title: GMBI_LCL_096


title: GMBI_LCL_088

status: Public on Sep 15 2013

type: RNA

city: Rochester

first: Stephen

middle: T

last: Turner

state: MN

address: 200 1st St SW

department: Internal Medicine, Nephrology, Hypertension

country: USA

institute: Mayo Clinic

hyb_protocol: Labeled cRNAs were hybridized onto the Affymetrix Human Exon 1.0 ST Array according to Affymetrix protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw intensity data were processed using the Affymetrix Power Tool software (v.1.14.4). Probe summarization and probe set normalization were performed using Robust Multi-array Analysis (RMA), which included background correction, quantile normalization, log2-transformation, and probe set summarization.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell line

label_protocol: One μg of RNA was labeled using the WT Expression labeling assay

growth_protocol: Cell lines established from peripheral blood samples by Epstein-Barr virus transformation

extract_protocol: Standard RNA extraction protocol using Trizol. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Foster City, CA) and quantified by spectrophotometry using the Nanodrop ND-1000 (Nanodrop Inc., Wilmington, DE). All RNA samples used in the present study yielded both anA260/A280 absorbance ratio greater than 2.0 and a RNA Integrity Number (RIN) ≥ 8.

tag: age (yrs)

tag: gender

value: male

tag: tissue source

value: peripheral blood


title: GMBI_LCL_093

value: female


title: GMBI_LCL_092


title: GMBI_LCL_127


title: GMBI_LCL_094


title: GMBI_LCL_086


title: GMBI_LCL_084


title: GMBI_LCL_089


title: GMBI_LCL_078


title: GMBI_LCL_097


title: GMBI_LCL_095


title: GMBI_LCL_087


title: GMBI_LCL_080


title: GMBI_LCL_083


title: GMBI_LCL_090


title: GMBI_LCL_099


title: GMBI_LCL_081


title: GMBI_LCL_079


title: GMBI_LCL_076


title: GMBI_LCL_085


title: GMBI_LCL_091


title: GMBI_LCL_075


title: GMBI_LCL_077


title: GMBI_LCL_082


title: GMBI_LCL_072


title: GMBI_LCL_074


title: GMBI_LCL_071


title: GMBI_LCL_073


title: GMBI_LCL_070


title: GMBI_LCL_066


title: GMBI_LCL_069


title: GMBI_LCL_067


title: GMBI_LCL_064


title: GMBI_LCL_065


title: GMBI_LCL_056


title: GMBI_LCL_055


title: GMBI_LCL_057


title: GMBI_LCL_061


title: GMBI_LCL_068


title: GMBI_LCL_062


title: GMBI_LCL_048


title: GMBI_LCL_049


title: GMBI_LCL_051


title: GMBI_LCL_060


title: GMBI_LCL_050


title: GMBI_LCL_054


title: GMBI_LCL_046


title: GMBI_LCL_052


title: GMBI_LCL_053


title: GMBI_LCL_059


title: GMBI_LCL_063


title: GMBI_LCL_045


title: GMBI_LCL_047


title: GMBI_LCL_044


title: GMBI_LCL_040


title: GMBI_LCL_041


title: GMBI_LCL_032


title: GMBI_LCL_042


title: GMBI_LCL_038


title: GMBI_LCL_058


title: GMBI_LCL_033


title: GMBI_LCL_039


title: GMBI_LCL_037


title: GMBI_LCL_025


title: GMBI_LCL_027


title: GMBI_LCL_036


title: GMBI_LCL_034


title: GMBI_LCL_043


title: GMBI_LCL_031


title: GMBI_LCL_029


title: GMBI_LCL_024


title: GMBI_LCL_021


title: GMBI_LCL_028


title: GMBI_LCL_019


title: GMBI_LCL_023


title: GMBI_LCL_020


title: GMBI_LCL_016


title: GMBI_LCL_026


title: GMBI_LCL_017


title: GMBI_LCL_018


title: GMBI_LCL_035


title: GMBI_LCL_030


title: GMBI_LCL_022


title: GMBI_LCL_015


title: GMBI_LCL_014


title: GMBI_LCL_008


title: GMBI_LCL_007


title: GMBI_LCL_006


title: GMBI_LCL_013


title: GMBI_LCL_009


title: GMBI_LCL_002


title: GMBI_LCL_005


title: GMBI_LCL_001


title: GMBI_LCL_003


title: GMBI_LCL_011


title: GMBI_LCL_012


title: GMBI_LCL_010


title: GMBI_LCL_004


title: liver_Casp1KO_repl2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 24 arrays that were used in this experiment were provided as 1x24 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0). The SI samples were normalzed together, separately from the liver samples.

label: biotin

organism: Mus musculus

source_name: liver from Caspase-1 null mouse, maintained on chow, after overnight fast, replicate 2

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: Caspase-1 null mice were backcrossed ten generations to C57Bl/6 mice and age-matched wild-type C57Bl/6J mice were used as control mice. Mice were housed under standard conditions with a 12-hour light-dark cycle and were fed a standard mouse chow diet with free access to water. Experiments were performed in 14 to 16-week old animals.

extract_protocol: Total RNA was obtained by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by DNAse treatment and column purification using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: Animals were maintained on regular lab chow. Mice were used at age between 14-16 weeks. For sampling of liver tissue, mice were fasted over night (16hrs). For sampling of small intestine, overnight fasted mice first received an intragastric load of 200 µL olive oil (Carbonell, Cordoba, Spain), and 2 hrs later small intestines were removed. The small intestine was subsequently divided into duodenum, jejunum, and ileum, and the epithelial cell layer was scraped off. All tissue samples were immediately snap-frozen in liquid nitrogen and stored at -80°C for RNA isolation.

tag: strain

tag: genotype/variation

value: Caspase-1 null

tag: tissue

value: liver

tag: age

tag: sample type

value: fasted state


title: liver_WT_repl1

source_name: liver from wild type mouse (C57BL/6), maintained on chow, after overnight fast, replicate 1

value: wild type


title: jejunum_WT_repl3

source_name: jejunum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 3

value: jejunum

value: scraped off epithelial cells, 2hrs after oral lipid load


title: ileum_Casp1KO_repl1

source_name: ileum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 1

value: ileum


title: liver_WT_repl3

source_name: liver from wild type mouse (C57BL/6), maintained on chow, after overnight fast, replicate 3


title: liver_Casp1KO_repl1

source_name: liver from Caspase-1 null mouse, maintained on chow, after overnight fast, replicate 1


title: ileum_Casp1KO_repl3

source_name: ileum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 3


title: jejunum_Casp1KO_repl3

source_name: jejunum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 3


title: ileum_WT_repl3

source_name: ileum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 3


title: ileum_WT_repl1

source_name: ileum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 1


title: liver_Casp1KO_repl3

source_name: liver from Caspase-1 null mouse, maintained on chow, after overnight fast, replicate 3


title: duodenum_Casp1KO_repl3

source_name: duodenum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 3

value: duodenum


title: liver_WT_repl2

source_name: liver from wild type mouse (C57BL/6), maintained on chow, after overnight fast, replicate 2


title: ileum_Casp1KO_repl2

source_name: ileum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 2


title: ileum_WT_repl2

source_name: ileum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 2


title: jejunum_WT_repl2

source_name: jejunum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 2


title: jejunum_Casp1KO_repl2

source_name: jejunum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 2


title: duodenum_WT_repl3

source_name: duodenum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 3


title: jejunum_Casp1KO_repl1

source_name: jejunum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 1


title: duodenum_Casp1KO_repl2

source_name: duodenum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 2


title: duodenum_WT_repl1

source_name: duodenum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 1


title: jejunum_WT_repl1

source_name: jejunum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 1


title: A/WSN/33 Infected with miRNA Mimics miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 Replicate 3

city: Evanston

first: William

last: Buggele

state: IL

address: 2200 Campus Dr.

institute: Northwestern University

description: A549 cells were transfected with an equimolar solotuion of miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 mimics.  Fifteen hours after transfection, cells were infected with A/WSN/33 (moi 5pfu/cell) for 10 hours prior to RNA purification.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Quantile Normalization

source_name: A549 cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell line

tag: infection


title: duodenum_WT_repl2

source_name: duodenum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 2


title: A/WSN/33 Infected with miRNA Mimics miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 Replicate 2


title: A/WSN/33 Infected with miRNA Mimics miR-141, miR-374b, miR-449b, miR-518b, and miR-1263 Replicate 2

description: A549 cells were transfected with an equimolar solotuion of miR-141, miR-374b, miR-449b, miR-518b, and miR-1263 mimics.  Fifteen hours after transfection, cells were infected with A/WSN/33 (moi 5pfu/cell) for 10 hours prior to RNA purification.


title: A/WSN/33 Infected with miRNA Mimics miR-141, miR-374b, miR-449b, miR-518b, and miR-1263 Replicate 3


title: duodenum_Casp1KO_repl1

source_name: duodenum from Caspase-1 null mouse, maintained on chow, 2hrs after lipid load, replicate 1


title: A/WSN/33 Infected with miRNA Mimics miR-141, miR-374b, miR-449b, miR-518b, and miR-1263 Replicate 1


title: Mock Infected Sample Replicate 2

description: A549 cells were mock infected for 10 hours prior to RNA purification

value: mock


title: A/WSN/33 Infected Replicate 2

description: A549 cells were infected with A/WSN/33 (moi 5pfu/cell) for 10 hours prior to RNA purification.


