: G1E ER4 cell, after estradiol induction, 7hr


title: 14 h post-estradiol,biological rep1


title: ORMES-9 rep. 2

description: ORMES-9 rep. 2

value: ES cells


title: Human fetal lung 110 dpc biological replicate 2

description: human fetal lung 110 dpc biological replicate 2

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17486


title: Human fetal lung 94 dpc

description: human fetal lung 94 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19998


title: 3 h post-estradiol,biological rep2

source_name: G1E ER4 cell, after estradiol induction, 3hr

value: G1E ER4


title: 3 h post-estradiol,biological rep3


title: 7 h post-estradiol,biological rep2


title: Human fetal lung 108 dpc biological replicate 3

description: human fetal lung 108 dpc biological replicate 3

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18475


title: 7 h post-estradiol,biological rep3


title: Human fetal lung 101 dpc

description: human fetal lung 101 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18402


title: Human fetal lung 122 dpc

description: human fetal lung 122 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19896

value: Unknown

tag: microarray hybridization data 08/08/2006


title: 3 h post-estradiol,biological rep1


title: T00342932_60M1

city: Rostock

first: Eik

last: Hoffmann

address: Albert-Einstein-Str. 3

department: Institute of Biological Sciences

institute: University of Rostock

description: no additional information

hyb_protocol: Standard CodeLink Expression assay protocol was used.

data_processing: The GenePix scanned files were analyzed using the CodeLink EXP v 4.0 (http://www4.gelifesciences.com/aptrix/upp01077.nsf/Content/codelink_soft). The signal and background fluorescence intensities were calculated for each spot, to average the intensities of every pixel inside the target region. The intensity of each spot was calculated as the difference between mean signal intensity and mean local background intensity. Per spot and per chip intensity dependent (*LOWESS*) normalization was followed by a per gene normalization to the control samples within each replicate. Each time point/condition tested was repeated at least three times as biological replicates. The output Code Link files were analyzed by using GeneSpring GX 7.3 Expression analysis software (Agilent Technologies) which filters those genes which are absent in all the samples and we considered those genes which exhibit a signal intensity above the background level in at least one of the samples using the 'Filtering on Flags' tool. All the fold changes in signal intensity of the test samples were calculated by subtracting the mean of the signal intensity of the controls (uninfected macrophages) using the 'Filtering on Fold changes' tool. Genes showing 1.7 fold higher or lower expression against the controls were considered significant. All the analysis of the fold changes were performed using a p-value cut-off <0.01.

source_name: Mannan-coated beads internalized for 60 minutes

extract_protocol: Total RNA was isolated from J774 macrophage monolayers using RNeasy mini kit (QIAGEN).

treatment_protocol: J774.A1 cells (mouse macrophage-like cell line) were seeded onto 6-well plates one day before the experiment. Duplicates were incubated with serum-free DME medium either left untreated or containing 0.01% latex beads of 1 µm diameter coupled to the following ligands: avidin (Av), Fc fragment of mouse IgG (Fc), lipopolysaccharides from Klebsiella pneumoniae (LPS) and mannan from Saccharomyces cerevisae (Man) for 30 and 60 minutes.

value: macrophage


title: Human fetal lung 85 dpc

description: human fetal lung 85 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19908

value: Control

value: <2 hrs


title: T00342940_60M3

description: no additional information

scan_protocol: Standard CodeLink Expression assay protocol was used.


title: Human fetal lung 96 dpc

description: human fetal lung 96 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19313

value: training sample


title: pre-estradiol, biological rep3

source_name: G1E ER4 cell, before estradiol induction.


title: Human fetal lung 59 dpc

description: human fetal lung 59 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H19128


title: Human fetal lung 74 dpc

description: human fetal lung 74 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18877

value: test sample


title: Human fetal lung 83 dpc

description: human fetal lung 83 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18606

value: Male

value: Caucasian


title: T00343470_30M3

description: no additional information

source_name: Mannan-coated beads internalized for 30 minutes

label_protocol: Standard CodeLink Expression assay protocol was used.


