title: AE40T

description: frozen tissue extracted by Trizol


title: Adult at T10 in LD, time-series experiment 4

status: Public on Sep 01 2010

type: RNA

city: Reno

first: Alexander

middle: Martinus

last: van der Linden

state: NV

address: 1664 N. Virginia St.

department: Biology

country: USA

institute: University of Nevada

description:
C. elegans_LD10_4
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Whole Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

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

data_processing: The GeneChip Robust Multiarray Averaging (GC-RMA) method in the R v2.7.1 software package was used to derive log2 expression values for each probe set from Affymetrix generated .CEL files. Expression values were normalized and standardized as described Keegan et al. 2007. Briefly, for each time-point in a time-series experiment, the expression level relative to the mean (in log2 expression values) over that experiment was calculated. This normalization was performed separately for each independent time-series experiment. Arrays in the independent time-course experiments were standardized by setting the mean expression of each array to 0 and the variance to 1. For samples with biological replicates, the log2 expression values for each biological replicate were averaged, and the averaged log2 value was further processed with GC-RMA, standardized and normalized.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: C. elegans adults 10 hr time-point during LD entrainment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (GeneChip Expression Analysis Technical Manual, 701025 Rev.6, 2004, Affymetrix).

growth_protocol: Growth-synchronized populations of wild-type Bristol N2 late L1 larvae were transferred to plates seeded with E. coli HB101 bacteria. Two populations of worms were entrained to opposing light/dark or temperature cycles in two different incubators: 12 hr at 25ºC (W) followed by 12 hr at 15ºC (C), or 12 hr of light (L) followed by 12 hr of dark (D). After reaching adulthood, the two populations of worms were transferred to the same incubator and allowed to free-run at constant 15ºC (CC) or in constant darkness (DD). Non-entrained control experiments for light/dark were performed in parallel in the same incubator in complete darkness. Temperature cycling experiments were conducted in constant darkness in temperature programmable incubators (Tritech Research). Light/dark cycling experiments were conducted at 18ºC in programmable incubators (Precision Scientific; cold white light (light source F20T12/CW) at about 500-1000 lux). To inhibit progeny production during entrainment, L4 larvae were quickly transferred to plates containing bacteria and 25 μM FUDR.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Trizol-extracted total RNA was treated with DNAase (New England Biolabs) as described (www.wormbook.org).

treatment_protocol: Adults were harvested and washed at least twice in cold 1x M9 buffer (<15 min) every 4 hrs during the last day of entrainment and subsequent free-running days. Trizol Reagent (Invitrogen) was added to harvested worm samples and pellets were immediately frozen in liquid nitrogen.

tag: strain

value: Bristol N2

tag: genotype

value: wild-type

tag: developmental stage

value: adult

tag: tissue

value: whole body

tag: conditions

value: 12:12 hr light/dark (LD) cycles

tag: time

value: 10 hr

tag: experiment


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayB_081210

type: genomic

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayB_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

molecule: genomic DNA

organism: Mus musculus

source_name: Sample Type: Cells, Cell Type: CH12.LX

label_protocol: standard Affymetrix protocol

growth_protocol: Growth Media: RPMISAdvance, HIFBS, HEPES, Pen/Strepp, L Glutamine, Mercaptoethanol, Amount of Media: 25, Units of Media: ml

extract_protocol: Extraction Method:  Addition of lysis buffer followed by disruption with a Dounce homogenizer. Lysates sonicated and DNA sheared to an average length of 300-500bp

treatment_protocol: in vitro Treatment: TCDD, Units of Treatment Repeat: nM, Treatment Duration: 1, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: Media, Dose or Concentration: 10, Units of Dose or Concentration: nM

tag: array type

tag: pooled from multiple samples

value: No

tag: number of cells seeded

value: 1X10^5 cells/ml, 25ml in P150s

tag: units of harvest time point

value: hr

tag: antibody name

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

tag: sample type

value: ChIP


title: AE39T

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by Trizol

hyb_protocol: Total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the R function rma() in the Bioconductor package affy

label: Biotin

organism: Homo sapiens

source_name: tumor tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Total RNA was extracted and purified by standard Trizol method and followed with qualification check by Agilent 2100.

tag: tissue type

value: esophageal squamous cell carcinoma (ESCC)


title: AE38T

description: frozen tissue extracted by Trizol


title: Adult at T6 in LD, time-series experiment 4

description:
C. elegans_LD6_4
This Sample represents 2 biological replicates.
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 6 hr time-point during LD entrainment

value: 6 hr


title: Adult at T46 in DD, time-series experiment 2

description:
C. elegans_DD46_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 46 hr time-point during DD free-running

value: constant darkness (DD)

value: 46 hr


title: AE36T

description: frozen tissue extracted by Trizol


title: Adult at T2 in LD, time-series experiment 4

description:
C. elegans_LD2_4
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 2 hr time-point during LD entrainment

value: 2 hr


title: AE37T

description: frozen tissue extracted by Trizol


title: Male Breast 22

city: Bari

first: Pina

last: Iannelli

address: viale Orazio Flacco, 65

country: Italy

institute: National Cancer Centre "Giovanni Paolo II"

description: diagnosis at Regina Elena

hyb_protocol: standard Agilent CGH protocol

scan_protocol: standard Agilent CGH protocol

data_processing: Agilent Feature Extraction Software (8.1.1.1 for GPL2879, 9.5.1.1 for GPL5477)

source_name: breast

label_protocol: standard Agilent CGH protocol

extract_protocol: standard Agilent CGH protocol

tag: gender

value: male

value: breast cancer tumor


title: Male Breast 25

description: diagnosis at Regina Elena


title: Male Breast 18

description: diagnosis at Regina Elena


title: Adult at T38 in DD, time-series experiment 2

description:
C. elegans_DD38_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 38 hr time-point during DD free-running

value: Bristol N2

value: wild-type

value: 38 hr


title: Male Breast 23

description: diagnosis at Regina Elena


title: Male Breast 24

description: diagnosis at Regina Elena


title: AE32T

description: frozen tissue extracted by Trizol


title: Adult at T34 in DD, time-series experiment 2

description:
C. elegans_DD34_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 34 hr time-point during DD free-running

value: adult

value: whole body

value: 34 hr


title: AE35T

description: frozen tissue extracted by Trizol


title: Male Breast 21

description: diagnosis at Regina Elena


title: Adult at T26 in DD, time-series experiment 2

description:
C. elegans_DD26_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 26 hr time-point during DD free-running

