title: PLACEBO CLINICAL SUBJECT 2, 72 HOURS POST-DOSING

status: Public on Oct 06 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: 1 of 9 clinical subjects enrolled at the General Clincial Research Center at the University of North Carolina Hospital with IRB approval. Placebo subject, received a 4 gram bolus of palcebo 0 hours (morning of the 4th day)

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver system (v6.0) (Rosetta Biosoftware, Kirkland, WA). Each patient was normalized to there own 0 hr data. Significant differential expression was determined by comparing APAP treated subjects to placebos.

source_name: Stratagene Universal Human Reference total RNA

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Absolutely RNA Miniprep Kit: Glass fiber based, Stratagene, La Jolla, CA

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

source_name: Peripheral blood collected in PAXgene tubes, 72 hrs after APAP

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was isolated utilizing the PAXgene blood RNA isolation kit (PreAnalytiX/ QIAGEN, Hilden, Germany) according to the manufacturer’s protocol, including the optional on-column DNase digestion, except that the centrifugation time after proteinase K diges

tag: cell type

value: Peripheral blood

tag: time point

value: 72 hrs after APAP

value: 22 yr old

tag: ethnicity

value: Asian

tag: gender

value: female

tag: weight

value: 55 kgs


title: PLACEBO CLINICAL SUBJECT 1, 72 HOURS POST-DOSING

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: age

value: 36 yr old

value: Caucasian

value: 66 kgs


title: APAP CLINICAL SUBJECT 4, 96 HOURS POST-DOSING

description: 1 of 9 clinical subjects enrolled at the General Clincial Research Center at the University of North Carolina Hospital with IRB approval. IF APAP subject, received a 4 gram bolus of APAP 0 hours (morning of the 4th day)

source_name: Peripheral blood collected in PAXgene tubes, 96 hrs after APAP

value: 96 hrs after APAP

value: 27 yr old

value: African-American

value: 78 kgs


title: PLACEBO CLINICAL SUBJECT 2, 96 HOURS POST-DOSING


title: APAP CLINICAL SUBJECT 1, 18 HOURS POST- DOSING

source_name: Peripheral blood collected in PAXgene tubes, 18 hrs after APAP

value: 18 hrs after APAP

value: 45 yr old

value: male

value: 81 kgs


title: PLACEBO CLINICAL SUBJECT 1, 0 HOUR

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

source_name: Peripheral blood collected in PAXgene tubes, immediatedly prior to APAP administration

value: Peripheral blood


title: PLACEBO CLINICAL SUBJECT 2, 48 HOURS POST-DOSING

source_name: Peripheral blood collected in PAXgene tubes, 48 hrs after APAP

value: 48 hrs after APAP

value: 22 yr old


title: PLACEBO CLINICAL SUBJECT 3, 6 HOURS POST- DOSING

source_name: Peripheral blood collected in PAXgene tubes, 6 hrs after APAP

value: 6 hrs after APAP

value: 24 yr old

value: 54 kgs


title: PLACEBO CLINICAL SUBJECT 1, 6 HOURS POST- DOSING

value: 36 yr old

value: Caucasian

value: female


title: PLACEBO CLINICAL SUBJECT 2, (-)48 HOURS BEFORE DOSING

source_name: Peripheral blood collected in PAXgene tubes, 48 hrs before APAP

value: 48 hrs before APAP

value: Asian

value: 55 kgs


title: PLACEBO CLINICAL SUBJECT 1, 48 HOURS POST-DOSING

value: 66 kgs


title: APAP CLINICAL SUBJECT 4, 72 HOURS POST-DOSING

value: 72 hrs after APAP

value: 27 yr old

value: African-American

value: 78 kgs


title: PLACEBO CLINICAL SUBJECT 2, 18 HOURS POST- DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

value: Peripheral blood

value: 18 hrs after APAP


title: PLACEBO CLINICAL SUBJECT 3, 18 HOURS POST- DOSING

value: male


title: PLACEBO CLINICAL SUBJECT 3, (-)24 HOURS BEFORE DOSING

source_name: Peripheral blood collected in PAXgene tubes, 24 hrs before APAP

value: 24 hrs before APAP

value: 24 yr old


title: PLACEBO CLINICAL SUBJECT 2, 6 HOURS POST- DOSING

value: 6 hrs after APAP

value: 22 yr old


title: APAP CLINICAL SUBJECT 6, 6 HOURS POST- DOSING

value: 39 yr old

value: Caucasian

value: female


title: PLACEBO CLINICAL SUBJECT 3, 0 HOUR

value: immediatedly prior to APAP administration

value: 54 kgs


title: APAP CLINICAL SUBJECT 5, (-)24 HOURS BEFORE DOSING


title: PLACEBO CLINICAL SUBJECT 2, 0 HOUR

value: Asian

value: 55 kgs


title: PLACEBO CLINICAL SUBJECT 3, (-)48 HOURS BEFORE DOSING

value: 48 hrs before APAP


title: PLACEBO CLINICAL SUBJECT 3, 48 HOURS POST-DOSING

value: 48 hrs after APAP


title: PLACEBO CLINICAL SUBJECT 2, 24 HOURS POST-DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

source_name: Peripheral blood collected in PAXgene tubes, 24 hrs after APAP

value: 24 hrs after APAP


title: PLACEBO CLINICAL SUBJECT 3, (-)72 HOURS BEFORE DOSING

source_name: Peripheral blood collected in PAXgene tubes, 72 hrs before APAP

value: Peripheral blood

value: 72 hrs before APAP


title: PLACEBO CLINICAL SUBJECT 3, 96 HOURS POST-DOSING

value: 96 hrs after APAP

value: male


title: APAP CLINICAL SUBJECT 6, 48 HOURS POST-DOSING


title: APAP CLINICAL SUBJECT 4, 48 HOURS POST-DOSING

value: 27 yr old

value: African-American

value: 78 kgs


title: PLACEBO CLINICAL SUBJECT 1, (-)72 HOURS BEFORE DOSING

value: 36 yr old

value: Caucasian

value: 66 kgs


title: PLACEBO CLINICAL SUBJECT 3, 72 HOURS POST-DOSING

value: 72 hrs after APAP

value: 24 yr old

value: 54 kgs


title: APAP CLINICAL SUBJECT 6, (-)24 HOURS BEFORE DOSING

value: 24 hrs before APAP

value: 39 yr old

value: female

value: 55 kgs


title: APAP CLINICAL SUBJECT 6, (-)72 HOURS BEFORE DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

value: Peripheral blood


title: PLACEBO CLINICAL SUBJECT 2, (-)72 HOURS BEFORE DOSING

value: 72 hrs before APAP

value: 22 yr old

value: Asian


title: PLACEBO CLINICAL SUBJECT 1, (-)48 HOURS BEFORE DOSING

value: 48 hrs before APAP


title: PLACEBO CLINICAL SUBJECT 1, (-)24 HOURS BEFORE DOSING


title: APAP CLINICAL SUBJECT 6, 72 HOURS POST-DOSING


title: APAP CLINICAL SUBJECT 6, 24 HOURS POST-DOSING

value: 24 hrs after APAP


title: APAP CLINICAL SUBJECT 5, 48 HOURS POST-DOSING

value: 48 hrs after APAP

value: male

value: 78 kgs


title: PLACEBO CLINICAL SUBJECT 2, (-)24 HOURS BEFORE DOSING


title: PLACEBO CLINICAL SUBJECT 3, 24 HOURS POST-DOSING

value: Caucasian


title: APAP CLINICAL SUBJECT 6, 96 HOURS POST-DOSING

value: 96 hrs after APAP


title: APAP CLINICAL SUBJECT 5, 6 HOURS POST- DOSING

value: 6 hrs after APAP


title: APAP CLINICAL SUBJECT 5, 96 HOURS POST-DOSING


title: PLACEBO CLINICAL SUBJECT 1, 18 HOURS POST- DOSING

value: 18 hrs after APAP

value: 36 yr old

value: 66 kgs


title: APAP CLINICAL SUBJECT 5, 72 HOURS POST-DOSING

value: 72 hrs after APAP


title: APAP CLINICAL SUBJECT 5, 24 HOURS POST-DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.


title: APAP CLINICAL SUBJECT 5, (-)72 HOURS BEFORE DOSING

value: Peripheral blood


title: APAP CLINICAL SUBJECT 6, 0 HOUR

value: immediatedly prior to APAP administration

value: 39 yr old

value: female

value: 55 kgs


title: PLACEBO CLINICAL SUBJECT 1, 24 HOURS POST-DOSING

value: 24 hrs after APAP


title: APAP CLINICAL SUBJECT 6, 18 HOURS POST- DOSING


title: APAP CLINICAL SUBJECT 6, (-)48 HOURS BEFORE DOSING

value: 48 hrs before APAP


title: APAP CLINICAL SUBJECT 5, 0 HOUR

value: 22 yr old

value: male


title: APAP CLINICAL SUBJECT 5, (-)48 HOURS BEFORE DOSING

value: Caucasian

value: 78 kgs


title: APAP CLINICAL SUBJECT 4, 6 HOURS POST- DOSING

value: 6 hrs after APAP

value: 27 yr old

value: African-American


title: APAP CLINICAL SUBJECT 5, 18 HOURS POST- DOSING

value: 18 hrs after APAP


title: APAP CLINICAL SUBJECT 4, (-)48 HOURS BEFORE DOSING


title: APAP CLINICAL SUBJECT 3, 24 HOURS POST-DOSING

value: 28 yr old

value: 60 kgs


title: APAP CLINICAL SUBJECT 2, 24 HOURS POST-DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

value: Peripheral blood

value: 26 yr old

value: 73 kgs


title: APAP CLINICAL SUBJECT 1, 6 HOURS POST- DOSING

value: 45 yr old

value: 81 kgs


title: APAP CLINICAL SUBJECT 1, 96 HOURS POST-DOSING

value: 96 hrs after APAP


title: APAP CLINICAL SUBJECT 1, 0 HOUR

value: immediatedly prior to APAP administration


title: APAP CLINICAL SUBJECT 1, 24 HOURS POST-DOSING

value: 24 hrs after APAP

value: male


title: APAP CLINICAL SUBJECT 1, 72 HOURS POST-DOSING

value: 72 hrs after APAP


title: APAP CLINICAL SUBJECT 2, 6 HOURS POST- DOSING

value: 6 hrs after APAP

value: female


title: APAP CLINICAL SUBJECT 1, 48 HOURS POST-DOSING

value: 48 hrs after APAP

value: African-American


title: APAP CLINICAL SUBJECT 2, 18 HOURS POST- DOSING

value: 18 hrs after APAP


title: APAP CLINICAL SUBJECT 1, (-)72 HOURS BEFORE DOSING

value: 72 hrs before APAP


title: APAP CLINICAL SUBJECT 2, (-)48 HOURS BEFORE DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

value: 48 hrs before APAP


title: APAP CLINICAL SUBJECT 1, (-)48 HOURS BEFORE DOSING

value: Peripheral blood


title: APAP CLINICAL SUBJECT 2, (-)24 HOURS BEFORE DOSING

value: 24 hrs before APAP

value: 26 yr old

value: 73 kgs


title: APAP CLINICAL SUBJECT 4, 24 HOURS POST-DOSING

value: 27 yr old

value: 78 kgs


title: APAP CLINICAL SUBJECT 1, (-)24 HOURS BEFORE DOSING

value: 45 yr old

value: 81 kgs


title: APAP CLINICAL SUBJECT 4, (-)72 HOURS BEFORE DOSING


title: APAP CLINICAL SUBJECT 4, (-)24 HOURS BEFORE DOSING


title: APAP CLINICAL SUBJECT 2, (-)72 HOURS BEFORE DOSING


title: APAP CLINICAL SUBJECT 3, 48 HOURS POST-DOSING

value: 28 yr old

value: male

value: 60 kgs


title: APAP CLINICAL SUBJECT 2, 0 HOUR

value: immediatedly prior to APAP administration

value: female


title: APAP CLINICAL SUBJECT 4, 0 HOUR

value: African-American


title: APAP CLINICAL SUBJECT 3, 72 HOURS POST-DOSING

value: 72 hrs after APAP


title: APAP CLINICAL SUBJECT 2, 72 HOURS POST-DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.