title: pre-estradiol, biological rep1

value: G1E ER4


title: pre-estradiol, biological rep2


title: Human fetal lung 98 dpc

description: human fetal lung 98 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18875


title: Human fetal lung 113 dpc

description: human fetal lung 113 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18484


title: T00343471_60A1

description: no additional information

source_name: Avidin-coated beads internalized for 60 minutes


title: GPI+ cells of Wild type C57BL/6 in batch2, biological rep4

first: Valeria

last: Visconte

address: 10 Center Dr

department: 10-CRC Clinical Research Center

institute: NIH

description: gene expression from wild-type cells

hyb_protocol: Following fragmentation, RNA was hybridized to Affymetrix mouse genome 430.2 gene chips for 16 hours, washed and stained on an Affymetrix fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix genechip scanner.

data_processing: Image processing and expression analysis were performed using Affymetrix GCOS version 12.  The signal intensity values obtained for probe sets in the microarray were transformed using a quantile-normalizing transformation. Transformed data were subjected to principal component analysis to detect outliers. One-way ANOVA and post-hoc t-test were performed to evaluate each probe set.

source_name: mouse bone marrow, wild type, GPI+

label_protocol: Biotinylated cRNA was performed according to the standard protocols from Affymetrix from 500 nanograms of RNA in the first experiment and 1 microgram in the second experiment.

growth_protocol: Bone marrow cells were extracted from femurs and tibias from Pig-a knock-out, C57BL/6 mice, recipients of GPI-deficient cells (T-GPI-) and wild-type C57BL/6 bone marrow cells. Cells were counted and stained with a fluorescein-conjugated antibody mixture (FITC) containing specific GPI markers antibodies like CD24, CD48 and Gr-1, and were sorted into GPI-deficient and GPI-normal fractions by a FACSVantage cell sorter.

extract_protocol: Total RNA was  extracted using Rneasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Bone marrow cells from Pig-a knock-out donors  were incubated with 10nM aerolysin at 37C for 30 minutes to efficiently lyse GPI-normal cells. Enriched GPI-deficient cells were infused via laternal tail vein injection to lethally-irradiated C57/BL6 mice previously irradiated with 9 Gys total body irradiation.

tag: wild-type bone marrow cells


title: Human fetal lung 89 dpc

description: human fetal lung 89 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17920


title: T00340081_30A3

description: no additional information

source_name: Avidin-coated beads internalized for 30 minutes


title: T00343474_60A3

description: no additional information


title: T00343468_30M1

description: no additional information


title: Human fetal lung 78 dpc

description: human fetal lung 78 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17574

value: Unknown


title: GPI+ cells of Wild type C57BL/6 in batch2, biological rep3

description: gene expression from wild-type cells


title: T00340079_30A1

description: no additional information

value: macrophage


title: T00342935_60L3

description: no additional information

source_name: LPS-coated beads internalized for 60 minutes


title: GPI+ cells of Wild-type C57BL/6 in batch2, biological rep2

description: gene expression from wild-type cells


title: T00343473_60A2

description: no additional information


title: GPI+ cells of transplanted C57BL/6 with wild-type bone marrow cells in batch2, biological rep2

description: gene expression from wild-type cells

source_name: mouse bone marrow, transplanted, GPI+


title: T00340080_30A2

description: no additional information


title: KO2

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See http://www.nimblegen.com/.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 2003, 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 2003, 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: OASIS KO calvaria

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See http://www.nimblegen.com/.

tag: tissue

value: KO calvaria


title: GPI+ cells of Wild type C57BL/6 in batch2, biological rep1

description: gene expression from wild-type cells


title: T00343469_30M2

description: no additional information


title: Human fetal lung 133 dpc biological replicate 4

description: human fetal lung 133 dpc biological replicate 4

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1776

value: Female

value: African American

value: Control

value: 1 hrs

tag: microarray hybridization data 02/04/2006


title: Human fetal lung 87 dpc

description: human fetal lung 87 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18480

value: <2 hrs

value: test sample


title: 14 h post-estradiol,biological rep3


title: GPI+ cells of transplanted C57BL/6 with wild-type bone marrow cells in batch2, biological rep3

description: gene expression from wild-type cells


title: T00342934_60L2

description: no additional information


title: Human fetal lung 140 dpc biological replicate 2

description: human fetal lung 140 dpc biological replicate 2

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1635

value: Male

tag: microarray hybridization data 11/02/2005

value: training sample


title: GPI- cells of transplanted C57BL/6 with enriched bone marrow cells from Pig-a knock-out in batch2, biological rep4