value: 26 hr


title: Adult at T30 in DD, time-series experiment 2

description:
C. elegans_DD30_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 30 hr time-point during DD free-running

value: 30 hr


title: AE33T

description: frozen tissue extracted by Trizol


title: Adult at T42 in DD, time-series experiment 2

description:
C. elegans_DD42_2
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 42 hr time-point during DD free-running

value: 42 hr


title: Male Breast 19

description: diagnosis at Regina Elena


title: Male Breast 16

description: diagnosis at Regina Elena


title: Adult at T18 in LD, time-series experiment 3

description:
C. elegans_LD18_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 18 hr time-point during LD entrainment

value: 12:12 hr light/dark (LD) cycles

value: 18 hr


title: AE29T

description: frozen tissue extracted by Trizol

value: esophageal squamous cell carcinoma (ESCC)


title: AE30T

description: frozen tissue extracted by Trizol


title: Adult at T22 in LD, time-series experiment 3

description:
C. elegans_LD22_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 22 hr time-point during LD entrainment

value: 22 hr


title: Adult at T22 in LD, time-series experiment 6

description:
C. elegans_LD22_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.


title: AE31T

description: frozen tissue extracted by Trizol


title: Male Breast 17

description: diagnosis at Regina Elena


title: Male Breast 20

description: diagnosis at Regina Elena


title: AE25T

description: frozen tissue extracted by Trizol


title: AE24T

description: frozen tissue extracted by Trizol


title: Adult at T14 in LD, time-series experiment 3

description:
C. elegans_LD14_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 14 hr time-point during LD entrainment

value: 14 hr


title: AE18T

description: frozen tissue extracted by Trizol


title: Adult at T6 in LD, time-series experiment 3

description:
C. elegans_LD6_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

value: 6 hr


title: AE23T

description: frozen tissue extracted by Trizol


title: AE26T

description: frozen tissue extracted by Trizol


title: AE19T

description: frozen tissue extracted by Trizol


title: AE27T

description: frozen tissue extracted by Trizol


title: Adult at T2 in LD, time-series experiment 3

description:
C. elegans_LD2_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

value: 2 hr


title: AE15T

description: frozen tissue extracted by Trizol


title: AE22T

description: frozen tissue extracted by Trizol


title: AE21T

description: frozen tissue extracted by Trizol


title: AE20T

description: frozen tissue extracted by Trizol


title: AE13T

description: frozen tissue extracted by Trizol


title: AE16T

description: frozen tissue extracted by Trizol


title: AE28T

description: frozen tissue extracted by Trizol


title: AE12T

description: frozen tissue extracted by Trizol


title: AE10T

description: frozen tissue extracted by Trizol


title: AE11T

description: frozen tissue extracted by Trizol


title: AE09T

description: frozen tissue extracted by Trizol


title: AE08T

description: frozen tissue extracted by Trizol


title: AE34T

description: frozen tissue extracted by Trizol


title: AE17T

description: frozen tissue extracted by Trizol


title: PTB/nPTB_Knockdown_Rep2

city: Santa Clara

first: Jason

middle: Wray

last: Hubbard

state: CA

address: 3380 Central Expressway

institute: Affymetrix Inc

hyb_protocol: Hybridized for 16hrs at 45C using standard Affymetrix protocols

scan_protocol: Arrays scanned on GCS3000

data_processing: Array data was sketch-quantile normalized and PLIER was used for probeset summarization

label: DLR (biotin)

source_name: HeLa S3 Cell Line; PTB/nPTB RNAi

label_protocol: Labeled target was prepared from 1 µg of Total RNA using the Affymetrix WT Sense Target Labeling Kit

growth_protocol: HeLa S3 cells were grown in DMEM with glutamax and 10% FBS under standard conditions

extract_protocol: RNA was harvested with 1ml of TRI reagent (SIGMA) and extraction was carried out following manufacturer’s instructions

treatment_protocol: Transfections were carried out with Lipofectamine 2000 (Invitrogen). For siRNA transfections, typically cells were seeded at 2 x 105 cells/well and were transfected with 20pmols of siRNA and 2.5 ml of Lipofectamine 2000 twice during two consecutive days. Samples were harvested for protein or RNA extraction 3 days after the first transfection.

tag: cell line

value: HeLa S3


title: AE02T

description: frozen tissue extracted by Trizol


title: AE05T

description: frozen tissue extracted by Trizol


title: AE49N

description: frozen tissue extracted by Trizol

source_name: adjacent normal tissue


title: AE14T

description: frozen tissue extracted by Trizol


title: AE04T

description: frozen tissue extracted by Trizol


title: AE51N

description: frozen tissue extracted by Trizol


title: AE46N

description: frozen tissue extracted by Trizol


title: Adult at T10 in LD, time-series experiment 3

description:
C. elegans_LD10_3
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 10 hr time-point during LD entrainment

value: Bristol N2

value: 10 hr


title: AE07T

description: frozen tissue extracted by Trizol


title: AE52N

description: frozen tissue extracted by Trizol


title: AE01T

description: frozen tissue extracted by Trizol


title: AE45N

description: frozen tissue extracted by Trizol


title: PTB/nPTB_Knockdown_Rep3


title: AE43N

description: frozen tissue extracted by Trizol


title: AE41N

description: frozen tissue extracted by Trizol


title: AE42N

description: frozen tissue extracted by Trizol


title: AE50N

description: frozen tissue extracted by Trizol


title: AE03T

description: frozen tissue extracted by Trizol


title: AE44N

description: frozen tissue extracted by Trizol


title: AE39N

description: frozen tissue extracted by Trizol


title: AE48N

description: frozen tissue extracted by Trizol


title: Control_Rep3

source_name: HeLa S3 Cell Line; Mock RNAi


title: AE06T

description: frozen tissue extracted by Trizol

source_name: tumor tissue


title: AE40N

description: frozen tissue extracted by Trizol


title: AE53N

description: frozen tissue extracted by Trizol


title: AE38N

description: frozen tissue extracted by Trizol


title: AE47N

description: frozen tissue extracted by Trizol


title: PTB/nPTB_Knockdown_Rep1


title: AE32N

description: frozen tissue extracted by Trizol


title: AE33N

description: frozen tissue extracted by Trizol


title: AE29N

description: frozen tissue extracted by Trizol


title: AE36N

description: frozen tissue extracted by Trizol


title: AE37N

description: frozen tissue extracted by Trizol


title: AE31N

description: frozen tissue extracted by Trizol


title: AE30N

description: frozen tissue extracted by Trizol


title: Day 20, Hypoxia, Susceptible oysters, pool 3

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

country: France

institute: Ifremer

hyb_protocol: The slides were filled with a pre-hybridization buffer (Chip Spread buffer containing 4× SSC and 0.2% SDS) for 1 h at 42°C. Hybridization was conducted overnight at 42°C in the automatic station according to the manufacturer’s instructions. After hybridization, the arrays were washed twice with Ribowash solution (0.1 M Tris, 0.05 M EDTA, and 0.4 M NaCl) and once with 0.1× SSC, and finally centrifuged (6,000 rpm, 15 s, room temperature) for drying