title: A/WSN/33 Infected with miRNA Mimics miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 Replicate 1


title: A/WSN/33 Infected Replicate 3


title: Mock Infected Sample Replicate 3


title: Mock Infected Sample Replicate 1


title: Undifferentiated Pleomorphic Sarcoma sample 15

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Tumor sample Cy5-labeled mixed with reference sample Cy3-labeled

hyb_protocol: Hybridization procedures were performed using Gene Expression Hybridization Kit (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on an Agilent G2565B scanner (Agilent Technologies) Images were quantified using Agilent Feature Extraction Software (v.10.1.1.1)

data_processing: Agilent Feature Extraction Software (v 10.1.1.1) was used for background subtraction and LOWESS normalization.

source_name: soft tissue sarcoma sample

label_protocol: Tumor and reference samples (500ng) were differentially labeled using Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Not applicable

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

value: Undifferentiated Pleomorphic Sarcoma

tag: topology

value: Retroperitoneum

source_name: custom reference sample

value: pooled of 15 different human cell lines


title: Undifferentiated Pleomorphic Sarcoma sample 21

value: Extremity


title: A/WSN/33 Infected Replicate 1


title: Undifferentiated Pleomorphic Sarcoma sample 18


title: Undifferentiated Pleomorphic Sarcoma sample 20

value: Pelvis


title: Undifferentiated Pleomorphic Sarcoma sample 17

value: male


title: Undifferentiated Pleomorphic Sarcoma sample 23


title: Undifferentiated Pleomorphic Sarcoma sample 9


title: Undifferentiated Pleomorphic Sarcoma sample 22


title: Undifferentiated Pleomorphic Sarcoma sample 19


title: Undifferentiated Pleomorphic Sarcoma sample 16

value: Trunk


title: Undifferentiated Pleomorphic Sarcoma sample 12


title: Undifferentiated Pleomorphic Sarcoma sample 11

value: female


title: Undifferentiated Pleomorphic Sarcoma sample 13


title: Undifferentiated Pleomorphic Sarcoma sample 1


title: Undifferentiated Pleomorphic Sarcoma sample 7

value: Head and Neck


title: Undifferentiated Pleomorphic Sarcoma sample 14


title: Undifferentiated Pleomorphic Sarcoma sample 2


title: Undifferentiated Pleomorphic Sarcoma sample 8


title: Undifferentiated Pleomorphic Sarcoma sample 5


title: Leiomyosarcoma sample 24

value: Leiomyosarcoma


title: Undifferentiated Pleomorphic Sarcoma sample 3


title: Undifferentiated Pleomorphic Sarcoma sample 4


title: Undifferentiated Pleomorphic Sarcoma sample 6


title: Leiomyosarcoma sample 17


title: Leiomyosarcoma sample 18


title: Leiomyosarcoma sample 21


title: Leiomyosarcoma sample 13


title: Leiomyosarcoma sample 23


title: Leiomyosarcoma sample 20


title: Leiomyosarcoma sample 22


title: Leiomyosarcoma sample 7


title: Leiomyosarcoma sample 8


title: Leiomyosarcoma sample 5


title: Leiomyosarcoma sample 9


title: Leiomyosarcoma sample 19


title: Leiomyosarcoma sample 16


title: Leiomyosarcoma sample 15


title: Leiomyosarcoma sample 11


title: Leiomyosarcoma sample 10


title: Leiomyosarcoma sample 4


title: Leiomyosarcoma sample 2


title: Leiomyosarcoma sample 6


title: Leiomyosarcoma sample 14


title: EpiSCs_LB2_2_ amplified

city: Westmead

first: Yoji

last: Kojima

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

description:
Sample name: LB2_2a
RNA from cultured cell
amplified RNA

hyb_protocol: Standard Illumina protocol. RNA labelling, hybridization and scanning were performed by Australian Genome Research Facility

scan_protocol: iScan with iScan Control Software

data_processing: Raw data of 45281 probes were extracted with BeadStudio and quantile normalized with Beadarray package on R. Non-annotated probes in Bioconductor illuminaMousev2.db package were removed and remaining 31646 probes were used for the analysis.

source_name: EpiSCs

label_protocol: Standard Illumina protocol using Illumina TotalPrep kit (Ambion) starting from 230 ng total RNA. For amplified RNA, First round amplification was performed with MessageAmp II aRNA kit (Ambion) and labelled with Illumina TotalPrep kit starting from 10 ng aRNA with second round protocol in MessageAmp II aRNA kit.

growth_protocol: Epiblast stem cells (EpiSCs) were collected between 10th to 20th passage. Epiblast samples were dissected from E5.5 to E8.25 embryos classified by morphological criteria.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy columns following standard protocol. Concentration and integrity were tested by spectrophotometry with Bioanalyser.

treatment_protocol: EpiSCs were treated with collagenase to lift of from fibroblast layer. Epiblast samples were digested with trypsin followed by mechanical dissection.

tag: cell type

value: embryo derived stem cells

tag: Stage

tag: passage


title: EpiSCs_LMS3_1_amplified

description:
Sample name: LMS3_1a
RNA from cultured cell
amplified RNA

value: Late Midstreak(E6.75-E7.5)


title: EpiSCs_LB2_3_ amplified

description:
Sample name: LB2_3a
RNA from cultured cell
amplified RNA


title: EpiSCs_LB2_1_ amplified

description:
Sample name: LB2_1a
RNA from cultured cell
amplified RNA


title: epiblast_LB3

description:
Sample name: epiblast_LB3
RNA from cultured cell
amplified RNA

source_name: epiblast/ectoderm

value: dissected epiblast/ectoderm


title: EpiSCs_LMS3_2_amplified

description:
Sample name: LMS3_2a
RNA from cultured cell
amplified RNA


title: EpiSCs_PS5_2_amplified

description:
Sample name: PS5_2a
RNA from cultured cell
amplified RNA


title: EpiSCs_LMS3_3_amplified

description:
Sample name: LMS3_3a
RNA from cultured cell
amplified RNA


title: EpiSCs_PS5_3_amplified

description:
Sample name: PS5_3a
RNA from cultured cell
amplified RNA


title: Leiomyosarcoma sample 3


title: epiblast_EB3

description:
Sample name: epiblast_EB3
RNA from cultured cell
amplified RNA

value: Early Bud(E7.5-E8.0)


title: EpiSCs_PS5_1_amplified

description:
Sample name: PS5_1a
RNA from cultured cell
amplified RNA


title: epiblast_LB1

description:
Sample name: epiblast_LB1
RNA from single epi/ect
amplified RNA


title: EpiSCs_CAV2_1_amplified

description:
Sample name: CAV2_1a
RNA from cultured cell
amplified RNA


title: epiblast_EB2

description:
Sample name: epiblast_EB2
RNA from single epi/ect
amplified RNA


title: EpiSCs_CAV2_2_amplified

description:
Sample name: CAV2_2a
RNA from cultured cell
amplified RNA


title: epiblast_EB1

description:
Sample name: epiblast_EB1
RNA from single epi/ect
amplified RNA


title: epiblast_LS3

description:
Sample name: epiblast_LS3
RNA from single epi/ect
amplified RNA

value: Late Streak(E7.0-E7.5)