description: gene expression from knocked-out cells

source_name: mouse bone marrow, transplanted, GPI-

tag: knocked-out cells


title: GPI+ cells of transplanted C57BL/6 with wild-type bone marrow cells in batch2, biological rep1

description: gene expression from wild-type cells


title: T00342930_60L1

description: no additional information


title: GPI- cells of transplanted C57BL/6 with enriched bone marrow cells from Pig-a knock-out in batch2, biological rep3

description: gene expression from knocked-out cells


title: T00343467_30L3

description: no additional information

source_name: LPS-coated beads internalized for 30 minutes


title: WT2

description: Gene expression data from WT calvaria

source_name: WT calvaria

value: WT calvaria


title: Human fetal lung 130 dpc

description: human fetal lung 130 dpc

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1621

value: Caucasian


title: Human fetal lung 133 dpc biological replicate 3

description: human fetal lung 133 dpc biological replicate 3

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1690

value: Anencephaly


title: GPI- cells of transplanted C57BL/6 with enriched bone marrow cells from Pig-a knock-out in batch2, biological rep2

description: gene expression from knocked-out cells


title: T00343466_30L2

description: no additional information

value: macrophage


title: Human fetal lung 133 dpc biological replicate 2

description: human fetal lung 133 dpc biological replicate 2

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1631

value: 2 hrs


title: Human fetal lung 133 dpc biological replicate 1

description: human fetal lung 133 dpc biological replicate 1

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1589

value: Female

value: African American


title: T00340077_30L1

description: no additional information


title: GPI- cells of transplanted C57BL/6 with enriched bone marrow cells from Pig-a knock-out in batch2, biological rep1

description: gene expression from knocked-out cells


title: T00343478_60F3

description: no additional information

source_name: Fc-coated beads internalized for 60 minutes


title: IL10 mouse week 7 colon 77

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description:
This data relates to a submitted paper "Transcriptomic and proteomic analyses to characterize onset and progression of colon inflammation in interleukin-10 gene-deficient mice"
Further details :
The formaldehyde-fixed intestinal tissues were embedded in a paraffin block, cut into 5 µm thick sections and stained with haematoxylin and eosin. The stained sections were scored by a pathologist (who had no knowledge of the experiment protocol) for the following aspects of inflammation: inflammatory cell infiltration (monocytes, neutrophils, fibrin exudation and lymphangiectasis), tissue destruction (enterocyte loss, ballooning degeneration, oedema and mucosal atrophy) and tissue repair (hyperplasia, angiogenesis, granulomas and fibrosis). A rating score between 0 (no change from normal tissue section) and 3 (lesions involving most areas and all layers of the tissue section including mucosa, muscle and omental fat) was given for each aspect of inflammatory cell infiltration, tissue destruction, and tissue repair. For each intestinal section, the histological injury score (HIS) was calculated as: HIS = (inflammatory lesions score) × 2 + tissue destruction score + tissue repair score. Inflammatory cell infiltration represented the main characteristic of the observed inflammation, therefore the sum of inflammatory lesions was multiplied by 2 to give more weight to this value.
The concentration of serum amyloid A (SAA) was measured in plasma to complement the histology scores using a murine specific SAA kit (Tridelta Development Limited, Maynooth, County Kildare, Ireland), according to the manufacturer’s instructions.

hyb_protocol: Labelled cRNA was hybridized on an Agilent Technologies 44k (G4122-60510) mouse 60mer oligonucleotide array (containing 44,290 probe sets which represent 33,994 unique genes) using the in situ hybridization plus kit (Agilent Technologies) and following the manufacturer’s protocols.

scan_protocol: Arrays were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA). Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities. probe sets quantified. There are low, medium and high scan data available.