scan_protocol: Microarray slides were scanned using a Genepix 4000B microarray scanner (Axon Instruments Inc.) with standard dual laser excitation at 532 nm (17 mW) and 635 nm (10 mW) according to the following parameters: Cy5 Photo Multiplier Tube (PMT) 550 and Cy3 PMT 590. Images (16-bit TIF) were analyzed using GenePix pro 5.1 software (Axon Instruments Inc.) according to the manufacturer’s instructions

data_processing: Microarray data were initially processed using the language R/BioConductor (R Development Core Team 2008). LOESS normalization and background correction were performed with the limma package. Missing (NA) values where calculated with an application of the TMev Software (A.I. Saeed, N.K. Bhagabati, J.C. Braisted, W. Liang, V. Sharov, E.A. Howe, et al., TM4 Microarray Software Suite, in: DNA  Microarrays, Part B: Databases and Statistics, Academic Press, 2006: pp. 134-193).

organism: Magallana gigas

source_name: Pooled Digestive Gland, Susceptible Oysters, 20 day of Hypoxia exposure

label_protocol: Five μg of total RNA were directly labeled by reverse transcription using the Direct ChipShot Direct Labeling and Clean-Up Kit (Promega) according to the manufacturer’s recommendations.

extract_protocol: Total RNA extracted using Extract-all Reagent (Eurobio) manufacturer's instructions

treatment_protocol: Hypoxia exposure maintained for 20 d. The oxygen levels were reduced by bubbling nitrogen to obtain 2 mg O2 L-1 (30% oxygen saturation at 20°C)

tag: oyster line

value: Susceptible Oysters

value: Digestive Gland

source_name: Total RNA from pooled entire wild oysters

value: Wild Oysters

value: All Tissues


title: Day 20, Hypoxia, Susceptible oysters, pool 4


title: fem-1 oocyte D3 vs fem-1 oocyte D8 array #6 SL12.02.08

city: Princeton

first: Shijing

last: Luo

state: NJ

address: 160 Carl Icahn Lab, Princeton University

institute: Princeton University

description: fem-1(hc17) oocyte day8 #8 10.22.08 1st collection Cy3 vs. fem-1(hc17) oocyte day3 #5 9.23.08 1st collection 2nd tube Cy5, array #6, SL scanned 12.02.08

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-02 Scan Time : 10:25:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.3.1
Datafile type : Agilent result file

source_name: fem-1 D8

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

extract_protocol: Extraction method : Qiagen Rneasy Kit

value: Day 8 oocytes

source_name: fem-1 D3

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

value: Day 3 oocytes


title: Day 20, Hypoxia, Resistant oysters, pool 3

source_name: Pooled Digestive Gland, Resistant Oysters, 20 day of Hypoxia exposure

value: Resistant Oysters


title: Day 20, Hypoxia, Susceptible oysters, pool 2


title: Day 20, Hypoxia, Resistant oysters, pool 4


title: AE27N

description: frozen tissue extracted by Trizol


title: Day 20, Hypoxia, Susceptible oysters, pool 1


title: Day 20, Hypoxia, Resistant oysters, pool 1


title: sma-4(e729) L4 v N2 L4 #1 WS 4.10.7

description: sma-4(e729) L4 v N2 L4 #1 WS 4.10.7-repeat L4 collection 4.10.07 rehyb of samples from 4.6.

scan_protocol: Pixel Size : 5 Scan Date : 2007-04-10 Scan Time : 10:56:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file


title: AE35N

description: frozen tissue extracted by Trizol


title: fem-1 oocyte D3 vs fem-1 oocyte D8 array #5 SL12.02.08

description: fem-1(hc17) oocyte day8 #7 10.17.08 2nd collection Cy3 vs. fem-1(hc17) oocyte day3 #9 10.12.08 collection Cy5, array #5, SL scanned 12.02.08


title: AE34N

description: frozen tissue extracted by Trizol


title: sma-2x3 L4 v N2 L4 #3 WS 4.6.07

description: sma-2(e502)x3 L4 v N2 L4 #3 WS 4.6.07  L4 collection 4.6.07

scan_protocol: Pixel Size : 5 Scan Date : 2007-04-06 Scan Time : 14:09:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: N2 L4

source_name: sma-2x3 L4


title: fem-1 oocyte D3 vs fem-1 oocyte D8 array #8 SL12.02.08

description: fem-1(hc17) oocyte day8 #11 10.23.08 2nd collection Cy5 vs. fem-1(hc17) oocyte day3 #20 10.22.08 collection Cy3, array #8, SL scanned 12.02.08


title: fem-1 oocyte D3 vs fem-1 oocyte D8 array #3 SL9.13.08

description: fem-1(hc17) oocyte day8 #4 9.5.08 collection Cy5 vs. fem-1(hc17) oocyte day3 #2 9.8.08 collection Cy3, array #3, SL scanned 9.13.08