title: epiblast_LB2

description:
Sample name: epiblast_LB2
RNA from single epi/ect
amplified RNA


title: epiblast_OB1

description:
Sample name: epiblast_OB1
RNA from single epi/ect
amplified RNA


title: epiblast_LS2

description:
Sample name: epiblast_LS2
RNA from single epi/ect
amplified RNA


title: epiblast_LMS1

description:
Sample name: epiblast_LMS1
RNA from single epi/ect
amplified RNA


title: EpiSCs_CAV2_3_amplified

description:
Sample name: CAV2_3a
RNA from cultured cell
amplified RNA


title: epiblast_Cav1

description:
Sample name: epiblast_Cav1
RNA from single epi/ect
amplified RNA


title: epiblast_LS1

description:
Sample name: epiblast_LS1
RNA from single epi/ect
amplified RNA


title: epiblast_LMS2

description:
Sample name: epiblast_LMS2
RNA from single epi/ect
amplified RNA


title: epiblast_PS2

description:
Sample name: epiblast_PS2
RNA from single epi/ect
amplified RNA


title: epiblast_LMS3

description:
Sample name: epiblast_LMS3
RNA from single epi/ect
amplified RNA


title: epiblast_Cav2

description:
Sample name: epiblast_Cav2
RNA from single epi/ect
amplified RNA


title: iPSC3_3

description:
Sample name: iPSC3_3
RNA from cultured cell

source_name: iPSCs

value: reprogrammmed mouse cells

value: (C57BL6xC3H)F1 hybrid

value: made from tale tip fibroblast


title: epiblast_PS1

description:
Sample name: epiblast_PS1
RNA from single epi/ect
amplified RNA


title: iPSC3_1

description:
Sample name: iPSC3_1
RNA from cultured cell


title: EpiSCs_EpiSC9_T

description:
Sample name: EpiSC9_T
RNA from cultured cell

value: RNA sample from Dr Tesar


title: iPSC1_1

description:
Sample name: iPSC1_1
RNA from cultured cell


title: iPSC1_2

description:
Sample name: iPSC1_2
RNA from cultured cell


title: MEF_1

description:
Sample name: MEF_1
RNA from cultured cell

source_name: MEF

value: embryonic fibroblasts

value: ARC/s


title: EpiSCs_EpiSC9_1

description:
Sample name: EpiSC9_1
RNA from cultured cell

value: From Dr Tesar


title: iPSC2_3

description:
Sample name: iPSC2_3
RNA from cultured cell


title: iPSC3_2

description:
Sample name: iPSC3_2
RNA from cultured cell


title: ESC_2

description:
Sample name: ESC_2
RNA from cultured cell

source_name: ESCs

value: embryonic stem cells


title: iPSC2_2

description:
Sample name: iPSC2_2
RNA from cultured cell


title: EpiSCs_EpiSC9_2

description:
Sample name: EpiSC9_2
RNA from cultured cell


title: ESC_3

description:
Sample name: ESC_3
RNA from cultured cell


title: EpiSCs_LB2_3

description:
Sample name: LB2_3
RNA from cultured cell


title: EpiSCs_EpiSC9_3

description:
Sample name: EpiSC9_3
RNA from cultured cell


title: EpiSCs_LB1*_3

description:
Sample name: LB1*_3
RNA from cultured cell


title: ESC_1

description:
Sample name: ESC_1
RNA from cultured cell


title: EpiSCs_LB3_2

description:
Sample name: LB3_2
RNA from cultured cell


title: iPSC1_3

description:
Sample name: iPSC1_3
RNA from cultured cell


title: iPSC2_1

description:
Sample name: iPSC2_1
RNA from cultured cell


title: EpiSCs_LB3_1

description:
Sample name: LB3_1
RNA from cultured cell


title: EpiSCs_LB2_2

description:
Sample name: LB2_2
RNA from cultured cell


title: EpiSCs_LB3_3

description:
Sample name: LB3_3
RNA from cultured cell


title: MEF_2

description:
Sample name: MEF_2
RNA from cultured cell


title: EpiSCs_LB2_1

description:
Sample name: LB2_1
RNA from cultured cell


title: EpiSCs_LB1_3

description:
Sample name: LB1_3
RNA from cultured cell


title: EpiSCs_EB1b_3

description:
Sample name: EB1b_3
RNA from cultured cell


title: EpiSCs_LB1*_1

description:
Sample name: LB1*_1
RNA from cultured cell


title: EpiSCs_LB1*_2

description:
Sample name: LB1*_2
RNA from cultured cell


title: EpiSCs_LB1_2

description:
Sample name: LB1_2
RNA from cultured cell


title: EpiSCs_LMS4_2

description:
Sample name: LMS4_2
RNA from cultured cell


title: EpiSCs_EB1b_2

description:
Sample name: EB1b_2
RNA from cultured cell


title: EpiSCs_LB1_1

description:
Sample name: LB1_1
RNA from cultured cell


title: EpiSCs_LMS2_3

description:
Sample name: LMS2_3
RNA from cultured cell


title: EpiSCs_LMS5_3

description:
Sample name: LMS5_3
RNA from cultured cell


title: EpiSCs_LMS5_1

description:
Sample name: LMS5_1
RNA from cultured cell


title: EpiSCs_LMS5_2

description:
Sample name: LMS5_2
RNA from cultured cell


title: EpiSCs_LMS2_1

description:
Sample name: LMS2_1
RNA from cultured cell


title: EpiSCs_EB1a_1

description:
Sample name: EB1a_1
RNA from cultured cell


title: EpiSCs_LMS3_2

description:
Sample name: LMS3_2
RNA from cultured cell


title: EpiSCs_LMS3_1

description:
Sample name: LMS3_1
RNA from cultured cell


title: EpiSCs_EB1a_3

description:
Sample name: EB1a_3
RNA from cultured cell


title: EpiSCs_EB1b_1

description:
Sample name: EB1b_1
RNA from cultured cell


title: EpiSCs_LMS6_3

description:
Sample name: LMS6_3
RNA from cultured cell


title: EpiSCs_LMS3_3

description:
Sample name: LMS3_3
RNA from cultured cell


title: EpiSCs_LMS6_1

description:
Sample name: LMS6_1
RNA from cultured cell


title: EpiSCs_EB1a_2

description:
Sample name: EB1a_2
RNA from cultured cell


title: EpiSCs_LMS2*_1

description:
Sample name: LMS2*_1
RNA from cultured cell


title: EpiSCs_LMS2_2

description:
Sample name: LMS2_2
RNA from cultured cell


title: EpiSCs_LMS2*_2

description:
Sample name: LMS2*_2
RNA from cultured cell


title: EpiSCs_LMS4_1

description:
Sample name: LMS4_1
RNA from cultured cell


title: EpiSCs_LMS6_2

description:
Sample name: LMS6_2
RNA from cultured cell


title: EpiSCs_LMS4_3

description:
Sample name: LMS4_3
RNA from cultured cell


title: EpiSCs_LMS1_3

description:
Sample name: LMS1_3
RNA from cultured cell


title: EpiSCs_LMS1_2

description:
Sample name: LMS1_2
RNA from cultured cell


title: EpiSCs_PS5_3

description:
Sample name: PS5_3
RNA from cultured cell


title: EpiSCs_PS4_1

description:
Sample name: PS4_1
RNA from cultured cell


title: EpiSCs_PS5_1

description:
Sample name: PS5_1
RNA from cultured cell


title: EpiSCs_CAV4_3

description:
Sample name: CAV4_3
RNA from cultured cell


title: EpiSCs_PS5_2

description:
Sample name: PS5_2
RNA from cultured cell


title: EpiSCs_PS3_3

description:
Sample name: PS3_3
RNA from cultured cell


title: EpiSCs_CAV4_2

description:
Sample name: CAV4_2
RNA from cultured cell


title: EpiSCs_LMS1_1

description:
Sample name: LMS1_1
RNA from cultured cell


title: EpiSCs_PS4_2

description:
Sample name: PS4_2
RNA from cultured cell


title: EpiSCs_CAV3*_3

description:
Sample name: CAV3*_3
RNA from cultured cell


title: EpiSCs_CAV3_3

description:
Sample name: CAV3_3
RNA from cultured cell


title: EpiSCs_CAV4_1

description:
Sample name: CAV4_1
RNA from cultured cell


title: EpiSCs_CAV3_2

description:
Sample name: CAV3_2
RNA from cultured cell


title: EpiSCs_CAV3_1

description:
Sample name: CAV3_1
RNA from cultured cell


title: EpiSCs_CAV2*_3

description:
Sample name: CAV2*_3
RNA from cultured cell


title: EpiSCs_PS3_1

description:
Sample name: PS3_1
RNA from cultured cell


title: EpiSCs_CAV3*_1

description:
Sample name: CAV3*_1
RNA from cultured cell


title: EpiSCs_CAV2*_2

description:
Sample name: CAV2*_2
RNA from cultured cell


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 4

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description:
RELe 4
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.

hyb_protocol: Samples were hybridized for 16 h at 45ºC onto the GeneChip® Rat Gene 1.0 ST. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The CEL files were used to extract and normalize the data using Robust Multichip Average (RMA) implemented with the algorithm RMA Sketch for 1.0 ST arrays in the GeneChip Expression Console software version 1.1.2 (Affymetrix).

organism: Rattus norvegicus

source_name: Liver isolated from lean (fa/+) female Zucker rat, standard diet + RE (0.05% w/w), 64 days

label_protocol: RNA was processed according to the GeneChip® Whole Transcript (WT) Sense Target Labeling protocol (Affymetrix, Santa Clara, CA, USA). Amplified sense single-strand DNA was obtained using the Ambion® WT Expression Kit (Life Technologies). DNA was fragmented and labeled with the WT terminal Labeling kit.

growth_protocol: Rat livers were rapidly removed after the animals sacrifice, rinsed and snap frozen in liquid nitrogen and stored at -80ºC prior to RNA isolation.

extract_protocol: Total RNA was isolated from the rats livers using the RNeasy Plus Mini Kit (Qiagen, Madrid, Spain) (Ref.74134) following the manufacturer recommendations. RNA was eluted in RNase-free water, aliquoted and stored at –80ºC. Isolated RNA was quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of the resulting RNA was determined by using the Experion RNA HighSens Bioanalyzer (Bio-Rad Laboratories, Inc.).

treatment_protocol: Livers were removed after 64 days of supplementation from rats fed: 1) a standard diet (CT), n=7 arrays (7 female rats); 2) a rosemary extract (RE, 0.05% w/w) treated group, n=7 arrays (7 female rats).

value: Zucker

tag: genotype

value: fa/+

value: liver

tag: treatment

value: standard diet supplemented with a rosemary extract rich in carnosic acid

tag: time

value: 64 days


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 7

description:
RELe 7
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.

value: female


title: EpiSCs_CAV3*_2

description:
Sample name: CAV3*_2
RNA from cultured cell

value: embryo derived stem cells


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 6

description:
RELe 6
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 3

description:
RELe 3
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 5

description:
RELe 5
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.


title: EpiSCs_CAV2_3

description:
Sample name: CAV2_3
RNA from cultured cell


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 2

description:
RELe 2
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.


title: EpiSCs_CAV2_1

description:
Sample name: CAV2_1
RNA from cultured cell


title: EpiSCs_CAV2_2

description:
Sample name: CAV2_2
RNA from cultured cell


title: EpiSCs_CAV2*_1

description:
Sample name: CAV2*_1
RNA from cultured cell


title: EpiSCs_CAV1_2

description:
Sample name: CAV1_2
RNA from cultured cell


title: Control group: standard diet, Time: 64 days, rat 7

description:
CTLe 7
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.