title: APAP CLINICAL SUBJECT 3, (-)72 HOURS BEFORE DOSING

value: 72 hrs before APAP


title: APAP CLINICAL SUBJECT 3, 6 HOURS POST- DOSING

value: Peripheral blood

value: 6 hrs after APAP


title: SG200dhxt1 GM 1% Xylose 2

status: Public on Sep 30 2009

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

country: Germany

institute: Karlsruhe Institute of Technology

description: Experiment for measuring the effects of the deletion of the sugar transporter gene hxt1 in SG200 during growth on xylose.

hyb_protocol: Affymetrix EukGe2V4 protocol on GeneChip Fluidics Station 400

scan_protocol: Affymetrix GSC3000

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain SG200-deltahxt1 grown in 1% xylose for 6 hours to an OD600 of 1

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, exept for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: Pre-cultures of SG200-deltahxt1 were grown overnight in liquid array medium (6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, pH 7.0, filter sterilized) containing 1% glucose (w/v). SG200-deltahxt1 cells were shifted to fresh liquid array medium containing 1% xylose and incubated for 6 hours to an OD600 of 1.0. RNA samples were frozen in liquid nitrogen for two independently conducted replicates.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer`s instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

tag: strain

value: :SG200-deltahxt1 is a SG200-derived strain with a deletion of the hxt1 gene (um05023 replaced by hygromycin).


title: APAP CLINICAL SUBJECT 2, 96 HOURS POST-DOSING

value: 96 hrs after APAP

value: 26 yr old

value: 73 kgs


title: AFSC at 48hrs with 100mM ethanol exposure

city: Winston-Salem

first: Jennifer

middle: A

last: Hipp

address: Medical Center Blvd

department: Institute for Regenerative Medicine

institute: Wake Forest School of Medicine

description: Expression analysis of human amniotic fluid-derived stem cells treated with 100mM ethanol.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr.

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is scanned.

data_processing: The data were analyzed with Robust Multi-Chip Analysis (RMA).

label: biotin

source_name: Human AFSC after 48hours of parafilm sealed with 100mM ethanol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: AFSC were grown in alpha-MEM medium containing 15% ES-FBS, 1% glutamine and penicillin/streptomycin supplemented with 18% Chang B and 2% Chang C (Irvine Scientific).

extract_protocol: Total RNA was extracted byRNA Bee kit and was performed according to the manufacturer's instructions.

treatment_protocol: AFSC were treated with 100mM etahnol (Sigma-Aldrich) and sealed with parafilm with media being replaced every 24 hours.

tag: Derived from clonal A1 line


title: High TCF activity Huh7_S33Y#1

city: Istanbul

first: Ersen

last: Kavak

address: Bogazici Uni. North Campus, North otopark building, 212

department: Molecular Biology and Genetics

country: Turkey

institute: Bogazici University

description: Replicates were done by using the same total RNA preparation

hyb_protocol: Affymetrix's protocol for U133 2.0 Plus arrays was followed during sample hybridization. 15 ug of biotin labeled cRNA was used for hybridization.

scan_protocol: Arrays were washed and scanned using Affymetrix Array Station

data_processing: GenePattern software of MIT was used for RMA normalization of 6 samples in this series (3 replicates of Huh7-Vec and 3 replicates of Huh7-S33Y). And the value stated here is after RMA normalization with GenePattern.

label: Biotin

source_name: Huh7 stably expressing S33Y beta-catenin

label_protocol: Affymetrix's protocol for U133 2.0 Plus arrays was followed during sample processing. First and second strand cDNA synthesis were performed by using 10 ug of total RNA (quality was checked by gel electrophoresis), according to one-cycle cDNA synthesis protocol in the Affymetrix handbook.

extract_protocol: Total RNA was isolated from early passages of tranfected cells cell lines (referred to as “Huh7-S33Y” and “Huh7-Vec” based on construct integrated into genome of Huh7) using the guanidine isothiocyanate method.


title: APAP CLINICAL SUBJECT 4, 18 HOURS POST- DOSING

value: 18 hrs after APAP

value: 27 yr old

value: 78 kgs


title: APAP CLINICAL SUBJECT 2, 48 HOURS POST-DOSING

value: 48 hrs after APAP


title: APAP CLINICAL SUBJECT 3, 18 HOURS POST- DOSING

value: 28 yr old

value: male

value: 60 kgs


title: APAP CLINICAL SUBJECT 3, 0 HOUR

value: immediatedly prior to APAP administration

value: African-American


title: APAP CLINICAL SUBJECT 3, (-)48 HOURS BEFORE DOSING

value: Stratagene Universal Human Reference RNA, 10 human cell lines.

value: 48 hrs before APAP


title: High TCF activity Huh7_S33Y#3

tag: Huh7 stably expressing S33Y beta-catenin


title: AFSC at 48hrs without ethanol exposure

description: Expression analysis of human amniotic fluid-derived stem cells without ethanol.

source_name: Human AFSC after 48hours of parafilm sealed without ethanol


title: SG200dhxt1 GM 1% Xylose 1

value: SG200-deltahxt1 is a SG200-derived strain with a deletion of the hxt1 gene (um05023 replaced by hygromycin).


title: Control Huh7_PCI

type: SAGE

anchor: NlaIII

description: We performed SAGE experiments with Invitrogen's I-SAGE kit (Invitrogen, San Diego, CA USA) according to the manufacturer’s instructions and EMBO’s SAGE manual, by using 25 ug of total RNA from both samples. The kit manual was followed until preparation of 100 bp ditags. After this step, some minor modifications were made as described in the EMBO’s SAGE manual. Sequencing was performed using an Amersham 96 capillary automatic DNA sequencer.

source_name: Huh7 Cells with PCI-Neo stable integration into genome


title: APAP CLINICAL SUBJECT 3, (-)24 HOURS BEFORE DOSING

value: Peripheral blood

value: 24 hrs before APAP


title: Control Huh7_Vec#2

tag: Huh7 Cells with PCI-Neo stable integration into genome


title: Control Huh7_Vec#1


title: High TCF activity Huh7_S33Y

tag: Huh7 liver cancer cell line

tag: Stably expresses mutant(S33Y) beta-catenin


title: SG200 GM 1% Xylose 1

description: Control experiment (base line) for measuring the effects of the deletion of the sugar transporter gene hxt1 in SG200 during growth on xylose.

source_name: U. maydis strain SG200 grown in 1% xylose for 6 hours to an OD600 of 1

growth_protocol: Pre-cultures of SG200 were grown overnight in liquid array medium (6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, pH 7.0, filter sterilized) containing 1% glucose (w/v). SG200 cells were shifted to fresh liquid array medium containing 1% xylose and incubated for 6 hours to an OD600 of 1.0. RNA samples were frozen in liquid nitrogen for two independently conducted replicates.

value: SG200 is a haploid, solopathogenic FB1-derived strain (Kämper et al., 2006).


title: SG200dhxt1 GM 1% Glucose 1

description: Experiment for measuring the effects of the deletion of the sugar transporter gene hxt1 in SG200 during growth on glucose.

source_name: U. maydis strain SG200-deltahxt1 grown in 1% glucose for 6 hours to an OD600 of 1

growth_protocol: Pre-cultures of SG200-deltahxt1 were grown overnight in liquid array medium (6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, pH 7.0, filter sterilized) containing 1% glucose (w/v). SG200-deltahxt1 cells were shifted to fresh liquid array medium containing 1% glucose and incubated for 6 hours to an OD600 of 1.0. RNA samples were frozen in liquid nitrogen for two independently conducted replicates.


title: SG200 GM 1% Glucose 2

description: Control experiment (base line) for measuring the effects of the deletion of the sugar transporter gene hxt1 in SG200 during growth on glucose.

source_name: U. maydis strain SG200 grown in 1% glucose for 6 hours to an OD600 of 1

growth_protocol: Pre-cultures of SG200 were grown overnight in liquid array medium (6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, pH 7.0, filter sterilized) containing 1% glucose (w/v). SG200 cells were shifted to fresh liquid array medium containing 1% glucose and incubated for 6 hours to an OD600 of 1.0. RNA samples were frozen in liquid nitrogen for two independently conducted replicates.


title: High TCF activity Huh7_S33Y#2


title: SG200 GM 1% Glucose 1


title: SG200 GM 1% Xylose 2


title: Control Huh7_Vec#3


title: SG200dhxt1 GM 1% Glucose 2


title: Saos-2 parental cells replicate 3

status: Public on Sep 08 2009

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: Gene expression profile of Saos-2 parental cells sensitive to methotrexate.

hyb_protocol: Affymetrix protocol for HG U133 PLUS 2.0

data_processing: Value generated using MAS 5.0 non-scaled

source_name: Saos-2 parental cells

extract_protocol: RNeasy Mini Kit from Qiagen

value: osteosarcoma

tag: methotrexate sensitivity

value: sensitive


title: Saos-2 parental cells replicate 2

scan_protocol: Affymetrix protocol for HG U133 PLUS 2.0


title: MIA PaCa2 resistant cells replicate 1

description: Gene expression profile of MIA PaCa2 cells resistant to 10e-6M methotrexate.

source_name: MIA PaCa2 methotrexate-resistant cells

label_protocol: Affymetrix protocol for HG U133 PLUS 2.0

value: MIA PaCa2

value: pancreatic cancer

value: resistant


title: Saos-2 parental cells replicate 1


title: Saos-2 resistant cells replicate 2

description: Gene expression profile of Saos-2 cells resistant to 10e-6M methotrexate.

source_name: Saos-2 methotrexate-resistant cells


title: K562 parental cells replicate 1

description: Gene expression profile of K562 parental cells sensitive to methotrexate.

source_name: K562 parental cells

value: erythroblastic leukemia


title: MDA-MB-468 parental cells replicate 3

description: Gene expression profile of MDA-MB-468 cells sensitive to methotrexate.

source_name: MDA-MB-468 parental cells

value: breast cancer


title: MIA PaCa2 resistant cells replicate 2


title: MDA-MB-468 resistant cells replicate 3

description: Gene expression profile of MDA-MB-468 cells resistant to 10e-6M methotrexate.

source_name: MDA-MB-468 methotrexate-resistant cells


title: MIA PaCa2 resistant cells replicate 3


title: MDA-MB-468 parental cells replicate 2


title: MIA PaCa2 parental cells replicate 3

description: Gene expression profile of MIA PaCa2 cells sensitive to methotrexate.

source_name: MIA PaCa2 parental cells


title: K562 resistant cells replicate 2

description: Gene expression profile of K562 cells resistant to 10e-5M methotrexate.

source_name: K562 methotrexate-resistant cells


title: Saos-2 resistant cells replicate 1


title: Saos-2 resistant cells replicate 3


title: MIA PaCa2 parental cells replicate 2


title: MIA PaCa2 parental cells replicate 1


title: K562 resistant cells replicate 3


title: MDA-MB-468 resistant cells replicate 2


title: MDA-MB-468 parental cells replicate 1


title: K562 parental cells replicate 2


title: K562 resistant cells replicate 1


title: K562 parental cells replicate 3


title: MDA-MB-468 resistant cells replicate 1


title: MCF7 resistant cells replicate 3

description: Gene expression profile of MCF7 cells resistant to 10e-6M methotrexate.