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-13 Scan Time : 16:02:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: AE28N

description: frozen tissue extracted by Trizol


title: fem-1 oocyte D3 vs fem-1 oocyte D8 array #7 SL12.02.08

description: fem-1(hc17) oocyte day8 #9 10.22.08 2nd collection Cy5 vs. fem-1(hc17) oocyte day3 #6 9.23.08 2nd collection 2nd tube Cy3, array #7, SL scanned 12.02.08


title: Day 20, Hypoxia, Resistant oysters, pool 2


title: AE26N

description: frozen tissue extracted by Trizol


title: Control_Rep1


title: Control_Rep2


title: Day 20, Normoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, 20 day Normoxia


title: AE24N

description: frozen tissue extracted by Trizol


title: Day 20, Normoxia, Susceptible oysters, pool 2


title: AE20N

description: frozen tissue extracted by Trizol


title: Day 20, Normoxia, Susceptible oysters, pool 3


title: Day 20, Normoxia, Resistant oysters, pool 3

source_name: Pooled Digestive Gland, Resistant Oysters, 20 day Normoxia


title: N2 L4 v sma-2x3 L4 #2 DF WS 4.6.07

description: N2 L4 v sma-2x3 L4 #2 DF WS 4.6.07  L4 4.6.07 dye flip technical replicate

scan_protocol: Pixel Size : 5 Scan Date : 2007-04-06 Scan Time : 13:44:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: AE23N

description: frozen tissue extracted by Trizol


title: AE21N

description: frozen tissue extracted by Trizol


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #3 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #10 1.22.09 collection Cy3 vs. fem-1(hc17) oocyte day8 #11 10.23.08 collection Cy5, array #3, SL scanned 2.6.09

scan_protocol: Pixel Size : 5 Scan Date : 2009-02-06 Scan Time : 11:06:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sma-2;fem-1 day 8

source_name: fem-1 day 8


title: Day 20, Normoxia, Resistant oysters, pool 2


title: AE25N

description: frozen tissue extracted by Trizol


title: AE18N

description: frozen tissue extracted by Trizol


title: Day 20, Normoxia, Susceptible oysters, pool 1


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #6 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #7 1.19.09 collection Cy3 vs. fem-1(hc17) oocyte day8 #4 9.6.08 collection Cy5, array #6, SL scanned 2.6.09

scan_protocol: Pixel Size : 5 Scan Date : 2009-02-06 Scan Time : 11:14:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Day 20, Normoxia, Resistant oysters, pool 1


title: Day 20, Normoxia, Resistant oysters, pool 4


title: Day 10, Hypoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, 10 day of Hypoxia exposure


title: AE22N

description: frozen tissue extracted by Trizol


title: AE19N

description: frozen tissue extracted by Trizol


title: AE17N

description: frozen tissue extracted by Trizol


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #9 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #4 11.12.08 collection Cy3 vs. fem-1(hc17) oocyte day8 #2 8.17.08 collection Cy5, array #9, SL scanned 2.6.09

scan_protocol: Pixel Size : 5 Scan Date : 2009-02-06 Scan Time : 13:45:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: sma-2x3 L4 vs N2 L4 #1 WS 4.6.07

description: sma-2(e502)x3 L4 vs N2 L4 #1 WS 4.6.07  L4 4.6.07 dye flip


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #4 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #7 1.19.09 collection Cy3 vs. fem-1(hc17) oocyte day8 #9 10.22.08 collection Cy5, array #4, SL scanned 2.6.09


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #2 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #9 1.21.09 collection Cy3 vs. fem-1(hc17) oocyte day8 #9 10.22.08 collection Cy5, array #2, SL scanned 2.6.09


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #5 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #12 1.30.09 collection Cy5 vs. fem-1(hc17) oocyte day8 #3 9.3.08 collection Cy3, array #5, SL scanned 2.6.09


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #8 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #4 11.12.08 collection Cy5 vs. fem-1(hc17) oocyte day8 #7 10.17.08 collection Cy3, array #8, SL scanned 2.6.09


title: Day 10, Hypoxia, Susceptible oysters, pool 3


title: AE16N

description: frozen tissue extracted by Trizol


title: AE15N

description: frozen tissue extracted by Trizol


title: Day 10, Hypoxia, Resistant oysters, pool 3

source_name: Pooled Digestive Gland, Resistant Oysters, 10 day of Hypoxia exposure


title: Day 10, Hypoxia, Susceptible oysters, pool 2


title: AE13N

description: frozen tissue extracted by Trizol

source_name: adjacent normal tissue


title: Day 10, Hypoxia, Resistant oysters, pool 4


title: sma-2;fem-1 oocyte D8 vs fem-1 oocyte D8 array #1 SL2.6.09

description: sma-2(e502);fem-1(hc17) oocyte day8 #8 1.20.09 collection Cy5 vs. fem-1(hc17) oocyte day8 #8 10.22.08 collection Cy3, array #1, SL scanned 2.6.09


title: Day 10, Hypoxia, Resistant oysters, pool 2


title: AE14N

description: frozen tissue extracted by Trizol


title: AE11N

description: frozen tissue extracted by Trizol


title: Day 10, Normoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, 10 day Normoxia


title: AE08N

description: frozen tissue extracted by Trizol


title: AE10N

description: frozen tissue extracted by Trizol


title: Day 10, Hypoxia, Resistant oysters, pool 1


title: Day 10, Normoxia, Resistant oysters, pool 3

source_name: Pooled Digestive Gland, Resistant Oysters, 10 day Normoxia


title: Day 10, Normoxia, Susceptible oysters, pool 2


title: AE12N

description: frozen tissue extracted by Trizol


title: Day 10, Normoxia, Resistant oysters, pool 4


title: Day 10, Normoxia, Susceptible oysters, pool 3


title: AE06N

description: frozen tissue extracted by Trizol


title: AE04N

description: frozen tissue extracted by Trizol


title: AE09N

description: frozen tissue extracted by Trizol


title: Day 10, Normoxia, Susceptible oysters, pool 1


title: AE05N

description: frozen tissue extracted by Trizol


title: 2h_TGFbeta_total3

city: Heidelberg

last: Feuerborn

state: BW

address: Im Neuenheimer Feld 280

department: Department of cellular and molecular pathology

country: Germany

institute: DKFZ

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430_2.0 mouse arrays

scan_protocol: GeneChips were scanned using the using a GeneChip™ scanner 3000.

data_processing: CEL files were imported to R statistical package version 2.7.1 using R Affy package version 1.18.2. Microarray data was subjected to VSN normalization. Significance analysis was performed using the bioconductor package SAMR, which implements SAM statistics in R.

source_name: cell culture

label_protocol: Total RNA and enriched RNA were linearily amplified using GeneChip® Two-Cycle Synthesis Kit (Affymetrix) according to the suppliers instructions.