source_name: Liver isolated from lean (fa/+) female Zucker rat, standard diet, 64 days

value: standard diet


title: EpiSCs_CAV1_3

description:
Sample name: CAV1_3
RNA from cultured cell


title: Treated group: standard diet plus rosemary extract (RE, 0.05% w/w) rich in carnosic acid (CA, 40%), Time: 64 days, rat 1

description:
RELe 1
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet + RE group. Time: 64 days.


title: Control group: standard diet, Time: 64 days, rat 5

description:
CTLe 5
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: Control group: standard diet, Time: 64 days, rat 1

description:
CTLe 1
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: Control group: standard diet, Time: 64 days, rat 2

description:
CTLe 2
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: Control group: standard diet, Time: 64 days, rat 6

description:
CTLe 6
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: Control group: standard diet, Time: 64 days, rat 3

description:
CTLe 3
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: EpiSCs_CAV1_1

description:
Sample name: CAV1_1
RNA from cultured cell


title: WildType mice with dextran sulfate sodium, replicate 3

city: Nashville

first: amar

middle: b

last: singh

state: TN

department: Surgery

institute: Vanderbilt University

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

scan_protocol: Cartridges were scanned using Affymetrix scanners.

data_processing: The data were analyzed with Affymetrix's Expression Console using Affymetrix default analysis settings and RMA normalization method.

source_name: WT male mice, dextran sulfate sodium

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

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 8-10 weeks old male Villin-Claudin-2 transgenic mice and WT littermates were provided either normal drinking water (control) or Dextran Sodium Sulfate (DSS: 4% w/v) for 10 days.

value: wild type

value: colon epithelial cells

value: male

value: dextran sulfate sodium


title: Transgenic mice with dextran sulfate sodium, replicate 2

source_name: TG male mice, dextran sulfate sodium

value: Villin-Claudin-2 transgenic (Cl-2TG)


title: Transgenic mice with dextran sulfate sodium, replicate 1


title: Control group: standard diet, Time: 64 days, rat 4

description:
CTLe 4
Gene expression data from liver isolated from lean female Zucker rat (fa/+). Standard diet group. Time: 64 days.


title: Transgenic mice with dextran sulfate sodium, replicate 3


title: Transgenic mice with water, replicate 3

source_name: TG male mice, water

value: water


title: WildType mice with dextran sulfate sodium, replicate 2


title: WildType mice with dextran sulfate sodium, replicate 1


title: miR294_OSK_Day3_Rep3

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: RMB1018, 35 Medical Center Way

department: Urology

institute: UCSF

description:
replicate 3
Sample 13

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadarray in R, and significance in changes between sets determined using Limma

source_name: OSK-infected MEFs

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: transgene

value: OSK-infected MEFs


title: MEFs_Day3_Rep3

description:
replicate 3
Sample 14

source_name: MEFs

value: MEFs


title: Con_OSK_Day3_Rep3

description:
replicate 3
Sample 15


title: iPSCs_Rep3

description:
replicate 3
Sample 11

value: iPSCs


title: miR181_OSK_Day3_Rep2

description:
replicate 2
Sample 8


title: Transgenic mice with water, replicate 1

tag: gender


title: miR294_OSK_Day3_Rep2

description:
replicate 2
Sample 9


title: Transgenic mice with water, replicate 2


title: mir181_OSK_Day3_Rep3

description:
replicate 3
Sample 12


title: Con_OSK_Day3_Rep2

description:
replicate 2
Sample 6


title: MEFs_Day3_Rep2

description:
replicate 2
Sample 10


title: WildType mice with water, replicate 1

source_name: WT male mice, water


title: EpiSCs_LMS2*_3

description:
Sample name: LMS2*_3
RNA from cultured cell

value: Late Midstreak(E6.75-E7.5)


title: iPSCs_Rep2

description:
replicate 2
Sample 7


title: WildType mice with water, replicate 2


title: WildType mice with water, replicate 3


title: MEFs_Day3_Rep1

description:
replicate 1
Sample 4


title: miR181_OSK_Day3_Rep1

description:
replicate 1
Sample 3


title: metastasis- BCSC#1 (LM3#1)

city: Roma

first: alfredo

last: pagliuca

state: RM

address: viale regina Elena 299

department: EOMM

country: Italy

institute: ISS

hyb_protocol: as from Manufacturer's manual

scan_protocol: as from Manufacturer's manual

data_processing: Array Tools excel add-in was used for data extraction. Data was processed according to the justRMA procedure and normalization was performed using the median array as reference

source_name: cell culture

label_protocol: as from Manufacturer's manual

growth_protocol: standard

extract_protocol: Trizol

tag: condition

value: metastasis


title: metastasis- BCSC#1 (LM5#1)


title: EpiSCs_PS3_2

description:
Sample name: PS3_2
RNA from cultured cell

tag: strain


title: metastasis- BCSC#4 (LM2#4)


title: metastasis- BCSC#1 (LM2#1)


title: metastasis- BCSC#1 (LM3#4)


title: metastasis- BCSC#4 (LM1#4)


title: Con_OSK_Day3_Rep1

description:
replicate 1
Sample 5


title: miR294_OSK_Day3_Rep1

description:
replicate 1
Sample 1


title: fat pad xenograft - stem cells BCSC#1 (FPS2#1)

value: orthotopic from stem medium cultivated cells


title: iPSCs_Rep1

description:
replicate 1
Sample 2


title: metastasis- BCSC#1 (LM4#1)


title: metastasis- BCSC#1 (LM1#1)


title: fat pad xenograft - differentiated cells BCSC#1 (FPD2#1)

value: orthotopic from differentiation medium cultivated cells


title: fat pad xenograft - stem cells BCSC#1 (FPS1#1)


title: wild-type_N2_II

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

description: Mixed stage C. elegans wild-type N2 strains were cultured on E. coli HT115(DE3) pL4440 as a food source for 3-4 days.

hyb_protocol: Hybridization protocol according to manufacturers instruction (Affymetrix)

scan_protocol: Scan protocol according to manufacturers instruction (Affymetrix)

data_processing: Pre-processing using the software Expression Console (v.1.1, Affymetrix). Processing algorithm: Global Median, following Background correction (PM-GCBG) and the summarization method of Plier.

organism: Caenorhabditis elegans

source_name: Wild-type N2

label_protocol: GeneChip eukaryotic target labeling kit according to Affymetrix recomendations

growth_protocol: Mixed stage C. elegans ercc-1 and N2 strains were cultured on E. coli HT115(DE3) pL4440 as a food source for 3-4 days.

extract_protocol: TRIZOL from Invitrogen

tag: strain background

tag: genotype/variation

value: mixed


title: wild-type_N2_III


title: ercc-1_III

description: Mixed stage C. elegans ercc-1 strains were cultured on E. coli HT115(DE3) pL4440 as a food source for 3-4 days.

source_name: NER-deficient ercc-1

value: NER-deficient ercc-1


title: fat pad xenograft - stem cells BCSC#4 (FPS1#4)


title: ercc-1_IV


title: fat pad xenograft - differentiated cells BCSC#4 (FPD1#4)


title: ercc-1_II


title: wild-type_N2_I


title: wild-type_N2_IV


title: fat pad xenograft - differentiated cells BCSC#1 (FPD1#1)


title: BaitC

type: genomic

city: Singapore

first: Chin-Tong

last: Ong

address: 1 Research Link

department: Developmental Biology

country: Singapore

institute: Temasek Life Sciences Lab

description: BaitC 4C

hyb_protocol: Hybridization was performed by the FSU-NimbleGen Microarray Facility according to the NimbleGen protocol.

scan_protocol: Scanning was performed by the FSU-NimbleGen Microarray Facility according to the NimbleGen protocol.

data_processing:
Data processing was performed by the FSU-NimbleGen Microarray Facility.
Validation experiments were carried out only on intra-chromosomal interactions between distant insulator binding sites. Briefly, interacting 4C sites (identified by the microarray) that contained CP190 and/or dCTCF (from ChIP-seq) were determined using Galaxy. These sites were then ranked by their signal strength (defined by peak height and width). At least 50 interacting 4C sites from each bait and verified were subjected to PCR using site-specific primers in multiple 3C libraries. The map illustrated in Figure 5 showed only 4C interactions that are verified by site-specific primers in multiple 3C libraries.