source_name: MCF7 methotrexate-resistant cells


title: MCF7 resistant cells replicate 2


title: Caco2 Resistant cells replicate 3

description: Gene expression profile of Caco2 cells resistant to 10e-5M methotrexate.

hyb_protocol: Affymetrix protocol for HG U133 plus 2.0

source_name: Caco2 methotrexate-resistant cells

value: colon cancer


title: MCF7 parental cells replicate 3

description: Gene expression profile of MCF7 cells sensitive to methotrexate.

source_name: MCF7 parental cells


title: Caco2 parental cells replicate 3

description: Gene expression profile of Caco2 cells sensitive to methotrexate.

scan_protocol: Affymetrix protocol for HG U133 plus 2.0

source_name: Caco2 parental cells


title: MCF7 parental cells replicate 2


title: 3 days post detachment vs. 2 days post detachment

status: Public on Sep 01 2009

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

description: Biological replicate of 3D and biological replicate of 2D

hyb_protocol: Each mixed aliquot was transferred to a Microcon YM-30 Centrifugal Filter Unit (Millipore, Billerica, MA) to be concentrated. Before the samples were loaded on the GeneTAC HybStation (Genomic Solutions), 110 μl SlideHyb buffer 3 (Ambion, Austin, TX) was added to each concentrated mixture and subsequently incubated in 70 ºC for 5 minutes. An 18-hour step-down protocol was applied to all hybridizations; briefly, 3 hours at 60 ºC, 3 hours at 55 ºC, 12 hours at 50 ºC. The washing procedure followed the hybridizations, and was performed with three different washing buffers containing SSC buffer (Ambion) and sodium dodecyl sulfate (SDS) under different conditions: 30 seconds in each cycle at 50 ºC for three cycles with medium stringency wash buffer (2 × SSC and 0.1% SDS), 30 seconds in each cycle at 42 ºC for three cycles with high stringency wash buffer (0.2 × SSC and 0.1% SDS), and 30 seconds in each cycle at 42 ºC for three cycles with post wash buffer (0.2 × SSC). All slides were rinsed once in 0.2 × SSC and once in double distilled water after they were downloaded from the HybStation, and immediately dried by centrifugation at 1,000 g for two minutes.

scan_protocol: Hybridized cDNA microarrays were scanned by GenePix 4000B two-laser Scanner (Molecular Devices, Downingtown, PA), and GenePix Pro 6.0 (Molecular Devices) software was then used for image processing and spot intensity file creation.

data_processing: Data were processed with Limma ((Wettenhall and Smyth, 2004) package under R environment. The essential parameters used in the analyses- Background correction: MINIMUM; Within array normalization: LOESS; Between array normalization: Aquantile.

label: Alexa 555

organism: Dreissena polymorpha

source_name: Zebra mussel foot tissue

label_protocol: Started with 15 µg total RNA, the cDNA synthesis and dye labeling were performed by SuperScript Plus Indirect cDNA Labeling Kit (Invitrogen) containing Alexa Fluor 555 & 647 dyes. The Oligo(dT) primer was used in cDNA synthesis. The protocol is based on the manufacturer's instructions.

growth_protocol: The zebra mussels were collected from Zebra mussels used for total RNA extraction were obtained from the Huron River in Ann Arbor, MI, USA (Latitude: 42º16’12’’N; Longitude -83º43’34”W). The mussels were then allowed to acclimate for eight weeks in glass aquaria kept at room temperature and supplied with well water. The mussels were fed a pure culture of the algus Ankistrodesmus falcatus once a week.

extract_protocol: 5-PRIME PerfectPure RNA Tissue Kit (5 PRIME Inc, Gaithersburg, MD) following manufacturer's instructions.

treatment_protocol: The RNA samples from feet of fully attached zebra mussels were used as reference group. The detached zebra mussels were put back to water for re-attachment. The RNA samples from feet of the mussels at different time post detachment were collected, namely, 12 hours (12h), 1 day (1D), 2 days (2D), 3 days (3D), 4 days (4D), 7 days (7D), 21 days (21D).

tag: attachment status

value: 3 days post detachment

tag: tissue

value: foot

label: Alexa 647

value: 2 days post detachment


title: 21 days post detachment vs. 7 days post detachment

description: Biological replicate of 21D and biological replicate of 7D

value: 21 days post detachment

value: 7 days post detachment


title: Caco2 Resistant cells replicate 1

label_protocol: Affymetrix protocol for HG U133 plus 2.0


title: 4 days post detachment vs. 7 days post detachment

description: Biological replicate of 4D and biological replicate of 7D

value: 4 days post detachment


title: 7 days post detachment vs. 4 days post detachment

description: Biological replicate of 7D and biological replicate of 4D


title: 4 days post detachment vs. 3 days post detachment

description: Biological replicate of 4D and biological replicate of 3D


title: 2 days post detachment vs. 3 days post detachment

description: Biological replicate of 2D and biological replicate of 3D


title: 2 days post detachment vs. 1 day post detachment

description: Biological replicate of 2D and biological replicate of 1D

value: 1 day post detachment


title: 3 days post detachment vs. 4 days post detachment

description: Biological replicate of 3D and biological replicate of 4D


title: 7 days post detachment vs. 21 days post detachment

description: Biological replicate of 7D and biological replicate of 21D


title: Caco2 parental cells replicate 1


title: Caco2 Resistant cells replicate 2


title: MCF7 parental cells replicate 1


title: MCF7 resistant cells replicate 1


title: 1 day post detachment vs. 2 days post detachment

description: Biological replicate of 1D and biological replicate of 2D


title: 1 day post detachment vs. 12 hours post detachment

description: Biological replicate of 1D and biological replicate of 12h

value: 12 hours post detachment


title: Caco2 parental cells replicate 2


title: 21 days post detachment vs. reference

description: Biological replicate of 21D and biological replicate of R

value: Fully attached zebra mussel ( more than 4 weeks post attachment)


title: 12 hours post detachment vs. 1 day post detachment

description: Biological replicate of 12h and biological replicate of 1D


title: 7 days post detachment vs. reference

description: Biological replicate of 7D and biological replicate of R


title: Reference vs. 4 days post detachment

description: Biological replicate of R and biological replicate of 4D


title: Reference vs. 21 days post detachment

description: Biological replicate of R and biological replicate of 21D


title: 4 days post detachment vs. reference

description: Biological replicate of 4D and biological replicate of R


title: Reference vs. 3 days post detachment

description: Biological replicate of R and biological replicate of 3D


title: Reference vs. 7 days post detachment

description: Biological replicate of R and biological replicate of 7D


title: 3 days post detachment vs. reference

description: Biological replicate of 3D and biological replicate of R


title: Reference vs. 12 hours post detachment

description: Biological replicate of R and biological replicate of 12h


title: 1 day post detachment vs. reference

description: Biological replicate of 1D and biological replicate of R


title: 12 hours post detachment vs. reference

description: Biological replicate of 12h and biological replicate of R


title: Reference vs. 1 day post detachment

description: Biological replicate of R and biological replicate of 1D


title: Reference vs. 2 days post detachment

description: Biological replicate of R and biological replicate of 2D


title: 2 days post detachment vs. reference

description: Biological replicate of 2D and biological replicate of R


title: CLA 9 adipocyte c9t11 pro12pro

city: Kiel

first: Julia

last: Herrmann

address: hermann-Weigmann Str

department: PBE

institute: MIR/BFEL

description: Proben: 45

hyb_protocol: according to the manufacture's protocol (Affymetrix).

data_processing: Data was normalized using GCRMA (R, Bioconductor)  Mah N, Thelin A, Lu T, Nikolaus S, Kuhbacher T, Gurbuz Y, Eickhoff H, Kloppel G, Lehrach H, Mellgard B, Costello CM, and Schreiber S. A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics 16: 361-370. Epub 2003 Nov 2025., 2004.

source_name: CLA 9 adipocyte c9t11 pro12pro subject, 9

extract_protocol: RNA was extracted using Ambion kit according to the manufacturer's protocol for fatty tissue.

treatment_protocol: 4 wk c9t11

tag: intervention

tag: subject


title: CLA 9 adipocyte control pro12pro

description: Proben: 46

scan_protocol: according to the manufacture's protocol (Affymetrix).

source_name: CLA 9 adipocyte control pro12pro subject, 9

treatment_protocol: 4 wk control

value: control


title: CLA 8 adipocyte t10c12 ala12ala

description: Proben: 44

source_name: CLA 8 adipocyte t10c12 ala12ala subject, 8

label_protocol: according to the manufacture's protocol (Affymetrix).