growth_protocol: Cells were seeded 24 hrs before treatment and cultured under standard growth conditions (37°C, 5%CO2)

extract_protocol: RNA was extracted using Qiagen RNAeasy Mini Kit according to the manufacturer's instruction. 4sU labeled RNA was further enriched via mercury-based chromatography

treatment_protocol: Cells were treated with growth media containing 200µM 4sU or media containing 200µM 4sU and 5ng/ml TGF-b1

tag: treatment

tag: cell type

value: NMuMG


title: Day 10, Normoxia, Resistant oysters, pool 2


title: AE07N

description: frozen tissue extracted by Trizol


title: Day 2, Hypoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, 2 day of Hypoxia exposure


title: AE03N

description: frozen tissue extracted by Trizol


title: Day 10, Normoxia, Resistant oysters, pool 1

source_name: Total RNA from pooled entire wild oysters


title: AE02N

description: frozen tissue extracted by Trizol


title: AE01N

description: frozen tissue extracted by Trizol


title: 2h_TGFbeta_total2


title: 2h_TGFbeta_total1


title: 2h_TGFbeta_enriched3


title: Day 2, Hypoxia, Susceptible oysters, pool 3


title: 2h_TGFbeta_enriched1


title: Day 2, Hypoxia, Resistant oysters, pool 3

source_name: Pooled Digestive Gland, Resistant Oysters, 2 day of Hypoxia exposure


title: Day 2, Hypoxia, Resistant oysters, pool 4


title: Day 2, Hypoxia, Resistant oysters, pool 1


title: Day 2, Hypoxia, Susceptible oysters, pool 1


title: Day 2, Hypoxia, Resistant oysters, pool 2


title: 2h_TGFbeta_enriched2


title: 2h_co._total1


title: 2h_co._total3


title: Day 2, Normoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, 2 day Normoxia


title: Day 2, Normoxia, Susceptible oysters, pool 3


title: Day 2, Normoxia, Susceptible oysters, pool 1


title: Day 2, Normoxia, Susceptible oysters, pool 2


title: Day 2, Normoxia, Resistant oysters, pool 4

source_name: Pooled Digestive Gland, Resistant Oysters, 2 day Normoxia


title: 2h_co._total2


title: 2h_co._enriched1


title: 2h_co._enriched3


title: 2h_co._enriched2


title: Day 2, Normoxia, Resistant oysters, pool 3


title: Day 2, Normoxia, Resistant oysters, pool 2


title: Day 0, Normoxia, Susceptible oysters, pool 4

source_name: Pooled Digestive Gland, Susceptible Oysters, Starting point


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayG_081212

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

source_name: Sample Type: Cells, Cell Type: CH12.LX

value: No

value: 1X10^5 cells/ml, 25ml in P150s

value: hr

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

value: ChIP


title: ATDC5_CHX+PBS

city: los angeles

first: wei wei

last: chen

address: 10833 Le Conte Avenue

institute: UCLA

description: control

hyb_protocol: Target preparation and hybridization to the Affymetrix Murine 430 2.0 GeneChip was carried out following the standard protocol (http://www.affymetrix.com).

scan_protocol: Standard Affymetrix protocol.

data_processing:
The data obtained from the hybridization was preprocessed using Affymetrix GeneChip Command Console Software (AGCC) and Expression Console Software to generate probe set intensity data (Affymetrix, Santa Clara, CA).
MAS5.0 signal intensity data.

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA from ATDC5 cells for microarray and real-time PCR evaluation was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). Following ethanol precipitation, total RNA was applied to an RNeasy column (Qiagen, Valencia, CA) for further purification and treated with DNase according to the manufacturer’s protocol.

value: chondrogenic cell line ATDC5

tag: agent

value: CHX+PBS(control)


title: Day 2, Normoxia, Resistant oysters, pool 1

tag: tissue


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayG_081212

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Jurkat_pMIGR-EGFP-Bcl11b_overexpression

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

hyb_protocol: For hybridization 20 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, of which  15 µg fragmented cRNA were added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA and 10% DMSO in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Human Gene U133 Plus 2.0 were loaded with 200 µl hybridization cocktail (containing 10 µg of fragmented cRNA) and hybridized 16 h at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were washed and stained using the GeneChip FluidicsStation 450 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Scanner 3000 (Affymetrix, Santa Clara, CA, USA) under the control of GeneChip Operating Software GCOS (Affymetrix, Santa Clara, CA, USA).

data_processing: Analysis of CEL-files was performed in GeneChip Operating Software GCOS 1.4 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 500.

source_name: Jurkat cells

label_protocol: The GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA) were used for synthesis of labeled material for hybridization. The protocol started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of double stranded DNA, DNA purification, in-vitro transcription for amplification and labeling, and purification of resulting cRNA according to the manufacturer’s protocols. Concentration and quality of cRNA were measured with a NanoDrop ND-1000 photometer and an Agilent 2100 Bioanalyzer, respectively.

extract_protocol: Cell were lysed in Trizol Reagent (Invitrogen) and total RNA was extracted according to the manufacturer's instructions. RNA was quantified spectrophotometrically (NanoDrop ND-1000; Thermo Fisher Scientific, Wilmington, DE, USA) and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA)

treatment_protocol: The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above.   For recombinant retrovirus production, non-confluent GP2-293 cells were co-transfected with 10 μg of purified pVSV-G and empty pMIGR plasmid (mock) or pMIGR encoding BCL11B. The transfection procedure was performed using CalPhos Mammalian Transfection Kit (Clontech Laboratories, CA, USA) according to the manufacturer’s instructions. The retrovirus-containing media were collected 48h after transfection and used immediately or stored at 4˚C and used within 7 days. To transduce the target cells, the retroviral supernatants were supplemented with 8 μg/ml Polybrene (Sigma Chemicals, Germany) and added to exponentially growing Jurkat cells for 8 hours. The procedure was repeated three times. The efficiency of gene transfer was estimated by FACS detection of EGFP reporter gene.

tag: vector

tag: protocol

value: BCL11B overexpression


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayG_081212

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

treatment_protocol: in vitro Treatment: DMSO, Units of Treatment Repeat: nM, Treatment Duration: 1, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: Media


title: Jurkat_pMIGR-EGFP_control

growth_protocol: The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above.

value: pMIGR-EGFP

value: control


title: Day 0, Normoxia, Susceptible oysters, pool 3

value: Susceptible Oysters

value: Digestive Gland


title: Day 0, Normoxia, Susceptible oysters, pool 1

value: Wild Oysters

value: All Tissues


title: Day 0, Normoxia, Susceptible oysters, pool 2


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayG_090108

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayG_090108: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: ATDC5_CHX+Nell-1

description: treatment


title: Day 0, Normoxia, Resistant oysters, pool 4

source_name: Pooled Digestive Gland, Resistant Oysters, Starting point


title: Day 0, Normoxia, Resistant oysters, pool 3


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayD_081211

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayD_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayG_081212