data_processing:
Statistical analysis and quality assessment of the microarray data were performed using linear models for microarray analysis (Limma) within the Bioconductor framework [Smyth 2005]. Data quality was assessed on diagnostic plots (boxplots and density plots) and spatial images generated from the raw (non-processed) data. All arrays passed the quality control and were included in the analyses. Medium scan data were used for normalization. Intensity ratios for all microarray spots were normalized using a global loess smoothing procedure to remove the effect of systematic variation in the microarrays and no background correction was necessary due to homogeneous hybridization [Smyth and Speed 2003].
The normalized data from the arrays of each time point group were averaged. For each comparison of interest (IL10-/- 7 vs. C57 7 and IL10-/- 12 vs. C57 12), a list of differentially expressed genes was generated by calculating moderated t-statistics and false discovery rate using the Limma package, which implements an empirical Bayes approach to assign differential gene expression.
Probes from the microarray dataset that satisfied the cut-off criteria of a 1.5-fold change (FC) in expression (up- or down-regulated) and a FDR (q-value) less than 0.05 were considered significantly different and used for pathway and functional analysis.

label_protocol: Amplification and labeling was processed according to Agilent Technologies protocols. Briefly, cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies). cRNA was labelled with cyanine 3-CTP (samples) and cyanine 5-CTP (reference) dyes (10mM; Perkin-Elmer/NEN Life Science (NEL 580, 581), Boston, MA, USA) and the dye incorporation monitored spectrophotometrically using a Nanodrop ND-1000.

growth_protocol: Bodyweight was determined three times a week and the mice carefully monitored for disease symptoms (weight loss, soft faeces, inactivity, etc.). Throughout the experimental period, dietary intake was estimated and adjusted daily to equal the mean amount of food consumed by IL10-/- mice on the previous day to ensure similar intakes between control (C57) and IL10-/- mice. On the day prior to sampling, mice were subjected to a fast-feed period prior to sampling. The mice were euthanased by CO2 asphyxiation and cervical dislocation. The intestine was removed, cut open lengthwise and rinsed with 0.9% NaCl to remove traces of digesta. The intestine was divided into duodenum, jejunum, ileum and colon. One piece of each intact tissue was stored at room temperature in 10% phosphate buffered formaldehyde for histological analysis, another immediately frozen in liquid nitrogen and kept at −85°C for genomic analysis. Plasma was separated from the blood, frozen in liquid nitrogen and stored at −85°C for biochemical analysis.

extract_protocol: Total RNA was extracted from homogenized full-thickness colonic tissues in TRIzol reagent (Invitrogen, Auckland, NZ) and purified with RNeasy columns (QIAGEN, San Diego, CA, USA). Quantity and integrity of RNA were assessed by a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and an Agilent 2100 bioanalyser (Agilent Technologies, Santa Clara, CA, USA), respectively. Samples with a 28s/18s peak ratio ~2.0 and a RNA integrity number >8 were considered for microarray hybridization and quantitative real-time PCR. For the comparison of gene expression levels, colonic RNA of IL10-/- and C57 at 7 and 12 weeks of age were compared because of a low HIS variability in the colon within those time points. A reference design with 15 arrays was used, where each individual RNA sample was hybridized with a reference sample onto the array, in a total of 3 or 4 biological replicates per treatment. Reference RNA was prepared by pooling equal amounts of purified total RNA extracted from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice.

treatment_protocol:
A total of 30 male IL10-/- (B6.129P2-Il10<tm1Cgn>/J) and 30 male C57 control (C57BL/6J) mice were obtained from The Jackson Laboratory (Bar Harbor, Maine, USA). All mice were between 28 and 35 days of age at the start of the study. For convenience and consistency in reporting, their age was defined as 35 days or 5 weeks of age. The mice were housed individually in standard shoebox size cages containing untreated wood shavings and maintained in an air-conditioned animal room with a 12-h light-dark cycle. Animals had free access to water and were fed an AIN-76A standard powder diet prepared in-house. This study was approved by the AgResearch Ruakura Animal Ethics Committee in Hamilton, New Zealand according to the Animal Protection Act (1960) and Animal Protection Regulations (1987) and amendments.
Four days after arrival, all mice were inoculated orally with a mixture of Enterococcus faecalis strains and bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation.
Mice were randomly assigned to five sampling groups (7, 8.5, 10, 12 and 14 weeks of age).