title: CLA 9 adipocyte mixture pro12pro

description: Proben: 47

source_name: CLA 9 adipocyte mixture pro12pro subject, 9

treatment_protocol: 4 wk mixture

value: mixture


title: CLA 10 adipocyte c9t11 pro12pro

description: Proben: 4

source_name: CLA 10 adipocyte c9t11 pro12pro subject, 10


title: CLA 10 adipocyte control pro12pro

description: Proben: 1

source_name: CLA 10 adipocyte control pro12pro subject, 10


title: CLA 9 adipocyte t10c12 pro12pro

description: Proben: 48

source_name: CLA 9 adipocyte t10c12 pro12pro subject, 9


title: CLA 10 adipocyte t10c12 pro12pro

description: Proben: 2

source_name: CLA 10 adipocyte t10c12 pro12pro subject, 10


title: CLA 10 adipocyte mixture pro12pro

description: Proben: 3

source_name: CLA 10 adipocyte mixture pro12pro subject, 10


title: CLA 8 adipocyte mixture ala12ala

description: Proben: 41

source_name: CLA 8 adipocyte mixture ala12ala subject, 8


title: CLA 7 adipocyte t10c12 pro12pro

description: Proben: 39

source_name: CLA 7 adipocyte t10c12 pro12pro subject, 7


title: CLA 8 adipocyte c9t11 ala12ala

description: Proben: 42

source_name: CLA 8 adipocyte c9t11 ala12ala subject, 8


title: CLA 6 adipocyte c9t11 ala12ala

description: Proben: 33

source_name: CLA 6 adipocyte c9t11 ala12ala subject, 6


title: CLA 6 adipocyte t10c12 ala12ala

description: Proben: 36

source_name: CLA 6 adipocyte t10c12 ala12ala subject, 6


title: CLA 6 adipocyte mixture ala12ala

description: Proben: 34

source_name: CLA 6 adipocyte mixture ala12ala subject, 6


title: CLA 7 adipocyte control pro12pro

description: Proben: 37

source_name: CLA 7 adipocyte control pro12pro subject, 7


title: CLA 7 adipocyte c9t11 pro12pro

description: Proben: 38

source_name: CLA 7 adipocyte c9t11 pro12pro subject, 7


title: CLA 5 adipocyte t10c12 pro12pro

description: Proben: 30

source_name: CLA 5 adipocyte t10c12 pro12pro subject, 5


title: CLA 6 adipocyte control ala12ala

description: Proben: 35

source_name: CLA 6 adipocyte control ala12ala subject, 6


title: CLA 5 adipocyte c9t11 pro12pro

description: Proben: 31

source_name: CLA 5 adipocyte c9t11 pro12pro subject, 5


title: CLA 5 adipocyte mixture pro12pro

description: Proben: 29

source_name: CLA 5 adipocyte mixture pro12pro subject, 5


title: CLA 7 adipocyte mixture pro12pro

description: Proben: 40

source_name: CLA 7 adipocyte mixture pro12pro subject, 7


title: CLA 5 adipocyte control pro12pro

description: Proben: 32

source_name: CLA 5 adipocyte control pro12pro subject, 5


title: CLA 4 adipocyte control ala12ala

description: Proben: 27

source_name: CLA 4 adipocyte control ala12ala subject, 4


title: CLA 4 adipocyte mixture ala12ala

description: Proben: 25

source_name: CLA 4 adipocyte mixture ala12ala subject, 4


title: CLA 4 adipocyte t10c12 ala12ala

description: Proben: 28

source_name: CLA 4 adipocyte t10c12 ala12ala subject, 4


title: CLA 3 adipocyte control pro12pro

description: Proben: 13

source_name: CLA 3 adipocyte control pro12pro subject, 3


title: CLA 3 adipocyte t10c12 pro12pro

description: Proben: 15

source_name: CLA 3 adipocyte t10c12 pro12pro subject, 3


title: CLA 4 adipocyte c9t11 ala12ala

description: Proben: 26

source_name: CLA 4adipocyte c9t11 ala12ala subject, 4


title: CLA 3 adipocyte c9t11 pro12pro

description: Proben: 16

source_name: CLA 3 adipocyte c9t11 pro12pro subject, 3


title: CLA 2 adipocyte control ala12ala

description: Proben: 9

source_name: CLA 2 adipocyte control ala12ala subject, 2


title: CLA 2 adipocyte t10c12 ala12ala

description: Proben: 11

source_name: CLA 2 adipocyte t10c12 ala12ala subject, 2


title: CLA 2 adipocyte c9t11 ala12ala

description: Proben: 12

source_name: CLA 2 adipocyte c9t11 ala12ala subject, 2


title: CLA 1 adipocyte t10c12 ala12ala

description: Proben: 6

source_name: CLA 1 adipocyte t10c12 ala12ala subject, 1


title: Neuroblastoma case 429

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

country: Japan

institute: Hiroshima University

description: Gene expression data from human neuroblastoma tissue sample

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

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

source_name: human primary neuroblastoma tissue sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: These tissues samples were obtained at surgery and stored at -80C until use.

extract_protocol: Acid guanidinium thiocyanate-phenol-chloroform extraction of total RNA was performed according to the previous report (Anal. Biochem, 162: 156,1987).

treatment_protocol: These tissues samples were obtained at srugery without any other pretreatment.

tag: age (month) at surgery

tag: stage of disease (inss)

tag: mycn gene

value: amplified

tag: outcome of the patient

value: Died of disease

value: neuroblastoma tumor


title: CLA 1 adipocyte mixture ala12ala

description: Proben: 7

source_name: CLA 1 adipocyte mixture ala12ala subject, 1


title: CLA 2 adipocyte mixture ala12ala

description: Proben: 10

source_name: CLA 2 adipocyte mixture ala12ala subject, 2


title: CLA 8 adipocyte control ala12ala

description: Proben: 43

source_name: CLA 8 adipocyte control ala12ala subject, 8


title: Neuroblastoma case 452


title: CLA 1 adipocyte c9t11 ala12ala

description: Proben: 8

source_name: CLA 1 adipocyte c9t11 ala12ala subject, 1


title: Neuroblastoma case 434

value: single copy

value: Alive


title: Neuroblastoma case 430


title: CLA 1 adipocyte control ala12ala

description: Proben: 5

source_name: CLA 1 adipocyte control ala12ala subject, 1


title: Neuroblastoma case 424


title: Neuroblastoma case 428


title: Neuroblastoma case 413


title: Neuroblastoma case 418


title: Neuroblastoma case 426


title: Neuroblastoma case 402


title: Neuroblastoma case 379


title: Neuroblastoma case 423


title: Neuroblastoma case 400


title: Neuroblastoma case 410


title: Neuroblastoma case 365


title: Neuroblastoma case 364


title: Neuroblastoma case 384


title: Neuroblastoma case 373


title: Neuroblastoma case 351


title: Neuroblastoma case 346

source_name: human metastatic neuroblastoma tissue sample


title: Neuroblastoma case 338


title: Neuroblastoma case 314


title: Neuroblastoma case 320


title: Neuroblastoma case 360


title: Neuroblastoma case 401


title: Neuroblastoma case 342


title: Neuroblastoma case 313


title: Neuroblastoma case 419


title: Neuroblastoma case 296


title: Neuroblastoma case 280


title: Neuroblastoma case 288


title: Neuroblastoma case 311


title: Neuroblastoma case 259


title: Neuroblastoma case 189


title: Neuroblastoma case 194


title: 3213 transgenic enterocytes, biological rep2

city: Tampa

first: Ulka

last: Sachdev-Ost

state: FL

address: 12901 Bruce B. Downs Blvd.

institute: University of South Florida

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent GeneArray 3000 with 7G upgrade.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150. RMA was performed using BRB-Array Tools (Rich Simon, National Cancer Institute, http://linus.nci.nih.gov/BRB-ArrayTools.html).

organism: Mus musculus

source_name: 3213 transgenic villi enterocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The mice were held in our selected pathogen-free colony according to NIH guidelines for use of animals in research. The mice had access to food and water ad libitum, 24 hours a day.

extract_protocol: Total RNA was isolated from villi enterocytes with the PicoPure kit (Arcturus) and amplified twice with the RiboAmp kit (Arcturus).

treatment_protocol: The intestine was removed in its entirety from the abdominal cavity of mice, from the exit of the stomach to the entry into the large intestine. The intestines were then opened along their cephalocaudal axis, washed with phosphate-buffered saline, and rolled from the duodenum to the ileum. Rolls from wild-type, TAg and TAg mutant transgenic mice were then processed to isolate villi cell types by LCM. Briefly, the rolls were quickly frozen and stored at -80C. Frozen sections were cut and immediately dehydrated in graded alcohol solutions. The dried sections were examined microscopically and the top 2/3 of 50 villous segments from each section were collected using a laser capture microscope (Pix Cell II, Arcturus, Mt. View, CA).

value: 4.2 months

tag: gender

value: Male

tag: cell type

value: 3213 transgenic enterocytes

tag: biological replicate


title: Neuroblastoma case 151


title: Neuroblastoma case 287


title: Neuroblastoma case 163


title: Neuroblastoma case 209


title: N136 transgenic enterocytes, biological rep5

source_name: N136 transgenic villi enterocytes

tag: age

value: 3.5 months

value: N136 transgenic enterocytes


title: N136 transgenic enterocytes, biological rep3

value: 5 months

value: Female


title: Neuroblastoma case 147


title: Neuroblastoma case 160


title: N136 transgenic enterocytes, biological rep1


title: 3213 transgenic enterocytes, biological rep3

value: 4.5 months


title: N136 transgenic enterocytes, biological rep4

value: 3.3 months


title: N136 transgenic enterocytes, biological rep2


title: D44N transgenic enterocytes, biological rep2

source_name: D44N transgenic villi enterocytes

value: 3.8 months

value: D44N transgenic enterocytes


title: 3213 transgenic enterocytes, biological rep1


title: D44N transgenic enterocytes, biological rep3


title: D44N transgenic enterocytes, biological rep1


title: Neuroblastoma case 142


title: Neuroblastoma case 66


title: TAg transgenic enterocytes, biological rep2

source_name: TAg transgenic villi enterocytes

value: 2.4 months

value: TAg transgenic enterocytes


title: TAg transgenic enterocytes, biological rep1


title: TAg transgenic enterocytes, biological rep3


title: Neuroblastoma case 18


title: Neuroblastoma case 55

value: amplified

value: Died of disease


title: Neuroblastoma case 59

value: single copy

value: neuroblastoma tumor


title: non-transgenic enterocytes, biological rep3

source_name: non-transgenic villi enterocytes

value: 2.9 months

value: non-transgenic enterocytes


title: Neuroblastoma case 9

value: Alive


title: TAg transgenic enterocytes, biological rep4

value: Male


title: Neuroblastoma case 11


title: Neuroblastoma case 5


title: non-transgenic enterocytes, biological rep4


title: Neuroblastoma case 3


title: non-transgenic enterocytes, biological rep2


title: Neuroblastoma case 4


title: Late_Speen_1_control

status: Public on Aug 31 2009

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

hyb_protocol: A 16-hour hybridization was conducted at 42 degrees in a Hybex hybridization chamber (SciGene, Sunnyvale CA).

scan_protocol: Chips were washed and then scanned on a GenePix Professional 4200 Scanner (MDS Analytical Technologies, Sunnyvale, CA).

data_processing: Each array was normalized using loess normalization and then across arrays using the A-quantile normalization procedure.  Each probeset was then summarized using the median polish procedure.

organism: Xenopus tropicalis

source_name: Late Spleen Control

label_protocol: Double-stranded cDNAs were synthesized using Invitrogenâ€™s SuperScript cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). cDNA samples were fluorescently labeled with custom Cy3 and Cy5 labeled oligonucleotides from TRILink BioTechnologies (TRILink BioTechnologies, San Diego, CA).

growth_protocol: Frogs were housed individually at 18 degrees C, Batrachochytrium dendrobatidis was grown on 1% tryptone plates prior to inoculation

extract_protocol: RNA was extracted with a Qiagen RNeasy Mini Kit (Qiagen,Valencia, CA) with the standard protocol and a DNase digestion.

treatment_protocol: Infected frogs were inoculated with B. dendrobatidis at t=0.  Tissues were collected from infected (and paired control) frogs at t=72hrs (early time point) and when clinical symptoms of chytridiomycosis were evident t=1-3weeks (late time point)

value: spleen


title: Late_Liver_3_infected

source_name: Late Liver Infected

value: liver


title: Late_Liver_2_control

source_name: Late Liver Control


title: Late_Liver_3_control


title: Late_Liver_2_infected


title: Late_Speen_1_infected

source_name: Late Spleen Infected


title: Early_Liver_3_infected

source_name: Early Liver Infected


title: Late_Liver_1_control


title: Early_Liver_2_control

source_name: Early Liver Control


title: Early_Liver_3_control


title: Early_Liver_1_infected


title: Late_Liver_1_infected


title: Early_Liver_1_control


title: Early_Liver_2_infected


title: Early_Skin_3_infected

source_name: Early Skin Infected

value: skin


title: Late_Skin_2_infected

source_name: Late Skin Infected


title: Late_Skin_1_control

source_name: Late Skin Control


title: Late_Skin_3_control


title: Early_Skin_1_control

source_name: Early Skin Control


title: Late_Skin_2_control


title: Late_Skin_1_infected


title: Late_Skin_3_infected


title: Early_Skin_1_infected


title: Early_Skin_2_infected


title: Early_Skin_3_control


title: Early_Skin_2_control


title: VanXCol_rep4_mRNA

status: Public on Aug 15 2009

first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

description:
template is total RNA from Van x Col F1 hybrids followed by poly A-RNA purification and double-stranded cDNA synthesis,
labelled products were hybridized to the array in a total amount of 16ug