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: Labeling was performed by the FSU-NimbleGen Microarray Facility according to the NimbleGen protocol.

growth_protocol: Cells were cultured in Schneider's medium with 10% HI FBS.

extract_protocol: 4C libraries were prepared from S2-DRSC cells using DpnII enzymes according to Gondor et. al., Nature Protocol 2008 and Ong et. al., Cell 2013. The detailed protocol is described in the following steps: 1. 25 million S2-DRSC cells were centrifuged for 5 min at 1000 rpm. The cell pellet was resuspended with 10 ml of fresh medium. Cells were fixed by adding 278 μl of 37% (vol/vol) formaldehyde and incubated at RT for 10 min with gentle shaking.   2. The cross-linking was quenched by adding 1.142 ml of 1.25 M glycine to cells and incubating for 5 min at RT, followed by 15 min on ice. Fixed cells were then centrifuged for 5 min at 1000 rpm (Eppendorf 5810 R). After removing supernatant, the cell pellet was froze in liquid nitrogen and stored at −80 °C for later use.  3. Frozen cell pellet was thawed on ice and resuspended in cold lysis buffer (10 mM Tris pH 8, 10 mM NaCl and 0.2% NP-40 supplemented with Roche cOmplete Mini EDTA-free protease inhibitor cocktail). 1 ml of lysis buffer was used for 50 million cells.  4. The lysate was incubated on ice for at least 15 min, with gentle mixing every 5 min. After incubation, the cells were homogenized on ice with two rounds of 15 strokes in a Dounce homogenizer (pestle A). Cell lysate was then transferred to a 1.5 ml microfuge tube and centrifuged for 5 min at 3000 rpm at RT.   5. The pellet (from 50 million cells) obtained was resuspended in 500 μl of 1× DpnII restriction buffer. After centrifugation for 5 min at 3000 rpm at RT, the pellet collected was washed again with 500 μl of 1× DpnII restriction buffer.  6. After centrifugation, the pellet was resuspended in 500 μl of 1× DpnII restriction buffer and divided equally into 50 μl aliquot. Each aliquot, which contains nuclei from approximately 5 million cells, can be frozen in liqiud nitrogen and stored at -80 °C for several months. Frozen pellet of nuclei was thawed on ice before use.  7. The thawed aliquot was mixed thoroughly with 337 μl of 1 × restriction buffer, followed by 38 μl of 1% SDS. The mixture was then incubated for 1 hr at 37 °C with gentle shaking.  8. The activity of SDS was sequestered by adding 44 μl of 10% Triton X-100. 30 µl of the mixture was kept as undigested fraction.   9. 400 U of DpnII per tube (5 million cells) was mixed thoroughly with the nuclei and the mixture was incubated overnight at 37 °C with gentle shaking.  10. 200 U of DpnII was further added to each tube and incubated for additional 4 hr at 37 °C. 30 µl of the restriction mixture was kept as digested fraction.  11. The DpnII was inactivated by adding 86 μl of 10% SDS and incubating at 65 °C for 30 min.  12. Each reaction (~575 μl) was then transferred individually to a 15-ml falcon tube.  13. The ligation reaction was then assembled by adding the following reagents in the order of: 745 μl of 10% Triton X-100, 745 μl of 10 x T4 DNA ligase buffer, 80 μl of BSA (10mg/ml), 80 μl of 100 mM ATP, 5960 μl of water and 10 μl of T4 ligase (400U/ μl). The reaction was mixed thoroughly and incubated at 16 °C for 4 hr, followed by at RT for 1 hr to facilitate circularization of DNA.  14. After ligation, 50 μl of proteinase K (10mg/ml) was added and incubated overnight at 65 °C.  15. On the following day, 35 µg of RNase A (Sigma) was added and incubated at 37C for 30 min. This was followed by addition of 50 μl of proteinase K (10mg/ml) and 2 hr of incubation at 65 °C.  16. Each ligation reaction was transferred into 50-ml conical tubes containing 8 ml of phenol. The mixture was vortex for 2 min and centrifuged for 30 min at 4000 rpm and 4 °C (Eppendorf 5810R).  17. The upper aqueous layer was then transferred to a fresh 50-ml conical tube and added with 8 ml phenol/chloroform. The mixture was vortex and centrifuged for 30 min at 3000 rpm and 4 °C.  18. The upper aqueous layer was transferred to a fresh 50-ml conical tube and added with 7 ml of nuclease-free water, 1.5 ml of 3 M NaAc (pH 5.2), 35 ml of ethanol and incubated at −80 °C for at least 30 min. The mixture was then centrifuged for 1 hr at 4000 rpm and 4 °C.  19. After discarding the supernatant, the pellet was dissolved in 500 μl of 1 × TE buffer (pH 8) by incubating at 42 C for 10 min and then at RT for 10 min. The dissolved DNA was then transferred to a 1.5 ml microfuge tube.   20. After adding 500 μl of phenol/chloroform, the mixture was vortex for 1 min and centrifuged for 10 min at 14,000 rpm in a microfuge at RT.  21. The upper aqueous layer was transferred to a new microfuge tube and added with 0.1 volumes of 3 M NaAc (pH 5.2) and 2 volumes of cold ethanol. The mixture was incubated at −80 °C for at least 30 min and centrifuged for 20 min at 16,000 rpm at 4 °C.  22. The supernatant was discarded and the white pellet was resuspended with 1 ml of 70% ethanol. The mixture was centrifuge for 5 min at 16,000 rpm at 4 °C.   23. Ethanol wash described in steps 23 was repeated for at least seven more times.  24. After the final ethanol wash, the pellet was air-dried and dissolved in 50 μl of TE (pH 8).  25. Digestion efficiency was determined with the undigested and digested fractions using previously described method (Hagege et al., 2007). The DpnII digestion efficiency is between 70-95% depending on the DNA sites examined.   26. DNA concentration was measured with Qubit Fluorometer (Invitrogen). The yield of 3C library from 5 million cells was typically 40-50 ng/µl in 50 µl total volume.    Generation of 4C libraries  27. The following method was adapted from (Gondor et al., 2008). Duplicate inverse PCRs for each cross-linked sample was set up with the composition of one reaction as follow:  Water (final volume of 40 µl), 8 µl of 5x HF buffer, 2 µl each of forward and reverse primers (10 µM), 1.4 µl of dNTP (10 mM), 0.8 µl of MgCl2 (10 mM), 0.6 µl of DMSO, 0.6 µl of Phusion high-fidelity DNA polymerase (NEB) and 50 ng of 3C DNA.  28. The first inverse PCR was carried out with the following cycling parameters: (1) 30 sec 98 °C. (2) 4 cycles of 10 sec 98 °C, 40 min 65 °C, 5 min 72 °C. (3) 20 rounds of 7 sec 98 °C, 2 min 30 sec 58 °C, 5 min 72 °C. (4) 7 min 72 °C (5) forever 4 °C.  29. The inverse PCR product obtained was diluted 80 fold (i.e. 1 µl product with 79 µl TE buffer). The dilution concentration was determined empirically in which the linear phase of amplification was attained after 30 cycles of nested PCR (Figure S5B).  30. Three nested PCRs for each core inverse PCR product was set up with the composition of one reaction as follow:  Water (final volume of 20 µl), 4 µl of 5x HF buffer, 1 µl each of forward and reverse nested primers (10 µM), 0.7 µl of dNTP (10 mM), 0.4 µl of MgCl2 (10 mM), 0.3 µl of DMSO, 0.3 µl of Phusion high-fidelity DNA polymerase (NEB) and 0.2 ng of diluted inverse PCR DNA.  31. The nested PCR was carried out with the following cycling parameters: (1) 30 sec 98 °C. (2) 30 rounds of 10 sec 98 °C, 30 sec 55 °C, 2 min 72 °C. (3) 10 min 72 °C (4) forever 4 °C.  32. Nested PCR products were pooled and purified with QIAquick PCR purification kit (QIAGEN). Pooled 4C samples and DpnII digest genomic DNA were hybridized to Drosophila melanogaster ChIP-chip 2.1M Whole-Genome Tiling Array (Roche) at the NimbleGen Microarray Facility at Florida State University.    33. To reduce technical/biological variations, the 4C-chip assay was represented by four independently cross-linked samples (four separate 3C libraries) undergoing the 4C protocol. In total, there are 4 x 2 x 3 = 24 nested PCR reactions.

treatment_protocol: Libraries prepared with 4C protocol (Gondor et. al., Nature Protocol, 2008.) using DpnII. DNA were ligated and subjected to 2 separate rounds on inverse PCR using specific primers pair.

tag: molecule type

value: PCR products of 3C DNA

source_name: Unligated control of BaitC

treatment_protocol: Genomic DNA cut with DpnII

value: DpnII cut, unligated genomic DNA


title: BaitB

description: BaitB 4C

source_name: Unligated control of BaitB


title: BaitA

description: BaitA 4C

source_name: Unligated control of BaitA


title: Root_three-leaf stage_repeat 5

status: Public on Sep 14 2013

city: Hsinchu

first: Jia-Shing

last: Chen

address: 6F, No 6, Technology Road 5

country: Taiwan

institute: Phalanx biotech Group

description: To elucidate the genes regulating rice tissue development, comparisons between shoot and root gene expression profiles from the rice OneArray® microarray were normalized and analyzed using Rosetta software.

hyb_protocol: The pre-hybridization of RiOAv1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in dulication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4200AL scanner (635nm power 100; PMT340 ) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

organism: Oryza sativa Japonica Group

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: A japonica subspecies (Tainung 67, TNG67) was selected and cultured for study.

extract_protocol: RNA extraction by Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) . RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: A rice plant was selected at three-leaf stage. Total RNA was isolated from rice roots and shoots using the Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) according to manufacture’s protocols.

tag: variety

tag: developmental stage

value: three-leaf stage

tag: tissue

value: root


title: Root_three-leaf stage_repeat 3


title: sicy-192 gun1-101 cotyledons, biological rep1

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

country: Japan

institute: Shimane University

description: Gene expression data from 4-day-old sicy-192 gun1-101 cotyledons

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix ATH1 GeneChip arrays for 16 h at 45°C according to Affymetrix protocols.

scan_protocol: Arrays were washed on an Affymetrix Fluidics Station 450 and measured for fluorescence intensity with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were processed using Affymetrix Gene Chip Operating Software (GCOS; Version 1.4.0.036).