tag: strain

tag: background strain

value: C57 mice (C57BL/6J), control

tag: gender

value: male

tag: age

value: 5 weeks

value: colon tissue

source_name: Reference RNA of healthy growing Swiss Mice

label_protocol: As for channel 1 (but Cy5)

growth_protocol: Reference

extract_protocol: as for channel 1

treatment_protocol: Reference

tag: sample type

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice


title: GPI+ cells of Pig-a knock-out in batch1, biological rep3

description: gene expression from knocked-out cells

source_name: mouse bone marrow, Pig-a knock-out, GPI+


title: T00342929_60F2

description: no additional information

tag: cell type

tag: cell line


title: Human fetal lung 154 dpc

description: human fetal lung 154 dpc

source_name: whole lung human fetus

tag: LabID

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB0684

tag: Sex

value: Male

tag: Race

tag: Disease Status

value: Tuberous Sclerosis

value: 5 hrs

value: test sample


title: Human fetal lung 134 dpc

description: human fetal lung 134 dpc

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB1566

value: Control

tag: Post-Mortem Interval

value: 6 hrs

tag: cross validation

value: training sample


title: GPI+ cells of Pig-a knock-out in batch1, biological rep1

description: gene expression from knocked-out cells


title: Human fetal lung 140 dpc biological replicate 1

description: human fetal lung 140 dpc biological replicate 1

value: University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD) ID# UMB0045

value: 2 hrs


title: GPI- cells of Pig-a knock-out in batch1, biological rep3

description: gene expression from knocked-out cells

source_name: mouse bone marrow, Pig-a knock-out, GPI-


title: IL10 mouse week 7 colon 75

description:
This data relates to a submitted paper "Transcriptomic and proteomic analyses to characterize onset and progression of colon inflammation in interleukin-10 gene-deficient mice"
Further details :

The formaldehyde-fixed intestinal tissues were embedded in a paraffin block, cut into 5 µm thick sections and stained with haematoxylin and eosin. The stained sections were scored by a pathologist (who had no knowledge of the experiment protocol) for the following aspects of inflammation: inflammatory cell infiltration (monocytes, neutrophils, fibrin exudation and lymphangiectasis), tissue destruction (enterocyte loss, ballooning degeneration, oedema and mucosal atrophy) and tissue repair (hyperplasia, angiogenesis, granulomas and fibrosis). A rating score between 0 (no change from normal tissue section) and 3 (lesions involving most areas and all layers of the tissue section including mucosa, muscle and omental fat) was given for each aspect of inflammatory cell infiltration, tissue destruction, and tissue repair. For each intestinal section, the histological injury score (HIS) was calculated as:  HIS = (inflammatory lesions score) × 2 + tissue destruction score + tissue repair score. Inflammatory cell infiltration represented the main characteristic of the observed inflammation, therefore the sum of inflammatory lesions was multiplied by 2 to give more weight to this value.
The concentration of serum amyloid A (SAA) was measured in plasma to complement the histology scores using a murine specific SAA kit (Tridelta Development Limited, Maynooth, County Kildare, Ireland), according to the manufacturer’s instructions.

tag: tissue


title: WT1

description: Gene expression data from WT calvaria

value: WT calvaria


title: GPI- cells of Pig-a knock-out in batch1, biological rep2

description: gene expression from knocked-out cells


title: T00342928_60F1

description: no additional information

value: macrophage


title: GPI+ cells of Pig-a knock-out in batch1, biological rep2

description: gene expression from knocked-out cells


title: IL10 mouse week 7 colon 78

value: C57 mice (C57BL/6J), control

value: male


title: Human fetal lung 108 dpc biological replicate 2

description: human fetal lung 108 dpc biological replicate 2

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18475

value: Unknown

value: <2 hrs

tag: microarray hybridization data 05/27/2005


title: T00340076_30F3

description: no additional information

source_name: Fc-coated beads internalized for 30 minutes


title: IL10 mouse week 12 colon 95

value: 5 weeks

value: colon tissue

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice


title: IL10 mouse week 12 colon 96


title: IL10 mouse week 12 colon 94

source_name: RNA of healthy growing Swiss Mice


title: T00340075_30F2

description: no additional information


title: Human fetal lung 105 dpc

description: human fetal lung 105 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18450

value: Male


title: Human fetal lung 72 dpc

description: human fetal lung 72 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18419