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G, GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor package Affy

organism: Arabidopsis thaliana

source_name: total RNA of Van-0 (female) x Col-0 (male)

label_protocol: Invitrogen Bioprime random labeling

extract_protocol: Qiagen RNeasy Plant Mini kit

tag: genotype

value: F1 hybrids of Van-0 x Col-0;

value: whole seedling;

tag: stage

value: 7d on MS plate;

tag: growth condition

value: Percival chamber, 12h light/12h dark, 20 degree


title: CVmix1to1_rep1_mRNA

description:
template is 1:1 mixture of Col and Van total RNA followed by poly A-RNA purification and double-stranded cDNA synthesis,
labelled products were hybridized to the array in a total amount of 16ug

source_name: total RNA of Col-0 and Van at 1:1 mix

value: Col-0, Van-O;


title: VanXCol_rep1_mRNA


title: ColXVan_rep4_mRNA

description:
template is total RNA from Col x Van F1 hybrids followed by poly A-RNA purification and double-stranded cDNA synthesis,
labelled products were hybridized to the array in a total amount of 16ug

source_name: total RNA of Col-0 (female) x Van-0 (male)

value: F1 hybrids of Col-0 x Van-0;


title: ColXVan_rep3_mRNA


title: CVmix1to1_rep4_mRNA


title: CVmix1to1_rep3_mRNA


title: VanXCol_rep3_mRNA


title: CVmix1to1_rep2_mRNA


title: CVmix3to1_gDNA

type: genomic

description:
template is 3:1 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

molecule: genomic DNA

source_name: genomic DNA of Col-0 and Van-0 at 3:1 mix

extract_protocol: Qiagen DNeasy Plant Mini kit


title: Van_rep3_gDNA

description:
template is Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Van-0


title: VanXCol_rep2_mRNA


title: Van_rep2_gDNA


title: ColXVan_rep1_mRNA


title: Van_rep4_gDNA


title: ColXVan_rep2_mRNA


title: CVmix1to1_exp2_rep1_gDNA

description:
template is 1:1 mixture of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 1:1 mix


title: CVmix5to1_gDNA

description:
template is 5:1 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 5:1 mix


title: Van_rep1_gDNA


title: CVmix1to1_exp2_rep3_gDNA


title: CVmix2to1_gDNA

description:
template is 2:1 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 2:1 mix


title: CVmix1to1_exp2_rep4_gDNA


title: CVmix1to1_exp2_rep2_gDNA


title: CVmix1to5_gDNA

description:
template is 1:5 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 1:5 mix


title: gonad_insitu_resistant_date4

city: Plouzane

first: Arnaud

last: Huvet

address: Ifremer centre de Brest BP 70

department: Physiologie Fonctionnelle des Organismes Marins

country: France

institute: IFREMER

hyb_protocol: Equimolar amounts of cDNA samples and cDNA reference, labeled with Cy5 and Cy3 respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA). Hybridizations were performed at the INRA IFR 140 transcriptomic facility (Rennes, France). Following pre-hybridization (with ChipSpread buffer, containing 4×SSC and 0.2% SDS), hybridization was conducted overnight at 42°C in a humidified chamber, according to manufacturer’s instructions. The arrays were washed twice with Ribowash solution (0.1 M Tris, 0.05 M EDTA, and 0.4 M NaCl), twice with 0.1×SSC and finally centrifuged to dry.

scan_protocol: After the hybridization step, microarray slides were scanned using a Scanner Genepix 4000B (Axon Instruments Inc.) according to the following parameters: Cy 5 Photo Multiplier Tube (PMT): 550 and Cy 3 PMT: 590.

data_processing: This process was repeated for each of the hybridized slides. The images (16-bits TIF images) were then analyzed with Genepix pro 5.1 software (Axon Instruments Inc.) according to manufacturer’s instructions. Spots were filtered for quality according to the following criteria: spot shape, median intensity of the spot, homogeneity of the local background pixels and spot pixel intensities. Spots showing inadequate signals were eliminated, as were those with noisy backgrounds and those with more than 20% saturated pixels in both channels. Transformation and normalization of hybridization data were performed to minimize variation arising from technical differences in RNA quality, probe labeling, and hybridization conditions between experiments. First, a logarithmic transformation was performed for each signal intensity (giving “log values”). The “log values” were median centered. Correction was next performed for differences in the variance across the range of gene expression levels using the formula: (corrected Cy5 log value)i = (Cy5 log value)i – (Cy3 log value)i + (mean Cy3 log value), where Cy5 log value represents sample signal intensity, Cy3 log value represents the reference signal intensity, and mean Cy3 log value represents the mean of all green values obtained for the gene “i” across the different conditions.

organism: Magallana gigas

source_name: pool of 8 resistant oyster gonad, sampled the 20th June 2005

extract_protocol: Total RNA was isolated using Extract-All (Eurobio), RNA quality was assessed by Agilent 6000 nano reagents (Agilent), and RNA concentration was measured using an ND-1000 spectrophotometer (Nanodrop).

treatment_protocol: in situ rearing before summer mortality (South Britanny, France)

tag: sample

value: pool of 8 gonad oysters

tag: line

value: resistant

tag: sampling

value: 1 week before the mortality peak

tag: field

value: in situ rearing (South Britanny, France)

value: males and females

value: gonad

source_name: pool of 10 wild oyster

label_protocol: 5µg of total RNA directly labeled by reverse transcription using the Direct ShipShot labeling kit (Promega). All these Cy3 reference samples were pooled and then divided once more into several samples to obtain homogeneous reference.

extract_protocol: Total RNA was isolated using Extract-All (Eurobio). RNA quality was assessed by Agilent 6000 nano reagents (Agilent). RNA concentration was measured using an ND-1000 spectrophotometer (Nanodrop).

value: pool of 10 oysters

value: no selection (wild oysters)

value: the 10th May 2007

value: Brest, France

value: all tissues (whole oyster)


title: gonad_insitu_sensitive_date4

source_name: pool of 8 sensitive oyster gonad, sampled the 20th June 2005

label_protocol: 5µg of total RNA directly labeled by reverse transcription using the Direct ShipShot labeling kit (Promega).

value: sensitive

value: 10 days before the mortality peak

tag: tissue


title: gonad_insitu_sensitive_date3

source_name: pool of 8 sensitive oyster gonad, sampled the 6th June 2005

value: 2 weeks before the mortality peak


title: gonad_insitu_resistant_date3

source_name: pool of 8 resistant oyster gonad, sampled the 6th June 2005


title: gonad_insitu_sensitive_date2

source_name: pool of 8 sensitive oyster gonad, sampled the 25th May 2005

value: 3 weeks before the mortality peak


title: gonad_insitu_resistant_date2

source_name: pool of 8 resistant oyster gonad, sampled the 25th May 2005


title: gonad_insitu_resistant_date1

source_name: pool of 8 resistant oyster gonad, sampled the 9th May 2005

value: 1 month before the mortality peak


title: gonad_insitu_sensitive_date1

source_name: pool of 8 sensitive oyster gonad, sampled the 9th May 2005


title: AML8 5-aza-dC H3K27me3

city: Bethesda

first: Thomas

last: Paul

state: MD

address: 37 Convent Dr.

department: Laboratory of Cellular Oncology

institute: NCI-CCR

description: Input

hyb_protocol: 3 ug DNA IP and Input was co-hybridized according to Agilent protocol 65 degrees, 48 h.

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: The value is log2R normalized using Agilent feature extraction

source_name: AML8 5-aza-dC H3K27me3

label_protocol: Two micrograms of amplified ChIP DNA or amplified input DNA was labeled with Cy3 (input) or Cy5 (IP)-dUTP (Perkin Elmer, Boston, MA) using the CGH labeling kit (Invitrogen, Carlsbad, CA).

growth_protocol: StemSpan Serum-Free Expansion Medium supplemented with StemSpan CC-100 cytokine cocktail (Stem Cell Technologies) to a final concentration of 100 ng/mL rhFlt-3 Ligand, 100 ng/mL rhStem Cell Factor, 20 ng/mL rhIL-3, and 20 ng/mL rh IL-6 and 2uM 5-aza-dC

extract_protocol: Chromatin immunoprecipitation assays were conducted as previously described (1Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ.Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res. 2008 18:521-32). AML cell lines were fixed in 0.8% formaldehyde for 6 min at 25oC. Following nuclei lysis, these samples were sonicated using a probe sonicator (Misonix, Inc; Farmingdale, NY) on ice for 15 cycles (20 sec per cycle) with a power level 3 with 1 min intervals of cooling. AML clinical samples  were fixed in 1% formaldehyde for 10 min at 25oC and sonicated as above for eight 20 second cycles. Chromatin sheering was monitored by agarose gel electrophoresis and optimized to a size range of 200bp- 600bp. Chromatin (150-200ug) was immunoprecipitated with rabbit polyclonal antibodies H3me3K27 (Upstate # 07–449), H3K4me3 (Abcam #ab8580), and EZH2 (Active Motif# 39103). A 10% aliquot of each sample was removed as an input fraction. ChIP enriched DNA and input DNA was amplified using the Genomeplex whole genome amplification kit (WGA2, Sigma).

tag: source

value: Primary patient blasts

tag: antibody

source_name: AML8 5-aza-dC Input


title: CVmix1to2_gDNA

description:
template is 1:2 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 1:2 mix

value: Col-0, Van-O;

value: whole seedling;

value: 7d on MS plate;

value: Percival chamber, 12h light/12h dark, 20 degree


title: AML8 5-aza-dC H3K4me3

description: Input

source_name: AML8 5-aza-dC H3K4me3


title: AML8 TSA H3K27me3

description: Input

source_name: AML8 TSA H3K27me3

growth_protocol: StemSpan Serum-Free Expansion Medium supplemented with StemSpan CC-100 cytokine cocktail (Stem Cell Technologies) to a final concentration of 100 ng/mL rhFlt-3 Ligand, 100 ng/mL rhStem Cell Factor, 20 ng/mL rhIL-3, and 20 ng/mL rh IL-6 and 250 nM TSA

source_name: AML8 TSA Input


title: AML8 H3K27me3

description: Input

source_name: AML8 H3K27me3

growth_protocol: StemSpan Serum-Free Expansion Medium supplemented with StemSpan CC-100 cytokine cocktail (Stem Cell Technologies) to a final concentration of 100 ng/mL rhFlt-3 Ligand, 100 ng/mL rhStem Cell Factor, 20 ng/mL rhIL-3, and 20 ng/mL rh IL-6

tag: p15ink4b dna methylation

value: partial

source_name: AML8 Input


title: AML8 H3K4me3

description: Input

source_name: AML8 H3K4me3


title: AML8 TSA H3K4me3

description: Input

source_name: AML8 TSA H3K4me3


title: AML7 H3K27me3

description: Input

source_name: AML7 H3K27me3

source_name: AML7 Input


title: AML6 H3K27me3

description: Input

source_name: AML6 H3K27me3

source_name: AML6 Input


title: CVmix1to1_rep3_gDNA

description:
template is 1:1 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 1:1 mix


title: AML5 H3K4me3

description: Input

source_name: AML5 H3K4me3

value: No

source_name: AML5 Input


title: AML6 H3K4me3

description: Input

source_name: AML6 H3K4me3


title: CVmix1to1_rep2_gDNA


title: AML5 H3K27me3

description: Input

source_name: AML5 H3K27me3


title: AML3 H3K27me3

description: Input

source_name: AML3 H3K27me3

source_name: AML3 Input


title: CVmix1to3_gDNA

description:
template is 1:3 mix of Col and Van genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0 and Van-0 at 1:3 mix


title: Col_rep4_gDNA

description:
template is Col genomic DNA,
labelled products were hybridized to the array in a total amount of 16ug

source_name: genomic DNA of Col-0


title: AML7 H3K4me3

description: Input

source_name: AML7 H3K4me3


title: Col_rep3_gDNA


title: AML2 H3K27me3

description: Input

source_name: AML2 H3K27me3

source_name: AML2 Input


title: AML3 H3K4me3

description: Input

source_name: AML3 H3K4me3


title: Col_6ug_gDNA

description: labelled products were hybridized to the array in a total amount of 6ug