organism: Arabidopsis thaliana

source_name: Four-day-old sicy-192 gun1-101 cotyledons

label_protocol: Total RNA samples were reverse-transcribed, yielding double-strand cDNA, which was transcribed in vitro in the presence of biotin-labeled nucleotides with an IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA), and purified.

growth_protocol: Wild-type, sicy-192, and sicy-192 gun1-101 plants were grown on MS medium containing 100 mM sucrose in a growth chamber kept at 25°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness for 4 days.

extract_protocol: Total RNA was semi-automatically purified from various organs of Arabidopsis plants using a QuickGene RNA cultured cell Kit and QuickGene-Mini80 (FUJIFILM corporation, Tokyo, Japan). The quality and purity of the RNA were confirmed for microarray analysis with an Ultrospec 2100 pro (GE Healthcare UK Ltd, Amersham Place, England).

treatment_protocol: At 4 days of age, cotyledons were collected as samples.

tag: ecotype

value: cotyledons


title: Root_three-leaf stage_repeat 2


title: sicy-192 gun1-101 cotyledons, biological rep2


title: Shoot_three-leaf stage_repeat 3

value: shoot


title: Root_three-leaf stage_repeat 4


title: wild-type cotyledons, biological rep2

description: Gene expression data from 4-day-old wild-type cotyledons

source_name: Four-day-old wild-type cotyledons

value: wild-type


title: wild-type cotyledons, biological rep1


title: Shoot_three-leaf stage_repeat 5


title: Shoot_three-leaf stage_repeat 1


title: sicy-192 cotyledons, biological rep1

description: Gene expression data from 4-day-old sicy-192 cotyledons

source_name: Four-day-old sicy-192 cotyledons


title: Root_three-leaf stage_repeat 1


title: sicy-192 cotyledons, biological rep2


title: Shoot_three-leaf stage_repeat 4


title: Shoot_three-leaf stage_repeat 2


title: genomic DNA from microdissected human kidney79

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

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

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

data_processing: GenomeStudio V2011.1; methylation module 1.9.0

label: Cy5 and Cy3

source_name: kidney 79

label_protocol: Standard Illumina Protocol

extract_protocol: 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4°C in RNALater for glomerular and tubular compartments using fine tip forceps. The corresponding tubulointerstitial and vascular compartment was placed into RLT solution. For easier designation we called this component tubules. Dissected tissue was homogenized using a Powergen125 (Fisher) homogenizer and stored at -80°C. Genomic DNA was prepared using DNA extraction kit (Qiagen) according to manufacturer's instructions.

value: kidney tubule


title: genomic DNA from microdissected human kidney82

source_name: kidney 82


title: genomic DNA from microdissected human kidney85

source_name: kidney 85


title: ercc-1_I


title: genomic DNA from microdissected human kidney83

source_name: kidney 83


title: genomic DNA from microdissected human kidney80

source_name: kidney 80


title: genomic DNA from microdissected human kidney84

source_name: kidney 84


title: genomic DNA from microdissected human kidney77

source_name: kidney 77


title: genomic DNA from microdissected human kidney81

source_name: kidney 81


title: genomic DNA from microdissected human kidney71

source_name: kidney 71


title: genomic DNA from microdissected human kidney78

source_name: kidney 78


title: genomic DNA from microdissected human kidney75

source_name: kidney 75


title: genomic DNA from microdissected human kidney76

source_name: kidney 76


title: genomic DNA from microdissected human kidney57

source_name: kidney 57


title: genomic DNA from microdissected human kidney72

source_name: kidney 72


title: genomic DNA from microdissected human kidney68

source_name: kidney 68


title: genomic DNA from microdissected human kidney59

source_name: kidney 59


title: genomic DNA from microdissected human kidney60

source_name: kidney 60


title: genomic DNA from microdissected human kidney74

source_name: kidney 74


title: genomic DNA from microdissected human kidney61

source_name: kidney 61


title: genomic DNA from microdissected human kidney58

source_name: kidney 58


title: genomic DNA from microdissected human kidney69

source_name: kidney 69


title: genomic DNA from microdissected human kidney70

source_name: kidney 70


title: genomic DNA from microdissected human kidney64

source_name: kidney 64


title: genomic DNA from microdissected human kidney63

source_name: kidney 63


title: genomic DNA from microdissected human kidney73

source_name: kidney 73


title: genomic DNA from microdissected human kidney65

source_name: kidney 65


title: genomic DNA from microdissected human kidney66

source_name: kidney 66


title: seedling in potassium deficient medium, biological rep 2

city: NEW DELHI

first: GIRDHAR

middle: KUMAR

last: PANDEY

state: DELHI

address: BENITO JUAREZ ROAD

department: Plant Molecular Biology

country: India

institute: Delhi University South Campus

description: Seedling in potassium deficient medium after 5 days

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v5.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChipOperating Software (GCOS 1.2.1) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa Indica Group

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Seeds of indica rice (Oryza sativa subsp. indica cv. IR64) were surface sterilized and grown hydroponically in culture solution . Seedlings were grown in hydroponically in RGM, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 16 h light and 8 h dark photoperiod with 70 % humidity.

extract_protocol: Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions

treatment_protocol: After 5 days of normal growth, one half of the rice seedlings were transferred to nutrient media with normal concentration of potassium (KP, 0.409 mM K2SO4) and other one half to medium without potassium (KM, 0 mM).  After 5 days, potassium (0.409 mM K2SO4) was resupplied to the plants grown in KM medium for 6 h.

value: Seedling

tag: cultivar

value: potassium deficient medium

value: 5 d


title: seedling in potassium deficient medium, biological rep 3

source_name: Seedling in potassium deficient medium after 5 days


title: genomic DNA from microdissected human kidney62

source_name: kidney 62


title: seedling in potassium deficient medium, biological rep 1


title: genomic DNA from microdissected human kidney67

source_name: kidney 67


title: genomic DNA from microdissected human kidney54

source_name: kidney 54


title: genomic DNA from microdissected human kidney56

source_name: kidney 56


title: genomic DNA from microdissected human kidney55

source_name: kidney 55


title: seedling at 0 hr , biological rep 3

description: Rice seedling before transferred to potassium stravation medium

value: 0 h


title: seedling in potassium sufficient medium, biological rep 3

description: Seedling in potassium sufficient medium after 5 days

value: potassium sufficient medium


title: seedling in potassium sufficient medium, biological rep 2

source_name: Seedling in potassium sufficient medium after 5 days


title: seedling at 0 hr , biological rep 2

source_name: Rice seedling before transferred to potassium stravation medium


title: genomic DNA from microdissected human kidney50

source_name: kidney 50


title: seedling in potassium sufficient medium, biological rep 1


title: seedling at 0 hr , biological rep 1


title: genomic DNA from microdissected human kidney48

source_name: kidney 48


title: genomic DNA from microdissected human kidney51

source_name: kidney 51


title: genomic DNA from microdissected human kidney49

source_name: kidney 49


title: seedling after potassium resupply, biological rep 2

description: Rice seedling after 6hr potassium resupply

value: potassium resupply

value: 6 h


title: genomic DNA from microdissected human kidney52

source_name: kidney 52


title: seedling after potassium resupply, biological rep 1

source_name: Rice seedling after 6hr potassium resupply


title: genomic DNA from microdissected human kidney46

source_name: kidney 46


title: seedling after potassium resupply, biological rep 3


title: genomic DNA from microdissected human kidney45

source_name: kidney 45


title: 1705-383_24hr

city: Melbourne

first: Maya

last: Kansara

state: Victoria

address: St Andrews Place

department: Research

institute: Peter MacCallum Cancer Centre

description: RB1-383 pGIPZ (OpenBiosystems)(shRB1),  human osteoblast cell line (hOB), irradiated (IR)

hyb_protocol: Labelled RNA was hybridised to Human Gene 1.0 ST arrays. Hybridisation was performed according to the manufacturers instructions (Affymetrix , Santa Clara, CA).

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

data_processing: The data were RMA normalised using the R package Affy

label_protocol: Affymetrix Gene Chip® WT terminal labelling and hybridization was performed according to manufacturers instructions (Affymetrix , Santa Clara, CA).

growth_protocol: Cells were maintained at 37°C and 5% CO2 in alpha MEM (modified Eagles's medium) containing 10% (v/v) FCS, 50 U.mL-1 penicillin and 50 ug.mL-1 streptomycin, 2mM L-glutamine, 100 uM L-ascorbate-2-phosphate

extract_protocol: Total RNA was extracted from cell pellets using Trizol reagent (Invitrogen)  and RNAeasy isolation kit (Qiagen). The quality of RNA was measured using Bioanalyzer (Agilent Technologies).