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Day 0, Normoxia, Resistant oysters, pool 1


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayD_090108

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayD_090108: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayD_081211

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayD_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayE_081211

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayE_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayD_081211

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayD_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayD_081211

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayD_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Day 0, Normoxia, Resistant oysters, pool 2


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayF_090108

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayF_090108: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayD_081211

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayD_081211: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayF_081212

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayF_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayF_081212

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayF_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Day 2, Hypoxia, Susceptible oysters, pool 2


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayF_081212

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayF_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayF_081212

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayF_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayF_081212

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayF_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: 70-4

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: Afferent Lymph was collected from up to 5 pen raised, nematode naïve, outbreed Romney sheep (Tag No’s 1001, 1002, 1003, 1004, 1006). During this time a Pre-Infection sample was collected, the sheep were immunised by 3 truncated (2 week) T. colubiformis infections (40,000 Tc) followed by a Challenge Infection with 40,000 T. colubiformis L3 (Challenge Infection weeks 1-3). The Challenge Infection will enable us to determine changes in gene expression when the sheep gut rejects the parasitic nematodes.

hyb_protocol: Micro array slides were prehybridized in a preheated (42oC) 0.22 µm filtered solution of 5 x SSC, 0.1% SDS and 0.25% BSA (A-788; Sigma Chemical company, St. Louis, MO, USA) for 20 min at 42oC. Slides were rinsed in deionised water then isopropanol and air dried before hybridization. cDNA labeled samples were heat-denatured (95oC for 5 min) and mixed with 60 µL of pre-warmed (68oC) SlideHyb No1 (Ambion, Austin, TX, USA) added. The final cDNA labeled solution was loaded onto the slides with lifter coverslips (Erie Scientific, Portsmouth, NH, USA). Hybridizations were conducted for 20 h at 52oC in sealed humidified chambers (CMT Hybridization Chambers, Corning, NY, USA). Following hybridization, slides were washed for 5 min each in (1) 2 x SSC, 0.1% SDS, (2) 1 x SSC and (3) 0.1 x SSC then centrifuged at 1000 g for 5 min

scan_protocol: The slides were stored in the dark to minimize photo bleaching, and scanned for both dye channels at 532 and 635 nm within two days using an GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with a 10-μm resolution. The photomultiplier tube voltage was adjusted to obtain an equal global intensity in both channels.

data_processing: The normalization method used as in PubMed ID 15231532 [Bioinformatics. 2004 Nov 22;20(17):3196-205].

organism: Ovis aries

source_name: Pre-Infection Pool

label_protocol: Fluorescent-labeling reactions used the SuperScript Indirect cDNA Labeling System (Invitrogen, Auckland, NZ). cDNA synthesised from 20µg total appropriately pooled RNA was labeled in the presence of either mono-functional N-hydroxysuccinimide (NHS)-ester Cy5 or Cy3 dyes (Amersham Biosciences, Piscataway, NJ, USA). Labeled cDNAs were purified to remove unincorporated dyes using the supplied SNAP columns, combined and concentrated to 10 µL by ethanol precipitation.

growth_protocol: Lymph cells were collected daily, RNA extracted and pooled for each weekly period for all sheep

extract_protocol: Total RNA was extracted using Trizol® Reagent (Invitrogen Auckland, NZ), a modification of the acid guanidinium thiocyanate-phenol-chloroform extraction method according to the manufacturers’ protocol and incorporated the optional step (for tissues with high content of protein, fat, polysaccharides) during sample homogenization. The appropriate RNA samples were pooled and further purified using an RNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: Pre-Infection Pool

value: Afferent Lymph collected over a 12 week period from sheep 1001-6

tag: strain

source_name: Challenge Infection week 2 Pool

treatment_protocol: Challenge Infection week 2 Pool


title: 70-3

value: up to 5 pen raised, nematode naïve, outbreed Romney sheep


title: 70-26

source_name: Challenge Infection week 3 Pool

treatment_protocol: Challenge Infection week 3 Pool


title: 70-16

source_name: Challenge Infection week 3 pool

treatment_protocol: Challenge Infection week 3 pool

source_name: Challenge Infection week 2 pool

treatment_protocol: Challenge Infection week 2 pool


title: 70-21

description: Afferent Lymph was collected over a 8 week period from up to 5 pen raised, nematode naïve, outbreed Romney sheep (Tag No’s 1001, 1002, 1003, 1004, 1006). During this time a Pre-Infection sample was collected, the sheep were immunised by 3 truncated (2 week) T. colubiformis infections (40,000 Tc L3, Immunising Infections 1-3). The treatment regime (shown below) will enable us to determine changes in gene expression during the development of immunity

source_name: Immunising Infection 3 Pool

treatment_protocol: Immunising Infection 3 Pool

value: Afferent Lymph collected over a 8 week period from sheep 1001-6

source_name: Immunising Infection 1 Pool

treatment_protocol: Immunising Infection 1 Pool


title: 70-28

source_name: Challenge Infection week 1 Pool

treatment_protocol: Challenge Infection week 1 Pool


title: Male Breast 13

description: diagnosis at Bari

source_name: breast

value: male

value: breast cancer tumor


title: 70-20

source_name: Immunising Infection 2 Pool

treatment_protocol: Immunising Infection 2 Pool


title: 70-15


title: 70-22


title: 70-23


title: Male Breast 14

description: diagnosis at Bari


title: 70-24


title: 70-27


title: Male Breast 12

description: diagnosis at Bari


title: Male Breast 15

description: diagnosis at Bari


title: Male Breast 11

description: diagnosis at Bari


title: Male Breast 10

description: diagnosis at Bari


title: 70-19


title: 70-14

source_name: Immunising Infection 2 pool

treatment_protocol: Immunising Infection 2 pool

source_name: Immunising Infection 1 pool

treatment_protocol: Immunising Infection 1 pool


title: 70-2

source_name: Pre-Infection pool

treatment_protocol: Pre-Infection pool

source_name: Immunising Infection 3 pool

treatment_protocol: Immunising Infection 3 pool


title: Male Breast 9

description: diagnosis at Bari


title: Male Breast 8

description: diagnosis at Bari


title: 70-18

source_name: Pre Infection pool

treatment_protocol: Pre Infection pool


title: 70-1


title: Male Breast 7

description: diagnosis at Bari


title: 70-11


title: Male Breast 5

description: diagnosis at Bari


title: 70-25


title: 70-17


title: Male Breast 3

description: diagnosis at Bari


title: Male Breast 4

description: diagnosis at Bari


title: Male Breast 6

description: diagnosis at Bari


title: Male Breast 2

description: diagnosis at Bari


title: Male Breast 1

description: diagnosis at Bari


title: 70-9

description: Afferent Lymph was collected over a 8 week period from up to 5 pen raised, nematode naïve, outbreed Romney sheep (Tag No’s  1001, 1002, 1003, 1004, 1006). During this time a Pre-Infection sample was collected, the sheep were immunised by 3 truncated (2 week) T. colubiformis infections (40,000 Tc L3, Immunising Infections 1-3). The treatment regime (shown below) will enable us to determine changes in gene expression during the development of immunity