title: Van_15ug_gDNA

description: labelled products were hybridized to the array in a total amount of 15ug

source_name: genomic DNA of Van-0


title: AML2 H3K4me3

description: Input

source_name: AML2 H3K4me3


title: Col_rep2_gDNA


title: Col_rep1_gDNA


title: AML1 H3K4me3

description: Input

source_name: AML1 H3K4me3

source_name: AML1 Input


title: CVmix1to1_rep1_gDNA

source_name: genomic DNA of Col-0 and Van-0 at 1:1 mix


title: AML1 H3K27me3

description: Input

source_name: AML1 H3K27me3


title: Van_12ug_gDNA

description: labelled products were hybridized to the array in a total amount of 12ug


title: KG-1a EZH2

description: Input

source_name: KG-1a EZH2

growth_protocol: RPMI-1640 medium containing 10% FBS and penicillin-streptomycin

tag: cell line

source_name: KG-1a Input

value: full


title: AML-193 5-aza-dC+TSA H3K4me3

description: Input

source_name: AML-193 5-aza-dC+TSA H3K4me3

growth_protocol: Iscove's modified Dulbecco's medium (IMDM) supplemented with 20% fetal calf serum (FCS), 2 ng/mL recombinant granulocyte-macrophage colony-stimulating factor (rhGM-CSF) and 2 ng/mL recombinant human interleukin

source_name: AML-193 5-aza-dC+TSA Input


title: AML-193 EZH2

description: Input

source_name: AML-193 EZH2

source_name: AML-193 Input


title: HL-60 EZH2

description: Input

source_name: HL-60 EZH2

source_name: HL-60 Input


title: Kasumi-1 EZH2

description: Input

source_name: Kasumi-1 EZH2

growth_protocol: RPMI-1640 medium containing 20% FBS and penicillin-streptomycin

source_name: Kasumi-1 Input


title: Col_15ug_gDNA

source_name: genomic DNA of Col-0


title: U-937 EZH2

description: Input

source_name: U-937 Input


title: Van_18ug_gDNA

description: labelled products were hybridized to the array in a total amount of 18ug

source_name: genomic DNA of Van-0


title: Col_9ug_gDNA

description: labelled products were hybridized to the array in a total amount of 9ug


title: Col_18ug_gDNA


title: KG-1 EZH2

description: Input

source_name: KG-1 EZH2

source_name: KG-1 Input


title: AML-193 5-aza-dC+TSA H3K27me3

description: Input

source_name: AML-193 5-aza-dC+TSA H3K27me3


title: KG-1 5-aza-dC+TSA H3K4me3

description: Input

source_name: KG-1 5-aza-dC+TSA H3K4me3

growth_protocol: RPMI-1640 medium containing 10% FBS and penicillin-streptomycin, 2 uM 5-aza-dC,  250 nM TSA

source_name: KG-1 5-aza-dC+TSA Input


title: HL-60 H3K27me3

description: Input


title: KG-1a H3K27me3

description: Input

source_name: KG-1a H3K27me3

source_name: KG-1a Input


title: AML-193 H3K27me3

description: Input


title: Kasumi-1 H3K27me3

description: Input

source_name: Kasumi-1 H3K27me3


title: KG-1 H3K4me3

description: Input

source_name: KG-1 H3K4me3


title: KG-1a H3K4me3

description: Input

source_name: KG-1a H3K4me3


title: AML-193 H3K4me3

description: Input

source_name: AML-193 H3K4me3

source_name: AML-193 Input


title: KG-1 H3K27me3

description: Input

source_name: KG-1 H3K27me3


title: Kasumi-1 H3K4me3

description: Input

source_name: Kasumi-1 H3K4me3

source_name: Kasumi-1 Input


title: U-937 H3K27me3

description: Input

source_name: U-937 Input


title: Van_6ug_gDNA

source_name: genomic DNA of Van-0


title: HL-60 H3K4me3

description: Input

source_name: HL-60 H3K4me3

source_name: HL-60 Input


title: hir1-null mutant nucleosome profile

status: Public on Aug 14 2009

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: hir1-null mutant nucleosome profile

hyb_protocol: Biotinylated samples were hybridized at 45°C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix 7G scanner.

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1 and visualized with the Integrated Genome Browser. Treatment and control samples were quantile normalized in pairs using perfect match probes only with a bandwidth of 20.

organism: Saccharomyces cerevisiae

source_name: Nucleosomal DNA from hir1-null mutant yeast

label_protocol: DNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and a DNase I mix at 37°C until the average fragment size was approximately 50 bp. The fragmentation reaction was stopped by incubating at 95°C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP using terminal deoxynucleotidyl transferase at 37°C for 2 hours.

growth_protocol: Cell cultures of 200mL were grown to mid log phase (OD600 0.8 to 1.0) in rich medium (YPD) at 30°C while shaking at 225 rpm.

extract_protocol: Cells were pelleted, washed once with PBS and resuspended in zymolyase buffer with freshly added 10 mM β-mercaptoethanol. Zymolyase was added to a final concentration of 0.25 mg/mL and cells were spheroplasted at 30°C while gently rolling for 30 min. After zymolyase treatment, cells were pelleted at 6000rpm for 15 minutes and resuspended in micrococcal nuclease (MNase) buffer with freshly added 1 mM β-mercaptoethanol and 500 μM spermidine. The crosslinked genomic DNA was digested with different amounts of MNase (0, 25, 50, 75, 100, and 150 U) at 37°C for 30 min, after which reactions were stopped by adding 5% SDS, 50 mM EDTA. The digested samples were then treated with 2 mg/mL proteinase K and incubated at 65°C overnight. DNA was isolated by phenol/chloroform extraction and concentrated via ethanol precipitation. Following RNA digestion with RNase A, samples were run on agarose gel and the sample with the highest proportion of mononucleosomal DNA fragments was used for hybridizations.

treatment_protocol: Histone-DNA interactions were cross-linked by the addition of methanol-free formaldehyde (final concentration of 2%) into the culture for 30 minutes. Glycine was then added to a final concentration of 125mM for 5 minutes to neutralize the cross-linking reaction.

tag: strain

tag: genotype/variation

value: hir1-null mutant

source_name: RNase treated genomic DNA

extract_protocol: DNA was isolated by phenol/chloroform extraction, concentrated via ethanol precipitation and digested with RNase A.


title: Wild type nucleosome profile

description: Wild type nucleosome profile

source_name: Nucleosomal DNA from wild type yeast

value: wild type


title: Col_12ug_gDNA

source_name: genomic DNA of Col-0


title: hir1-null mutant vs. WT nucleosome changes


title: rtt106-null mutant vs. WT nucleosome changes

source_name: Nucleosomal DNA from rtt106-null mutant yeast

value: rtt106-null mutant


title: rtt106-null mutant nucleosome profile

description: rtt106-null mutant nucleosome profile


title: U-937 H3K4me3

description: Input


status: Public on Aug 07 2009

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 260 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: Gene expression data from PD22-PD25 chase Bu (1-2 Division) cells, mouse 3

hyb_protocol: Labelled cDNA are hybridized to Gene Chip MOE 430 2.0 according to manufactuer's manual (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray 3000 scanner.

data_processing: The data were analyzed with GCOS software using Affymetrix default analysis settings and global scaling as normalization method to generate present calls and signal values (Affymetrix).

label: GeneChip IVT labelling

source_name: Tet-off H2BGFP mouse skin after PD22-PD25 Doxycycline chase

label_protocol: 5 ng of high quality RNA (Bioanalyzer, Agilent) were amplified (Ovation Amplification; Nugene) in the Cornell Microarray Core Facility. GeneChip IVT labelling was performed according to manufacturer's instructions (Affymetrix).

growth_protocol: Mice are housed in the Biotechnology Building mouse facility of Cornell University approved by Cornell IACUC.

extract_protocol: Total RNA was extracted using Absolutely RNA kit (Stratagene) according to the manufacturer's instructions.

treatment_protocol: K5tTA (FvB) x pTREH2B-GFP (CD1) mice were fed doxy at 1g/KG of food (Bio-serv) to repress H2BGFP expression.

value: skin

tag: cell type

value: bulge

value: K5tTA x pTRE-H2B-GFP

tag: protocol

value: Doxycycline chase

tag: cell division

value: 1-2 Division


description: Gene expression data from PD22-PD25 chase Bu (1-2 Division) cells, mouse 1

tag: genotype

tag: age


title: Van_9ug_gDNA

tag: stage

tag: growth condition


description: Gene expression data from PD22-PD25 chase Bu (0 Division) cells, mouse 3

value: 0 Division


description: Gene expression data from PD22-PD25 chase Bu (0 Division) cells, mouse 2


title: PD22-PD25 chase NonBu cells, mouse 1

description: Gene expression data from PD22-PD25 chase NonBu cells, mouse 1

value: non-bulge


title: PD22-PD25 chase NonBu cells, mouse 2

description: Gene expression data from PD22-PD25 chase NonBu cells, mouse 2


description: Gene expression data from PD22-PD25 chase Bu (0 Division) cells, mouse 1


description: Gene expression data from PD18-PD21 chase Bu (1-2 Division) cells, mouse 1

source_name: Tet-off H2BGFP mouse skin after PD18-PD21 Doxycycline chase


description: Gene expression data from PD18-PD21 chase Bu (0 Division) cells, mouse 3


description: Gene expression data from PD18-PD21 chase Bu (0 Division) cells, mouse 2


description: Gene expression data from PD18-PD21 chase Bu (1-2 Division) cells, mouse 3


title: PD18-PD21 chase NonBu cells, mouse 1

description: Gene expression data from PD18-PD21 chase NonBu cells, mouse 1


description: Gene expression data from PD18-PD21 chase Bu (0 Division) cells, mouse 1


title: PD22-PD25 chase NonBu cells, mouse 3

description: Gene expression data from PD22-PD25 chase NonBu cells, mouse 3


title: S1_DMSOtreated_rep3_vs_CHO-WT_DAPTtreated_rep3

status: Public on Aug 01 2009

city: Lausanne

first: Patrick

middle: C

last: Fraering

state: Vaud

address: station no15

department: Life Sciences / Brain Mind Institute

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
dye-swap
CHO cells: abolished g-secretase activity through DAPT (carrier: DMSO) treatment
S1 cells: 8fold enhanced g-secretase acitivity through stable NCT,APH1-a2,PS1 and PEN2 overexpression, treated with DAPT carrier DMSO only but not with DAPT

hyb_protocol: Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC,  1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.

scan_protocol: Agilent microarray scanner, 10 μm resolution

data_processing: GenePix Pro 6.0 was used to analyse the images and  generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values. Bioconductor open source software was used for data processing.

organism: Cricetulus griseus

source_name: S1 cells treated with DMSO

label_protocol: Total RNA from CHO cells was amplified using the MessageAmpTM aRNA  kit (Ambion, NY, U.S.A.). 5 microgram of amplified RNA were reverse transcribed into cyanin3 or cyanin 5 labeled cDNA, purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL4371)

growth_protocol: The S-1 cell line was derived from Chinese Hamster Ovary cells (CHO) and overexpresses Flag-PEN2, APH1-a2-HA, PS1 and NCT-GST. S-1 cells were cultured in 10cm dishes as biological triplicates in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% Fetal Bovine Serum (FBS) and Penicillin/Streptomycin, supplemented with 200 µg/ml G418, 25 µg/ml puromycin, 250 µg/ml zeocin, 250 µg/ml hygromycin and 10µg/mL blasticidin. S1 cells exhibit 8fold enhanced activity levels. S1 cells were also treated with 0.05% DMSO which is needed as a carrier of DAPT in the CHO-WT cells with abolished g-secretase activity. The CHO-WT cells used here are rooted in the same mother cell line as S1, but they were not transfected, thus do not overexpress g-secretase and were treated with DAPT (10uM) in 0.05% DMSO a strong g-secretase inhibitor, so their g-secretase activity was abolished. As in the case of S1 they were cultured in 10cm dishes as biological triplicates in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% Fetal Bovine Serum (FBS) and Penicillin/Streptomycin.