treatment_protocol: Subconfluent hOB shEV and shRB1 cells were irradiated at 4 Gy using a 137Cesium source at a dose rate of 1.7 min/Gy and cell pelllets collected 0, 2, 4, 8, 16  and 24 hrs after irradiation

tag: cell line

value: Normal bone cell line 1705

tag: phenotype

value: RB1 knockdown

tag: cell type

value: human osteoblast (hOB)


title: 1705-383_4hr


title: 1705-383_8hr


title: 1705-383_16hr


title: genomic DNA from microdissected human kidney53

source_name: kidney 53


title: genomic DNA from microdissected human kidney44

source_name: kidney 44


title: 1705_383_2hr


title: genomic DNA from microdissected human kidney42

source_name: kidney 42


title: 1705-EV_24hr

description: Empty vector-non silencing-pGIPZ, OpenBiosystems (EV), human osteoblast cell line (hOB), irradiated (IR)

value: Parental


title: genomic DNA from microdissected human kidney43

source_name: kidney 43


title: 1705_383_0hr

description: RB1-383 pGIPZ (OpenBiosystems)(shRB1),  human osteoblast cell line (hOB)


title: Ruptured4

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

country: China

institute: Shandong University

description:
miRNA level in plasma
array12

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Plasma from patients with ruptured intracranial aneurysm

label_protocol: miRNA was labeled by miRNA Complete Labeling and Hyb Kitn(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instruction's labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

value: pooled plasma sample


title: Ruptured3

description:
miRNA level in plasma
array11


title: genomic DNA from microdissected human kidney39

source_name: kidney 39


title: 1705-EV_8hr


title: 1705_EV_4hr


title: Ovaries, 8wks, SD (16hrs of Light) M21

city: Ithaca

first: Ned

last: Place

state: NY

address: 240 Farrier Road

department: Population Medicine & Diagnostic Sciences

institute: Cornell University

description: Gene expression in ovary from female hamster raised in SD(10 hours of light per day) by 8wks of age

hyb_protocol: Cy3-labelled cRNA was hybridized to 4X44K microarray and washed, according to manufacturer's protocols. Briefly, Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 44K custom high-definition whole-genome oligo array (G2519F-014868) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Agilent microarray scanner was used to scan the microarry using one color scan setting.

data_processing: The Scanned images were analyzed with Agilent Feature Extraction software by obtaining fluorecent signal.

organism: Phodopus sungorus

source_name: Ovaries, 8wks, SD (16hrs of Light)

label_protocol: One ug of total RNA is amplified and labeled with Cyanine-3 (Cy3) using Ambion Amino Allyl MessageAmp™ II aRNA  Amplification Kit.

extract_protocol: Both ovaries from each hamster were homogenized with a Polytron, and total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was purified again with Rneasy Kit (Qiagen, Valencia, CA), examined its quantity and quality with and Agilent Bioanlyzer 2100 (Agilent Technologies,Palo Alto, CA).

treatment_protocol: Female hamsters from both LD and SD groups were euthanized by CO2 Chamber at the age of 3 week or  8 week, respectively. Ovaries were asecptically removed,snap-frozen on dry ice, and stored at -80 degree until RNA extraction.

tag: treatment

value: 16hrs of Light

value: Ovaries

tag: Sex

value: female

tag: age


title: 1705-EV_16hr


title: Ovaries, 8wks, SD (16hrs of Light) M06


title: 1705-EV_2hr


title: genomic DNA from microdissected human kidney32

source_name: kidney 32


title: genomic DNA from microdissected human kidney36

source_name: kidney 36


title: genomic DNA from microdissected human kidney37

source_name: kidney 37


title: Unruptured4

description:
miRNA level in plasma
array8

source_name: Plasma from patients with unruptured intracranial aneurysm


title: genomic DNA from microdissected human kidney38

source_name: kidney 38


title: genomic DNA from microdissected human kidney41

source_name: kidney 41


title: Ovaries, 8wks, SD (16hrs of Light) M35


title: Unruptured3

description:
miRNA level in plasma
array7


title: genomic DNA from microdissected human kidney30

source_name: kidney 30


title: genomic DNA from microdissected human kidney35

source_name: kidney 35


title: genomic DNA from microdissected human kidney34

source_name: kidney 34


title: 1705-EV_0hr

description: Empty vector-non silencing-pGIPZ, OpenBiosystems (EV), human osteoblast cell line (hOB)


title: genomic DNA from microdissected human kidney33

source_name: kidney 33


title: Ruptured2

description:
miRNA level in plasma
array10


title: Unruptured2

description:
miRNA level in plasma
array6


title: genomic DNA from microdissected human kidney47

source_name: kidney 47


title: genomic DNA from microdissected human kidney28

source_name: kidney 28


title: 695_383_24hr_repeat

value: Normal bone cell line 695


title: genomic DNA from microdissected human kidney31

source_name: kidney 31

value: kidney tubule


title: Ovaries, 3wks, SD (10hrs of Light) M05

description: Gene expression in ovary from female hamster raised in SD(10 hours of light per day) by 3wks of age

source_name: Ovaries, 3wks, SD (10hrs of Light)

value: 10hrs of Light


title: genomic DNA from microdissected human kidney40

source_name: kidney 40


title: genomic DNA from microdissected human kidney29

source_name: kidney 29


title: genomic DNA from microdissected human kidney27

source_name: kidney 27


title: Unruptured1

description:
miRNA level in plasma
array5


title: Control4

description:
miRNA level in plasma
array4

source_name: Plasma from healthy control


title: Control3

description:
miRNA level in plasma
array3


title: Ruptured1

description:
miRNA level in plasma
array9

source_name: Plasma from patients with ruptured intracranial aneurysm


title: Ovaries, 8wks, LD (16hrs of Light) M47

description: Gene expression in ovary from female hamster raised in LD(16 hours of light per day) by 8wks of age

source_name: Ovaries, 8wks, LD (16hrs of Light)


title: Ovaries, 3wks, SD (10hrs of Light) M39


title: 695_383_16hr_repeat


title: Ovaries, 8wks, SD (16hrs of Light) M09

source_name: Ovaries, 8wks, SD (16hrs of Light)


title: genomic DNA from microdissected human kidney26

source_name: kidney 26


title: Ovaries, 8wks, LD (16hrs of Light) M64


title: genomic DNA from microdissected human kidney25

source_name: kidney 25


title: Ovaries, 3wks, SD (10hrs of Light) M43


title: Ovaries, 3wks, SD (10hrs of Light) M34


title: Ovaries, 8wks, LD (16hrs of Light) M54


title: Ovaries, 8wks, LD (16hrs of Light) M44


title: 695_383_8hr_repeat


title: 695_383_4hr_repeat


title: 695_383_2hr_repeat


title: Control1

description:
miRNA level in plasma
array1new


title: Control2

description:
miRNA level in plasma
array2new


title: 695_383_0hr_repeat


title: 695-383_24hr


title: genomic DNA from microdissected human kidney24

source_name: kidney 24


title: 695-383_8hr


title: shKDM4C 3, clone 1, rep 2

first: Vivian

middle: G

last: Cheung

state: PA

address: 3615 Civic Center Blvd

institute: University of Pennsylvania/HHMI

description: gene expression data from primary fibroblasts expressing shRNA targeting KDM4C or a control constuct

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2 Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

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 500.

source_name: primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 3, clone 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary fibroblasts were grown in MEM supplemented with 10% FBS, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin, and .5ug/mL Puromycin

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Primary fibroblasts were transfected with shRNA constructs targeting KDM4C or a control construct (SureSilencing shRNA Plasmids, SABiosciences) and selected for stable selection of the constructs with 1ug/mL Puromycin

value: neonatal foreskin

value: primary dermal fibroblasts

tag: shRNA transfection

value: shKDM4C construct 3


title: Ovaries, 3wks, LD (16hrs of Light) M24

description: Gene expression in ovary from female hamster raised in LD(16 hours of light per day) by 3wks of age

source_name: Ovaries, 3wks, LD (16hrs of Light)


title: Ovaries, 3wks, LD (16hrs of Light) M17


title: Ovaries, 3wks, LD (16hrs of Light) M13


title: 695-383_16hr


title: shKDM4C 2, clone 2, rep 1

source_name: primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 2, clone 2

value: shKDM4C construct 2


title: genomic DNA from microdissected human kidney20

source_name: kidney 20


title: 695_383_0hr

description: RB1-383 pGIPZ (OpenBiosystems)(shRB1), human osteoblast cell line (hOB)


title: genomic DNA from microdissected human kidney23

source_name: kidney 23


title: 695-383_4hr


title: genomic DNA from microdissected human kidney22

source_name: kidney 22


title: genomic DNA from microdissected human kidney19

source_name: kidney 19


title: genomic DNA from microdissected human kidney21

source_name: kidney 21


title: shKDM4C 3, clone 1, rep 1


title: 695-383_2hr


title: 142A4_2cell_46hR29.5hG_r4

city: Quebec

first: Ernesto

last: Orozco-Lucero

state: Quebec

address: 2440, Boul. Hochelaga

department: Animal Science

country: Canada

institute: Laval University

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Auto-gain scanning with Tecan technology (PowerScanner)