label_protocol: Fluorescent-labeling reactions used the SuperScript Indirect cDNA Labeling System (Invitrogen, Auckland, NZ). cDNA synthesised from 20µg total appropriately pooled RNA was labeled in the presence of either mono-functional N-hydroxysuccinimide (NHS)-ester Cy5 or Cy3 dyes (Amersham Biosciences, Piscataway, NJ, USA).  Labeled cDNAs were purified to remove unincorporated dyes using the supplied SNAP columns, combined and concentrated to 10 µL by ethanol precipitation.

extract_protocol: Total RNA was extracted using Trizol® Reagent (Invitrogen Auckland, NZ), a modification of the acid guanidinium thiocyanate-phenol-chloroform extraction method according to the manufacturers’ protocol and incorporated the optional step (for tissues with high content of protein, fat, polysaccharides) during sample homogenization.  The appropriate RNA samples were pooled and further purified using an RNeasy kit (Qiagen, Hilden, Germany).


title: N35

status: Public on Aug 31 2010

city: RIYADH 11211

first: ABDUL

middle: KHALID

last: SIRAJ

state: KSA

department: HUMAN CANCER GENOMIC

country: Saudi Arabia

institute: KING FAISAL SPECIALIST HOSPITAL & RESEARCH CENTER

description: Gene expression data from Normal paired Tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using a commercially available software package, Partek Genomics Suite 6.4 (Partek Incorporated, Missouri, USA), PLIER algorithm using default analysis settings and global scaling as normalization method and t-test  to assess differentially expressed genes. The Strand Genomics Avadis software package (Strand Genomics Pvt Ltd, http://www.strandgenomics.com) was employed for hierarchical clustering of differentially expressed genes.

source_name: normal paired tissue

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

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

value: Female


title: N31

value: Male


title: N33


title: N32


title: N28


title: N29


title: N27


title: N21


title: N23


title: N24


title: N22


title: N26


title: N25


title: N20


title: N19


title: N15


title: N16


title: N14


title: N8


title: N3


title: Control_Rep5

source_name: HeLa S3 Cell Line; Mock RNAi

treatment_protocol: Transfections were carried out with Lipofectamine 2000 (Invitrogen). For siRNA transfections, typically cells were seeded at 2 x 105 cells/well and were transfected with 20pmols of siRNA and 2.5 ml of Lipofectamine 2000 twice during two consecutive days. Samples were harvested for protein or RNA extraction 3 days after the first transfection.

value: HeLa S3


title: CC46

description: Gene expression data from Colon Tumour Sample

source_name: colon tumour


title: CC45


title: N2


title: PTB/nPTB_Knockdown_Rep3

source_name: HeLa S3 Cell Line; PTB/nPTB RNAi


title: PTB/nPTB_Knockdown_Rep2


title: CC40


title: PTB/nPTB_Knockdown_Rep4


title: CC42


title: CC43


title: CC41


title: N11


title: CC36


title: CC35


title: Control_Rep2


title: CC37


title: CC38


title: PTB/nPTB_Knockdown_Rep1


title: PTB/nPTB_Knockdown_Rep5


title: CC44


title: CC34


title: PTB/nPTB_Knockdown_Rep6


title: Control_Rep1


title: N12


title: CC33


title: N9


title: Control_Rep4


title: Control_Rep3


title: Control_Rep6


title: CC28


title: CC26


title: CC32


title: CC29


title: CC16


title: CC20


title: CC27


title: CC22


title: CC13


title: CC11


title: CC25


title: CC6


title: CC21


title: CC23


title: CC18


title: CC24


title: CC12


title: CC2


title: CC8


title: Biliary Atresia Patient 46

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from human liver.

hyb_protocol: Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45 degC  on the human HG-U133 Plus 2.0 GeneChip array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data was analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to the median of all samples.

source_name: Human Liver Wedge Biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).

extract_protocol: RNeasy Mini Kit (QIAGEN, California, USA)

treatment_protocol: Flash Frozen

value: Liver Wedge Biopsy

tag: molecular group

value: Unclassified


title: CC17


title: Biliary Atresia Patient 47

description: Gene expression data from human liver.


title: CC30


title: CC3


title: Biliary Atresia Patient 44

description: Gene expression data from human liver.


title: Biliary Atresia Patient 41

description: Gene expression data from human liver.

value: Inflammation


title: Biliary Atresia Patient 43

description: Gene expression data from human liver.


title: Biliary Atresia Patient 42

description: Gene expression data from human liver.


title: Biliary Atresia Patient 45

description: Gene expression data from human liver.


title: Biliary Atresia Patient 39

description: Gene expression data from human liver.


title: Biliary Atresia Patient 34

description: Gene expression data from human liver.


title: Biliary Atresia Patient 36

description: Gene expression data from human liver.


title: Biliary Atresia Patient 35

description: Gene expression data from human liver.


title: Biliary Atresia Patient 26

description: Gene expression data from human liver.

value: Fibrosis


title: Biliary Atresia Patient 38

description: Gene expression data from human liver.


title: Biliary Atresia Patient 24

description: Gene expression data from human liver.


title: Biliary Atresia Patient 28

description: Gene expression data from human liver.


title: Biliary Atresia Patient 31

description: Gene expression data from human liver.


title: Biliary Atresia Patient 30

description: Gene expression data from human liver.


title: Biliary Atresia Patient 19

description: Gene expression data from human liver.


title: Biliary Atresia Patient 22

description: Gene expression data from human liver.


title: Biliary Atresia Patient 21

description: Gene expression data from human liver.