value: Control


title: IL10 mouse week 12 colon 92


title: C57 mouse week 7 colon 46


title: C57 mouse week 7 colon 45


title: T00343476_60C2

description: no additional information

source_name: uninfected/untreated control 60 minutes


title: T00343475_60C1

description: no additional information


title: T00343477_60C3

description: no additional information


title: Human fetal lung 76 dpc biological replicate 2

description: human fetal lung 76 dpc biological replicate 2

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18401

value: training sample


title: GPI- cells of Pig-a knock-out in batch1, biological rep1

description: gene expression from knocked-out cells


title: Human fetal lung 108 dpc biological replicate 1

description: human fetal lung 108 dpc biological replicate 1

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18355

value: test sample


title: C57 mouse week 7 colon 43


title: T00340073_30C1

description: no additional information

source_name: uninfected/untreated control 30 minutes

value: macrophage


title: KO1

value: KO calvaria


title: Human fetal lung 103 dpc

description: human fetal lung 103 dpc

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18356

value: Female


title: RT_30_13_284_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2

status: Public on Sep 09 2009

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: Gene expression changes in female mouse lung tissue treated for 90 days with NPTH

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Grouped-Batch-Profile normalization

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

value: tissue

value: lung

tag: array type

value: Affymetrix Mouse 430_2

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: Good

tag: sample preservation

value: RNA later

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental stage

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

value: 18 weeks


title: T00340074_30F1

description: no additional information

tag: cell type

tag: cell line


title: Human fetal lung 63 dpc biological replicate 2

description: human fetal lung 63 dpc biological replicate 2

tag: LabID

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H18338

tag: Sex

tag: Race

value: Pacific Islander

tag: Disease Status

value: Control

tag: Post-Mortem Interval

value: <2 hrs

tag: cross validation

value: training sample


title: Human fetal lung 63 dpc biological replicate 1

description: human fetal lung 63 dpc biological replicate 1

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17657

value: Unknown

tag: microarray hybridization data 05/27/2005

value: test sample


title: RT_3_13_254_NPTH-3_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3, Units of Dose or Concentration: ppm

tag: sample type

value: tissue

tag: tissue

value: lung

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: gender

tag: age


title: C57 mouse week 12 colon 64

tag: strain

tag: background strain

value: C57 mice (C57BL/6J), control

value: male

value: 5 weeks

value: colon tissue

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice


title: T00340082_30C2

description: no additional information

tag: cell type

value: macrophage

tag: cell line


title: RT_3_13_255_NPTH-3_Lung_07008_Mouse430_2_RSTLRI000_2

value: Affymetrix Mouse 430_2

value: ul

tag: rna integrity number

tag: bioanalyzer results

value: Good

tag: sample preservation

value: RNA later

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental stage

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

value: 18 weeks


title: Human fetal lung 76 dpc biological replicate 1

description: human fetal lung 76 dpc biological replicate 1

tag: LabID

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17470

tag: Sex

value: Unknown

tag: Race

tag: Disease Status

value: Control

tag: Post-Mortem Interval

tag: microarray hybridization data 05/27/2005

tag: cross validation

value: test sample


title: C57 mouse week 12 colon 65

tag: strain

tag: background strain

value: C57 mice (C57BL/6J), control

tag: gender

value: male

tag: age

tag: tissue

tag: sample type


title: C57 mouse week 7 colon 44

value: 5 weeks

value: colon tissue


title: RT_3000_13_210_MECL-3000_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3000, Units of Dose or Concentration: ppm

value: tissue

value: lung

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: T00340083_30C3

description: no additional information

tag: cell type

value: macrophage

tag: cell line


title: C57 mouse week 12 colon 66

tag: strain

tag: background strain

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice


title: C57 mouse week 12 colon 63

tag: gender

tag: age

value: pooled RNA from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice


title: RT_3925_13_209_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TCFM

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Trichlorofluoromethane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 3925, Units of Dose or Concentration: mg/kg

tag: sample type

tag: tissue

value: Affymetrix Mouse 430_2

value: ug

value: good

value: RNA later

tag: individual

tag: developmental stage

value: adult

tag: sacrifice method


title: RT_4000_13_217_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 4000, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