extract_protocol: Total RNA extraction: was performed using the RNeasy Mini Kit (Qiagen, Basel, Switzerland), in the absence of DNAse treatment. RNA quality was assessed using the RNA 6000 Nanochip assay (Agilent Technologies, Meno Park, USA) and RNA concentration was determined using the ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, USA).

treatment_protocol: S1 triplicates were exposed for 24h to DMSO (0.05%) whereas CHO- triplicates were exposed for 24h to the γ-secretase inhibitor N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT, 10µM) and DMSO (0.05%).

value: S1 cells

tag: gamma secretase activity level

tag: agent

value: DMSO (DAPT carrier)

source_name: CHO cells treated with DAPT

value: CHO cells

value: abolished g-secretase activity

value: DAPT


description: Gene expression data from PD22-PD25 chase Bu (1-2 Division) cells, mouse 2


title: PD18-PD21 chase NonBu cells, mouse 3

description: Gene expression data from PD18-PD21 chase NonBu cells, mouse 3


title: CHO-WT_DAPTtreated_rep2_vs_S1_DMSOtreated_rep2

description:
CHO cells: abolished g-secretase activity through DAPT (carrier: DMSO) treatment
S1 cells: 8fold enhanced g-secretase acitivity through stable NCT,APH1-a2,PS1 and PEN2 overexpression, treated with DAPT carrier DMSO only but not with DAPT


title: control_shRNA_neuro2a

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: Alternative splicing is a key process underlying the evolution of increased proteomic and functional complexity and is especially prevalent in the mammalian nervous system. However, the factors and mechanisms governing nervous system-specific alternative splicing are not well understood. Through a genome-wide computational and expression profiling strategy, we have identified a tissue- and vertebrate-restricted Ser/Arg (SR)-repeat splicing factor, the neural-specific SR-related protein of 100 kDa (nSR100). We show that nSR100 regulates an extensive network of brain-specific alternative exons enriched in genes that function in neural cell differentiation. nSR100 acts by increasing the levels of the neural/brain-enriched polypyrimidine tract binding protein and by interacting with its target transcripts. Disruption of nSR100 prevents neural cell differentiation in cell culture and in the developing zebrafish. Our results thus reveal a critical neural-specific alternative splicing regulator, the evolution of which has contributed to increased complexity in the vertebrate nervous system.

hyb_protocol: Mixed labeled cDNAs were added to hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40 μg herring sperm DNA (Invitrogen, Carlsbad, USA). Hybridizations were carried out in a final volume of 0.5 ml injecting into an Agilent hybridization chamber at 42°C on a rotating platform in a hybridization oven (Robbins Scientific Corporation, Sunnyvale, USA) for 16–24 h. Slides were then washed (rocking for approximately 30 seconds in 6 × SSPE, 0.005% sarcosine, then rocking for approximately 30 seconds in 0.06 × SSPE) and scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA). Hybridizations were performed in duplicate with fluor reversal: that is, each mRNA sample was examined in duplicate, once in the Cy3 channel and once in the Cy5 channel, on separate arrays. Each array was hybridized with two samples simultaneously, each from an individual tissue.

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent, Palo Alto, USA).

data_processing:
Images were processed by the Agilent Feature Extraction software (version 9.5). Variance stabilizing normalization (vsn) was performed using the vsn package within Bioconductor (version 2.1).
Although Platform GPL8572 is an Agilent 244K array platform, only 104K probes were analyzed, and the rest of the probes may never be analyzed (so raw data and normalized data are unavailable for those probes) and they are not the same probes used to measure alternative splicing levels as the 104K probes represented below in the Sample data tables.  They also have nothing to do with the accompanying paper in which the 104K probes were used to measure alternative splicing.

label: Cy3, Cy5

source_name: Mouse neuro2A control

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with random nonamer primers (1 μg per reaction) and T18VN (0.25 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water. Purified cDNA was reacted with N-hydroxy succinimide esters of Cy3 or Cy5 (Amersham Pharmacia Biotech, Piscataway, USA) following the manufacturer's instructions.

extract_protocol: RNA was extracted using homogenization and Trizol reagent (Invitrogen, Carlsbad, USA) following the instructions from the manufacturer. Prior to cDNA synthesis, polyA+ RNA was purified from total RNA using the Nucleotrap mRNA Midi kit (Clontech) as recommended by the manufacturer with two rounds of purification.

value: neuro2A cells

value: expressing control shRNAs


title: Rap1 H4K16Q

city: Los Angles

first: Adam

middle: Samuel

last: Sperling

address: 332 Boyer Hall

department: Biological Chemistry

institute: UCLA

description: Rap1 ChIP in H4 K16Q yeast

hyb_protocol: Done according to Affymetrix 500K protocol

data_processing:
Data were quantile normalized to 13 input samples in the Affymetrix Tiling Analysis Software using the following parameters: PM only; Bandwidth = 50. Log2 (IP/input) is reported in bar files.
.bar files were generated by quantile normalization of 2 sample files and 13 control files.

source_name: Rap1 ChIP

growth_protocol: Grown to log phase in YPD

extract_protocol: Done as in Hecht et al., Nature 1996.

value: H4 K16Q

source_name: input DNA

tag: sample type

value: input DNA


title: Spleen

source_name: Mouse spleen

tag: tissue

value: spleen


title: CHO-WT_DAPTtreated_rep1_vs_S1_DMSOtreated_rep1

value: 8fold enhanced g-secretase acitivity through stable NCT,APH1-a2,PS1 and PEN2 overexpression


title: nSR100_shRNA_neuro2a

source_name: Mouse neuro2A nSR100 knockdown

value: expressing nSR100-targeting shRNAs


title: Muscle

source_name: Mouse skeletal muscle

value: skeletal muscle


title: Kidney

source_name: Mouse kidney

value: kidney


title: Heart

source_name: Mouse heart

value: heart


title: Brain

source_name: Mouse brain

value: brain


title: Sir3 H35KG

description: Sir3 ChIP in H3 K9,14,18,23,27G yeast

scan_protocol: Done according to Affymetrix 500K protocol

source_name: Sir3 ChIP


title: Sir3 gcn5

description: Sir3 ChIP in gcn5 deletion yeast

label_protocol: Done according to Affymetrix 500K protocol

value: gcn5 deletion


title: Rap1 wild type

description: Rap1 ChIP in wild type yeast

value: Wild Type


title: Liver

source_name: Mouse liver

value: liver


title: Sir3 H4K16Q

description: Sir3 ChIP in H4 K16Q yeast


title: Sir3 wild type

description: Sir3 ChIP in wild type yeast


title: Sir3 H3d4-30

description: Sir3 ChIP in H3 del 4-30 yeast


title: Rap1 H3d4-30

description: Rap1 ChIP in H3 del 4-30 yeast


title: KG-1 5-aza-dC+TSA H3K27me3

description: Input

source_name: KG-1 5-aza-dC+TSA H3K27me3

source_name: KG-1 5-aza-dC+TSA Input


title: PD18-PD21 chase NonBu cells, mouse 2

description: Gene expression data from PD18-PD21 chase NonBu cells, mouse 2

value: skin

value: non-bulge

value: K5tTA x pTRE-H2B-GFP

value: Doxycycline chase


title: M505-184/05

city: saint-pée sur nivelle

first: catherine

last: kolditz

address: quartier Ibarron

institute: INRA

description: microarray hybridization were performed at the INRA UMR1067 transcriptome facility (St-Pée-sur-Nivelle. France). The hybridization procedure was performed as described in Panserat et al., 2008.

hyb_protocol: Five muscle RNA samples from each experimental condition were used for microarray hybridisation at the INRA UMR1067 transcriptome facility (St-Pée-sur-Nivelle. France). A first hybridisation was performed at 42°C for 48h using a 33P-labeled oligonucleotide sequence (TAATACGACTCACTATAGGG) present at the extremity of each PCR product to monitor the amount of cDNA in each spot. After stripping (3 hours at 68°C, 0.1× SSC, 0.2% SDS), arrays were prehybridised for 1 h at 65°C in hybridisation solution (5× Denhardt's solution, 5× SSC, 0.5% SDS). RNA was degraded by treatment at 68°C for 30 min with 1 microl 10% SDS, 1microl 0.5 M EDTA and 3 microl 3 M NaOH, and then equilibrated at room temperature for 15 min. Neutralization was performed by adding 10 microl 1 M Tris- HCl plus 3 microl 2N HCl. Two micrograms of PolydA 80mers were then added to the solution to saturate the polyA tails. Arrays were incubated with the corresponding denatured labelled cDNA for 40h at 65°C in hybridisation solution. After 3 washes (1 hour at 68°C, 0.1× SSC 0.2% SDS), arrays were exposed for 60 hours to phosphor-imaging plates before scanning using a phosphorimager (FUJIBAS 5000).

scan_protocol: Scanner: BAS-5000 Fuji - Feature extraction software: AGScan

data_processing: Spots with an oligonucleotide signal lower than three times the background level (calculated for each membrane as the median value of the empty spots) were excluded from the analysis. After this filtering step, signal processing was performed using the oligonucleotide data to correct each spot signal acording to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

organism: Oncorhynchus mykiss

source_name: L-LE

label_protocol: Labelled cDNA samples were prepared from 3 microg of RNA by simultaneous reverse transcription and labelling for 1 hour at 42°C in the presence of 50 microCi [alpha-33P] dCTP, 5 microM cold dCTP, 0.8 mM each dATP, dTTP, dGTP and 200 units SuperScriptTM III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) in 30 microl final volume.

extract_protocol: Total RNA was extracted from individual muscles  using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA). Eight individual samples per experimental condition were used as biological replicates. Total RNA was quantified using spectrophotometry based on absorbance at 260nm and integrity was monitored using the Agilent 2100 Bioanalyzer (Agilent Technologies, Kista, Sweden).

tag: group

value: L-LE group, third tank

value: muscle sample number 505

value: Lean muscle line (L line)

tag: diet

value: fed a high fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months


title: M563-184/59

source_name: L-HE

value: L-HE group, first tank

value: muscle sample number 563

value: lean muscle line (L line)

value: fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months


title: D.rerio_embryo_CR_vs_PBS_embryo_120hpiB

status: Public on Jul 31 2009

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) according to Agilent protocol G4140-90050 v.5.7 (www.Agilent.com) for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: Microarray data were processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies).

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of UniGene clusters (UniGene build #105). The significance cut-off for ratios of infected versus control was set at P ≤ 10-4.