title: Biliary Atresia Patient 29

description: Gene expression data from human liver.


title: Biliary Atresia Patient 32

description: Gene expression data from human liver.


title: Biliary Atresia Patient 33

description: Gene expression data from human liver.


title: Biliary Atresia Patient 40

description: Gene expression data from human liver.


title: Biliary Atresia Patient 13

description: Gene expression data from human liver.


title: Biliary Atresia Patient 27

description: Gene expression data from human liver.


title: Biliary Atresia Patient 18

description: Gene expression data from human liver.


title: Biliary Atresia Patient 16

description: Gene expression data from human liver.


title: Biliary Atresia Patient 15

description: Gene expression data from human liver.


title: Biliary Atresia Patient 23

description: Gene expression data from human liver.


title: Biliary Atresia Patient 25

description: Gene expression data from human liver.


title: Biliary Atresia Patient 37

description: Gene expression data from human liver.


title: Biliary Atresia Patient 20

description: Gene expression data from human liver.


title: Biliary Atresia Patient 14

description: Gene expression data from human liver.


title: Biliary Atresia Patient 11

description: Gene expression data from human liver.


title: Biliary Atresia Patient 17

description: Gene expression data from human liver.


title: Biliary Atresia Patient 12

description: Gene expression data from human liver.


title: Biliary Atresia Patient 10

description: Gene expression data from human liver.


title: Biliary Atresia Patient 9

description: Gene expression data from human liver.


title: Biliary Atresia Patient 8

description: Gene expression data from human liver.


title: Biliary Atresia Patient 7

description: Gene expression data from human liver.


title: Biliary Atresia Patient 6

description: Gene expression data from human liver.


title: Biliary Atresia Patient 5

description: Gene expression data from human liver.


title: Biliary Atresia Patient 2

description: Gene expression data from human liver.


title: Biliary Atresia Patient 3

description: Gene expression data from human liver.


title: Skin Type VI, Patient 8

first: Vincent

last: Hearing

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

hyb_protocol: Oligo-cDNA microarray hybridization was performed according to the National Cancer Institute in-house protocol. A universal human reference RNA (Stratagene, La Jolla, CA) was used as a control. cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C.

scan_protocol: Scanned on GenePix 4000B. Images were quantified using GenePix Pro (version 5.0.1.24).

data_processing: The data were processed by filtered 11,771 out of 36,288 spots with at least half of the corresponding intensity measures (CIMs) less than the mean of the background signal of the array plus three times the standard deviation of the background for further analysis. Data were then processed by subtracting background signals, conducting loess within-array and quantile between-array on the common reference channel normalization. One spot, Block 45, Column 18, Row 14, an empty well but passing the filtering criteria, was excluded from the data matrix.

source_name: Skin Type VI, Patient 8

extract_protocol: Total RNA from fibroblats was prepared using RNAeasy kit (Qiagen, Valencia, CA).

tag: phototypes

value: Type VI

source_name: Universal Human Reference RNA

tag: reference

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together. Provided by Stratagene (La Jolla, CA).


title: Cerebullum_wild-type control_AG1_rep3

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Gene expression profiling data from cerebellum

hyb_protocol: Cy3-labeled cRNA (1.65 μg) from each sample was hybridized to an Agilent Mouse Genome microarrays in a 4x44k format, i.e., four samples were simultaneously processed on one chip.

scan_protocol: According to Agilent protocol. Scanner Name: Agilent Technologies Scanner G2505B US23502303.

data_processing: Intensity data were extracted from the scanned image with background subtracted and normalized using Feature Extraction 9.5 (Agilent Technologies) followed by global scaling so that the median intensity for each array is 1000.

source_name: cerebellum from Npc1 (BALB/cNctr-Npc1m1N/J) mice

label_protocol: 500 ng of total RNA was converted into labeled cRNA with nucleotides coupled to the fluorescent dye Cy3 using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol: Npc1(BALB/cNctr-Npc1m1N/J) heterozygous male and female mice on BALB/c background were purchased from Jackson Laboratory (Bar Harbor, MN) and housed in the vivarium under protocols approved by the local IACUC. Mice had free access to water and food; Npc1-/- mice were produced by in-house breeding.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy Mini Kit according to the manufacturer instructions (Qiagen, Valencia, CA).

treatment_protocol: Mice were genotyped using tail DNA with PCR methods described by Baudray (Baudray et al., 2003). Cerebelli were collected from 8 mice (4 Npc1+/+mice, and 4 Npc1-/- mice) at 3 weeks postnatal and were snap-frozen in liquid nitrogen.

value: cerebellum

value: Npc1 (BALB/cNctr-Npc1m1N/J)

tag: genotype/variation

value: wild-type


title: Biliary Atresia Patient 4

description: Gene expression data from human liver.


title: Skin Type VI, Patient 7

source_name: Skin Type VI, Patient 7

label_protocol: cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C.


title: Cerebullum_wild-type control_AG1_rep1


title: Skin Type VI, Patient 16

source_name: Skin Type VI, Patient 16


title: Cerebullum_wild-type control_AG1_rep4


title: Skin Type I, Patient 26

source_name: Skin Type I, Patient 26

value: Type I


title: Skin Type VI, Patient 17

source_name: Skin Type VI, Patient 17


title: Skin Type III, Patient 6

source_name: Skin Type III, Patient 6

value: Type III


title: Skin Type VI, Patient 28

source_name: Skin Type VI, Patient 28


title: Skin Type III, Patient 9

source_name: Skin Type III, Patient 9


title: Cerebullum_wild-type control_AG1_rep2


title: Skin Type I, Patient 19

source_name: Skin Type I, Patient 19


title: Skin Type I, Patient 15

source_name: Skin Type I, Patient 15


title: Skin Type III, Patient 14

source_name: Skin Type III, Patient 14


title: Skin Type III, Patient 23

source_name: Skin Type III, Patient 23


title: Cerebellum_NPC_AG1_rep3


title: Cerebellum_NPC_AG1_rep1


title: Cerebellum_NPC_AG1_rep2


title: Biliary Atresia Patient 1

description: Gene expression data from human liver.


title: Cerebellum_NPC_AG1_rep4


title: Skin Type III, Patient 13

source_name: Skin Type III, Patient 13


title: Skin Type I, Patient 4

source_name: Skin Type I, Patient 4


title: Skin Type I, Patient 12

source_name: Skin Type I, Patient 12