value: Good

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

value: 18 weeks


title: RT_0_13_117_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with CTRL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: RT_4000_13_220_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2

tag: gender


title: RT_0_13_173_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with CTRL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: age


title: RT_0_13_134_Lu_CCO3_Mouse430_2_RSTLRI601_1

tag: sample type


title: RT_0_13_120_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2

tag: tissue


title: RT_0_13_294_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: individual


title: RT_0_13_240_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2

tag: developmental stage


title: RT_0_13_54r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sacrifice method


title: RT_0_13_97_Lu_CCO2_Mouse430_2_RSTLRI601_1

tag: array type


title: Human fetal lung 110 dpc biological replicate 1

description: human fetal lung 110 dpc biological replicate 1

tag: LabID

value: University of Washington Center for Birth Defects Research (Seattle, WA) ID# H17486

tag: Sex

value: Unknown

tag: Race

tag: Disease Status

value: Control

tag: Post-Mortem Interval

tag: microarray hybridization data 05/27/2005

tag: cross validation

value: training sample


title: RT_1200_13_97_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with PGBE

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Propylene glycol mono-t-butyl ether, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 1200, Units of Dose or Concentration: ppm

value: tissue

value: lung

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: RT_0_13_295_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample type

tag: tissue

tag: ncbi taxonomy id

tag: individual

tag: developmental stage

tag: sacrifice method

tag: gender

tag: age


title: RT_10_13_262_NPTH-10_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: array type


title: RT_0_13_99_Lu_CCO2_Mouse430_2_RSTLRI601_1

tag: amount to core


title: RT_0_13_60_Lu_CCO3_Mouse430_2_RSTLRI601_1

tag: units of amount


title: RT_0_13_237_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2

tag: ratio


title: RT_0_13_260_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: dilution


title: Granulocytes_cultured18h_G-CSF/dex_donorC

city: Amsterdam

first: Agata

last: Drewniak

address: Plesmanlaan 125

department: Blood Cell Research

country: Netherlands

institute: Sanquin Research

description: Biological replicate 3 of 3

hyb_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

data_processing: The default Agilent normalization procedure, called Linear & Lowess, was applied.Exact protocol and parameter settings are described in the Agilent Feature Extraction Software User Manual 8.5 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=37629).

label_protocol: Dye Coupling Reaction (Amersham, England)

growth_protocol: ex vivo isolated granulocytes

extract_protocol: Total RNA extracted using Trizol according to the  manufacturer's instruction followed by additional purification using nucleospin RNA isolation kit (Machery-Nagel, Düren, Germany)

tag: granulocytes cultured

tag: HBSS medium + G-CSF&dex 18hours

source_name: pooled Total RNA from freshly isolated control granulocytes

tag: granulocytes

tag: percoll isolated granulocytes


title: RT_0_13_293_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample type

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: RT_100_13_179_MECL-100_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

tag: tissue

tag: ncbi taxonomy id

tag: individual

tag: developmental stage

tag: sacrifice method


title: RT_1000_13_252_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TDPP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tris(2,3-dibromopropyl)phosphate, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1000, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: gender

tag: age


title: RT_05_13_241_NPTH-05_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: ratio

tag: dilution


title: RT_1200_13_96_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with PGBE

tag: sample type


title: RT_10000_13_15_Lu_NAAC_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with NAAC

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 4-Nitroanthranilic acid, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 10000, Units of Dose or Concentration: ppm

tag: rna integrity number


title: RT_1250_13_2_Lu_BBMP_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with BBMP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,2-Bis(bromomethyl)-1,3-propanediol, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

tag: bioanalyzer results


title: RT_1250_13_267_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TFEL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tetrafluoroethylene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

tag: sample preservation


title: Granulocytes_cultured18h_donorB

description: Biological replicate 2 of 3

scan_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

tag: granulocytes cultured

tag: HBSS medium 18hours

tag: granulocytes

tag: percoll isolated granulocytes


title: Granulocytes_cultured18h_donorC

description: Biological replicate 3 of 3


title: RT_16000_13_39_Lu_MALA_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with MALA