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye(GE Healthcare) and column purified.

growth_protocol: Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean see salts).

extract_protocol: Embryos were directly homogenized in TRIZOL® Reagent. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RIN value of 9 and a minimum RIN value of 8.

treatment_protocol: For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were staged at 28 hours post fertilization (hpf) by morphological critera (Kimmel et al.) and approximately 50 cfu of E11 bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Infection experiments were carried out in triplicate on separate days and pools of 15-20 embryos were taken at 2, 24 and 120 hours post infection (hpi).

tag: reference

value: Common reference (CR) consisting of a mixture of samples from embryo infections

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye(GE Healthcare) and column purified.

value: 15-20 embryos

tag: time

value: 120 hours post injection

value: PBS


title: M660-184/56

source_name: F-LE

value: F-LE group, third tank

value: muscle sample number 660

value: fatty muscle line (F line)

value: fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months


title: M657-184/52

value: muscle sample number 657


title: D.rerio_embryo_CR_vs_PBS_embryo_120hpiC

value: 2 hours post injection


title: M544-184/14

source_name: F-HE

value: F-HE group, first tank

value: muscle sample number 544

value: Fatty muscle line (F line)


title: M542-184/11

value: muscle sample number 542


title: M506-184/08

value: L-LE group, third tank

value: muscle sample number 506

value: Lean muscle line (L line)

value: fed a high fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months


title: M582-184/23

value: L-LE group, first tank

value: muscle sample number 582

value: lean muscle line (L line)


title: M641-184/51

value: L-HE group, second tank

value: muscle sample number 641

value: fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months


title: M696-184/68

value: F-HE group, third tank

value: muscle sample number 696


title: M679-184/64

value: L-HE group, third tank

value: muscle sample number 679


title: D.rerio_embryo_CR_vs_PBS_embryo_120hpiA

value: Common reference (CR) consisting of a mixture of samples from embryo infections

value: 15-20 embryos

value: 2 hours post injection

value: PBS


title: M715-184/58

value: F-LE group, first tank

value: muscle sample number 715

value: fatty muscle line (F line)

value: fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months


title: Pros-814-3|17

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

state: WA

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

hyb_protocol: Sectored array chambers (4 chambers per array) (CombiMatrix 4×2K arrays™) were each filled with 30 μl of Pre-Hybridization Solution (CombiMatrix Corp) and incubated for 10 min at 45°C.  MicroRNA was mixed with 9 μl 20× SSPE (Ambion), 4.8 μl BSA at 50 mg/ml (Ambion), 3.6 μl deionized formamide (Sigma) and 7.5 μl of 10% SDS (Ambion) and heated to 95°C for 3 min.  30 μl of each sample were added to sectored hybridization chambers, sealed with aluminum tape, and incubated at 45°C for 16 hr with rotation.  After hybridization, arrays were washed 2 × with 2 × SSC with 0.1% SDS at room temperature (RT) for 10 sec (CombiMatrix Corp), 2 × with 2× SSC at RT for 10 sec and then washed 1 × with 0.2 × SSC at RT for 10 sec each.  Arrays were blocked with 5× PBS/Casein Blocking Buffer at RT for 10 min and then labeled with streptavidin-Cy5 labeling solution for fluorescence scanning and incubated for 30 min at RT.  Arrays were then washed 2 × with Biotin Wash Solution (2× PBST) for 30 sec each at room temp and again washed 2 × with 2 × PBS followed by scanning with an Axon instrument.

scan_protocol: Arrays were scanned with an Axon Instruments GenePix 4000B scanner

data_processing: Data were extracted from scanned images with the CombiMatrix software Microarray Imager.  For each miRNA mature region, two controls were written on the chip: a sense wild-type probe (s), an anti-sense wild-type (PM) form and a double mutant control (MM). This probe set was used to evaluate significance as well as intensity of each miRNA mature form. For each hybridization, the raw signal was extracted and probes were grouped by the miRNA that they were designed for. PM signal was log2 transformed, and Z-normalized. For the classifier and for the focused cancer versus normal hierarchical clustering, we used a simple heuristic to determine if a probe was indeed present. For each miRNA that was evaluated, we counted a signal significant if the signal for PM/MM >1.0. If so, then the Z-normalized log2 (signal) was used for that miRNA, otherwise the probe data for that particular probe was not used. Normalization was thus performed over anti-sense wild-type probes across the chip; however, only data from significant probes were used for clustering and classification.   Data Mining was performed using the WEKA package. Normalized probe intensity data was converted into ARFF format and input into the WEKA program. Hybridizations were grouped into two classes, ‘cancer’ and ‘normal’. We used the CfsSubsetEval routine to choose miRNA’s (attributes). This method gave the best classification of the data into the two classes. This routine assesses the predictive ability of each attribute as well as the degree of redundancy among each miRNA. It prefers attributes that are highly correlated within each class, but that have low inter-correlation. The choice of attributes was performed using 10-fold cross-validation, and selection of the 28 best attributes was based upon their being selected at least 30% of the time.    We next extracted signal from each hybridization for just this selected set of miRNA’s. Two different classifiers were used to distinguish cancer vs. normal samples. A Bayesian network and an instance-based method called K* were able to clearly differentiate the two classes within 36 samples. Clustering was next performed using the Cluster program from Eisen et al. Average linkage was used as the tree-building criteria and Spearman rank correlation was used as the distance function.

source_name: Serum,RNA

label_protocol: Approximately one μg of isolated RNA was labeled with a Mirus miRNA Biotin labeling kit (MIR8450) following manufacturers directions.  Briefly, 1 μg RNA was diluted to 86 μl with water and 10 μl of 10 × buffer was added followed by 4 μl LabelIT biotin labeling reagent and incubation at 37°C for 1 hr.  The reaction was stopped with 10 μl stop reagent and the sample precipitated as described above.  The dried pellet was resuspended in 5.1 μl water.

extract_protocol: An aliquot of 400 μl of each serum sample was mixed with 500 μl lysis buffer (RLT, Qiagen, Valencia, CA) and 800 μl acid phenol: Chloroform (Ambion, Foster City, CA), vortexed for 30 seconds and centrifuged at 16000 rcf for 10 min at 25°C.  The aqueous phase was extracted 2 × with an equal volume of acid phenol:chloroform and centrifuged at 16000 rcf for 10 min at 25°C.  The resulting aqueous phase was then precipitated with 0.1 vol 5 M NaCl, 2 μl precipitation enhancer (Mirus, Madison, WI), 2 μl GlycoBlue (Ambion) and 2.5 vol 100% ethanol at –20ºC for at least 1 hr.  After centrifugation at 4ºC for 30 min, the pellets were washed 2 × with 75% ethanol and then air-dried.  Precipitated RNA was resuspended in 50 μl molecular grade water (Ambion) and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Human serum samples were purchased from Bioreclamation, Inc, Hicksville, NY and include: stages 2 to 4 prostate, stages 1 to 4 colon, stage 4 ovarian, stage 4 breast, and stages 3 and 4 lung cancer sera; and sera from normal male and female donors. Samples were stored at minus 80ºC until use.

tag: gender

value: male

tag: tumor stage

tag: tumor site

value: Prostate


title: M698-184/50

value: muscle sample number 698

value: Fatty muscle line (F line)


title: lun-151-4|02

value: female

value: Lung


title: lun-153-3|35


title: Pros-812-3|08


title: lun-787-4|33


title: D.rerio_embryo_CR_vs_PBS_embryo_24hpiA

value: 24 hours post injection


title: D.rerio_embryo_CR_vs_PBS_embryo_24hpiC


title: D.rerio_embryo_CR_vs_PBS_embryo_24hpiB


title: M584-184/29

value: L-LE group, first tank

value: muscle sample number 584

value: lean muscle line (L line)


title: M525-184/09

value: F-LE group, second tank

value: muscle sample number 525


title: Pros-809-4|30


title: M658-184/53

value: F-LE group, third tank

value: muscle sample number 658


title: M678-184/63

value: L-HE group, third tank

value: muscle sample number 678

value: fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months


title: M504-184/04

value: L-LE group, third tank

value: muscle sample number 504

value: Lean muscle line (L line)

value: fed a high fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months


title: M562-184/17

value: L-HE group, first tank

value: muscle sample number 562


title: D.rerio_embryo_CR_vs_PBS_embryo_2hpiC

value: Common reference (CR) consisting of a mixture of samples from embryo infections

value: 15-20 embryos

value: 2 hours post injection

value: PBS


title: Pros-808-4|00

value: male

value: Prostate


title: Pros-14-3|13


title: Pros-11-3|12


title: D.rerio_embryo_CR_vs_PBS_embryo_2hpiB


title: Ova-782-4|09

value: female

value: Ovarian


title: D.rerio_embryo_CR_vs_PBS_embryo_2hpiA


title: D.rerio_embryo_CR_vs_E11_embryo_120hpiC

value: 120 hours post infection

tag: infection

value: 50 cfu of E11 M. marinum strain


title: Ova-781-4|34


title: Nor-M28-0|24

value: Normal


title: Nor-M24-0|26


title: D.rerio_embryo_CR_vs_E11_embryo_120hpiB


title: D.rerio_embryo_CR_vs_E11_embryo_24hpiC

value: 24 hours post infection


title: Nor-F4567-0|07


title: D.rerio_embryo_CR_vs_E11_embryo_120hpiA


title: D.rerio_embryo_CR_vs_E11_embryo_24hpiB


title: Nor-M-0|28


title: Nor-48-0|44


title: Nor-F4567-0|05


title: D.rerio_embryo_CR_vs_E11_embryo_24hpiA


title: Nor-47-0|45


title: D.rerio_adult_CR_vs_PBS_1dpi_6

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of UniGene clusters (UniGene build #105). The significance cut-off for ratios of infected versus control was set at P ≤ 10-4. For adult infection studies, where triplicate individuals are tested, an absolute fold change cut-off (≥ 1.5) was applied additionally.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).

extract_protocol: Adult fish were homogenized in liquid nitrogen using a mortar and pestle and portions of 50 -100 μg of powdered tissue were used for extraction of total RNA with 1 ml of TRIZOL® Reagent (Invitrogen) according to the manufacturer’s instructions. Embryos were directly homogenized in TRIZOL® Reagent. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RIN value of 9 and a minimum RIN value of 8.

treatment_protocol: This sample is a mixture of all RNA samples from early adult infection study (1 and 6 dpi infection with Mma20 and E11 strains and PBS-injected controls)

value: CR (common reference) is a mixture of all RNA samples from healthy and infected adult zebrafish used in this microarray study

growth_protocol: Infection experiments with adult fish were performed on young males selected from a wild type laboratory-breeding colony and acclimated to their new environment for one week in a quarantine area. These fish were kept at 28˚C on a 12:12 h light/dark rhythm throughout the experiment.

treatment_protocol: Zebrafish were inoculated intraperitoneally as previously described (Meijer et al., 2004) with phosphate-buffered saline (PBS) as a control.

value: adult zebrafish

value: PBS and harvested

value: 1 dpi (day post injection)


title: D.rerio_adult_CR_vs_PBS_1dpi_4


title: D.rerio_adult_CR_vs_PBS_1dpi_5


title: Nor-32-0|46


title: Nor-31-0|47


title: Nor-28-0|22


title: Nor-F4567-0|06


title: D.rerio_adult_CR_vs_PBS_1dpi_2


title: Nor-23-0|20


title: Nor-27-0|21


title: D.rerio_embryo_CR_vs_E11_embryo_2hpiA

value: 2 hours post infection


title: RP58-/-

city: Setagaya

first: Hiroshi

last: Asahara

state: Tokyo

department: Department of Systems BioMedicine

institute: National Research Institute for Child Health and Development

description: Gene expression data from RP58 KO mouse.

hyb_protocol: Hybridization of 10 ug cRNA to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using GeneChip Scanner 3000.

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Command Console using default parameters. We used the Expression Console Version 1.1 software for data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation.

source_name: muscle in diaphragm

label_protocol: Biotinylated cRNA were prepared from total RNA following standard Affymetrix® protocols.

extract_protocol: RNA of the culture was extracted using ISOGEN (NIPPONGENE).

tag: strain

value: skeletal muscle

tag: developmental stage