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Malathion, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 14800, Units of Dose or Concentration: ppm

tag: tissue

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental stage


title: Granulocytes_fresh_G-CSF/dex_invivo_donorA

description: Biological replicate 1 of 3

tag: granulocytes fresh

tag: donor treated with G-CSF/dex, cells isolated 18 h after treatment


title: Granulocytes_cultured18h_G-CSF/dex_donorA

description: Biological replicate 1 of 3

tag: HBSS medium + G-CSF&dex 18hours


title: Granulocytes_fresh_G-CSF/dex_invivo_donorC

description: Biological replicate 3 of 3


title: RT_20_13_272_NPTH-20_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 20, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: sacrifice method

tag: gender

tag: age


title: RT_200_13_28_Lu_DIAZ_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with DIAZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Diazinon, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: sample type

tag: bioanalyzer results

tag: sample preservation


title: Granulocytes_cultured18h_donorA

description: Biological replicate 1 of 3

tag: granulocytes cultured

tag: HBSS medium 18hours

tag: granulocytes

tag: percoll isolated granulocytes


title: Granulocytes_fresh_control_donorC

description: Biological replicate 3 of 3

tag: granulocytes fresh

tag: control


title: Granulocytes_fresh_G-CSF/dex_invivo_donorB

description: Biological replicate 2 of 3

tag: donor treated with G-CSF/dex, cells isolated 18 h after treatment


title: RT_16000_13_33_Lu_MALA_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with MALA

tag: tissue

tag: array type

tag: amount to core

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental stage


title: RT_2000_13_197_MECL-2000_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: sample type

tag: units of amount

tag: ratio

tag: dilution

tag: sacrifice method

tag: gender

tag: age


title: RT_200_13_72_Lu_COUM_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with COUM

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Coumarin, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 200, Units of Dose or Concentration: mg/kg

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation


title: Granulocytes_fresh_control_donorB

description: Biological replicate 2 of 3

tag: granulocytes fresh

tag: control

tag: granulocytes

tag: percoll isolated granulocytes


title: RT_2000_13_4_Lung_Naphthalenediamine_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with NAPD

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,5-Naphthalenediamine, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: tissue

tag: array type

tag: amount to core

tag: strain or line

tag: ncbi taxonomy id


title: RT_2000_13_5_Lung_Naphthalenediamine_Mouse430_2_IMFGN0023_8

source_name: female mouse lung tissue treated for 90 days with NAPD

tag: sample type

tag: units of amount

tag: ratio

tag: developmental stage


title: RT_3_13_251_NPTH-3_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3, Units of Dose or Concentration: ppm

tag: dilution

tag: individual

tag: sacrifice method

tag: gender

tag: age


title: TOC1-ox Arabidopsis seedlings replicate 3

city: Barcelona

first: Paloma

last: Mas

address: C/ Jordi Girona 18-26

department: Genetica Molecular

country: Spain

institute: Consorcio CSIC-IRTA-UAB (CRAG)

description: Genome expression data from TOC1-ox Arabidopsis seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner using AGCC software version 1.1

data_processing: Carmaweb software (https://carmaweb.genome.tugraz.at) was used for data processing with the gcRMA algorythm for normalization. Differentially expressed genes were identified using the empirical Bayes moderated t statistics from the LiMMA package. Genes with an FDR < 5% were selected as misregulated in TOC1-ox

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual Rev. 3, 2005, Affymetrix).

growth_protocol: Seedlings were grown on MS3 medium under 12-hour light:12-hour dark (LD) cycles for 12 days.

extract_protocol: Total RNA extractions were performed with Pure Link Total RNA Purification System (Invitrogen).

treatment_protocol: Samples were collected at Zeitgeber Time 15 (ZT15).

tag: ecotype

value: 12 days old seedlings


title: WT Arabidopsis seedlings replicate 3

description: Genome expression data from WT Arabidopsis seedlings

source_name: WT


title: RT_30_13_285_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

value: Affymetrix Mouse 430_2

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation


title: RT_2000_13_12_Lung_ethylenediamine_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with NEDD

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: N-(1-naphthyl)ethylenediamine dihydrochloride, Treatment Duration: 13, Units of Duration: week, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: tissue

tag: array type


title: TOC1-ox Arabidopsis seedlings replicate 2