data_processing: LOESS normalized within array, background subtracted and quantile normalized between array data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: All chemicals were obtained from Sigma-Aldrich, unless otherwise stated.    COCs were aspirated (10 cc syringe, 18G 1 1/2) from slaughterhouse Holstein cow’s ovaries. After 3 washes in TLH (HEPES-buffered Tyrode’s Lactate)/10% bovine serum/0.2 mM pyruvate, groups of up to 10 selected COCs (quality 1-3, Blondin & Sirard, 1995) with at least 5 cumulus layers were cultured under mineral oil in dishes (Nunc) and matured at 38.5°C/5% CO2/20% O2/100% humidity/22-24h in TCM-199 (Gibco)/10% FCS (HyClone, ThermoScientific)/0.1 μg/ml r-hFSH (Serono kit, Gonal F)/1 μg/ml estradiol/0.33 mM pyruvate/50 μg/ml gentamicin.        After IVM, COCs were washed twice in TLH. 5 COCs were added to 48-μl droplets of IVF medium (Tyrode’s Lactate solution/ 0.6% fatty acid free BSA/0.2 mM pyruvate, 10 μg/ml heparin/50 μg/ml gentamicin under mineral oil. 2 μl of 1 mM hypotaurine/2 mM penicillamine/250 mM epinephrine were added to each droplet 10 min before spermatozoa (cryopreserved mixture of ejaculates from 5 bulls, Centre d’Insémination Artificielle du Québec, St-Hyacinthe, QC, Canada). The spermatozoa were thawed in 37°C water for 1 min, put on a discontinuous Percoll gradient (2 ml of 45% Percoll over 2 ml of 90% Percoll), and centrifuged at 700g/30 min/26°C. After discarding the supernatant, the pellet of live spermatozoa was resuspended in IVF medium after being counted on a haemocytometer to obtain a concentration of 1000,000 cells/ml. 2 μl of the sperm suspension were added to each droplet and incubated at 38.5°C/5% CO2/20% O2/100% humidity/18h.        A 3-step mSOF culture system containing MEM essential and non-essential amino acids, 0.5 mM of glycyl-glutamine, and 0.4% fatty acid-free BSA under mineral oil was used. Incubation was performed at 38.5°C/6.5% CO2/5% O2/88.5% N2/100% humidity/8 d. After fertilization, presumptive zygotes were mechanically denuded and washed 3 times in TLH/fatty acid-free BSA and were placed in groups of 10 in 10 μl droplets of SOF1 with non-essential aa (1X) and 3μM EDTA. Embryos were transferred in new 10 μl droplets of SOF2 containing non-essential (1X) and essential (0.5X) aa 72 h post-fertilization and once again 120 h post-fertilization in 20 μl droplets of SOF3 containing non-essential (1X) and essential (1X) aa. Media was replaced 3 times to prevent toxicity due to ammonium accumulation and nutrients depletion. The glucose concentration used in SOF1, 2 and 3 was respectively 0.2, 0.5 and 1.0 mM (Cagnone et al., 2011).        All zygotes cleaved by 29.5- (early-) were separately cultured to distinguish them from those divided at 35- (middle-) and 46 hpi (late cleavers). Batches of 5 cumulus-free 2c-embryos were randomly frozen (-80°C) at each time point. Only the 29.5- and 46 hpi pools (4 replicates) have been used for microarray after total RNA extraction (PicoPure™ RNA Isolation [Arcturus] kit).

extract_protocol:
Total RNA extraction using the PicoPure RNA Isolation Kit from Life Technologies. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Life Technologies). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: time of embryo collection

value: 29.5 hpf (hours post-in-vitro fertilization)

value: 46 hpf (hours post-in-vitro fertilization)


title: shKDM4C 2, clone 2, rep 2


title: shKDM4C 2, clone 1, rep 2

source_name: primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 2, clone 1


title: Ovaries, 3wks, LD (16hrs of Light) M31


title: genomic DNA from microdissected human kidney18

source_name: kidney 18


title: 142A1_2cell_46hR29.5hG_r2


title: 141A3_2cell_29.5hR46hG_r4


title: shKDM4C 1, clone 2, rep 2

source_name: primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 1, clone 2

value: shKDM4C construct 1


title: 695_EV_16hr_repeat


title: 140A4_2cell_46hR29.5hG_r1


title: 695_EV_8hr_repeat


title: 695_EV_24hr_repeat


title: 695_EV_0hr_repeat


title: 695_EV_4hr_repeat1


title: genomic DNA from microdissected human kidney17

source_name: kidney 17


title: shKDM4C 1, clone 2, rep 1


title: shKDM4C 1, clone 1, rep 2

source_name: primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 1, clone 1


title: 140A3_2cell_29.5hR46hG_r2


title: 141A1_2cell_29.5hR46hG_r3


title: genomic DNA from microdissected human kidney13

source_name: kidney 13


title: shKDM4C 2, clone 1, rep 1


title: genomic DNA from microdissected human kidney15

source_name: kidney 15


title: 695_EV_2hr_repeat


title: shKDM4C 1, clone 1, rep 1


title: 140A1_2cell_29.5hR46hG_r1


title: 142A3_2cell_46hR29.5hG_r3


title: shControl clone 2, rep 2

source_name: primary fibroblasts expressing a control shRNA construct, clone 2

value: Control construct


title: genomic DNA from microdissected human kidney16

source_name: kidney 16


title: genomic DNA from microdissected human kidney14

source_name: kidney 14


title: 695-EV_24hr

value: human osteoblast (hOB)


title: 695-EV_16hr

value: Parental


title: genomic DNA from microdissected human kidney12

source_name: kidney 12


title: 695-EV_8hr


title: 695-EV_2hr


title: shControl clone 1, rep1

source_name: primary fibroblasts expressing a control shRNA construct, clone 1


title: 695_EV_0hr


title: shControl clone 2, rep 1


title: OVCA432-48h-miR-506

city: HOUSTON

first: wei

last: zhang

state: TX

address: 1515 Holcombe Blvd, Unit 85

department: Pathology

institute: M. D. Anderson Cancer Center

description: Transcriptional profiling of untreated  and miR-506 transfected with 48hours OVCA432 cells.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Total RNA from OVCA432-control

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

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

value: untreated

source_name: Total RNA from miR-506 treament OVCA432 for 48h


title: genomic DNA from microdissected human kidney11

source_name: kidney 11


title: MII-NF, GnRH Agonist, patient AT

status: Public on Sep 13 2013

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: CC of MII-NF oocyte from GnRH Agonist treated patient AT

hyb_protocol: GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, USA) were hybridized for 16 hours and washed using GeneChip Fluidics Station 450 according to manufacturer’s recommendations.

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

data_processing: Data were normalized using RMA algorithm from R/Bioconductor/XPS package.

label_protocol: 200 ng of RNA was amplified and converted to cDNA using the WT Expression Kit (Ambion, Austin, USA). The resulting cDNA was fragmented and labeled using the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, USA).

growth_protocol: Immediately after oocyte retrieval, CC surrounding the oocyte were removed with a sharp needle, washed in PBS, snap frozen in liquid nitrogen and stored at -80°C in vials until RNA isolation.

extract_protocol: RNA was extracted using TRI reagent (Sigma – Aldrich, St. Louis, USA) according to manufacturer’s instruction with small modification. Due to small sample volume, glycogen was used as a carrier to increase RNA yield. Briefly, CC from individual follicle were homogenized in 500 uL TRI reagent supplemented with 125 g of glycogen (Ambion, Austin, USA). After 2 min incubation at room temperature, 100 uL kloroform was added and sample vortexed vigorously. RNA was precipitated with isopropanol from aqueous phase and collected after 15 min centrifugation at 12,000 x g and 4°C. RNA pellet was washed 3 times by 75% ethanol, dried and dissolved in 15 uL of RNAse free water. The integrity of the RNA samples was assessed on Agilent 2100 Bioanalyzer to assure high quality of total RNA.

treatment_protocol: 21 patients undergoing classical IVF cycle at the Department of Obstetrics and Gynecology, University Medical Center Ljubljana were included. Eleven randomly selected patients were administered GnRH agonist buserelin acetate (Suprefact; Hoechst AG, Frankfurt/Main, Germany) from day 22 with a daily dose of 0.6ml (600pg) subcutaneously. When criteria for ovarian desensitization were fulfilled (eastradiol <0.05nmol/l, follicles <5mm in diameter), patients were subcutaneously administered 225IU of gonadotrophin folitropin alpha (Gonal F; Industria Farmaceutica Serono S.p.A, Bari, Italy). To other ten patients, 225 IU of gonadotrophin folitropin alpha was subcutaneously administered on day 2. When the dominant follicle measured ≥14mm in diameter, the GnRH antagonist cetrorelix acetate (Cetrotide; Asta Medica AG, Frankfurt, Germany) in a dose of 0.25mg was administered subcutaneously. Afterwards, all patients were administered 10.000 IU of the human chorionic gonadotrophin (hCG) (Pregnyl; N.V. Organon) when at least three follicles were ≥17mm and serum oestradiol was ≥0.40nmol/l per follicle; 34-36h later an ultrasound guided transvaginal oocyte retrieval was performed.

tag: patient

value: AT

tag: stimulus

value: GnRH Agonist

tag: oocyte maturity 3

value: MII-NF

tag: oocyte maturity 2

value: MII

tag: cell id


title: 695-EV_4hr

value: Normal bone cell line 695


title: MII-NF, GnRH Agonist, patient BF (2)

description: CC of MII-NF oocyte from GnRH Agonist treated patient BF

value: BF


title: SKOV3-48h-miR-506

description: Transcriptional profiling of untreated  and miR-506 transfected with 48hours SKOV3 cells.

source_name: Total RNA from SKOV3-control

source_name: Total RNA from miR-506 treament SKOV3 for 48h


title: HeyA8-48h-miR-506

description: Transcriptional profiling of untreated  and miR-506 transfected with 48hours HeyA8 cells.

source_name: Total RNA from HeyA8-control

source_name: Total RNA from miR-506 treament HeyA8 for 48h


title: MI, GnRH Agonist, patient AU

description: CC of MI oocyte from GnRH Agonist treated patient AU

value: AU

value: MI


title: MII-BL, GnRH Agonist, patient AT

description: CC of MII-BL oocyte from GnRH Agonist treated patient AT

value: MII-BL


title: MI, GnRH Agonist, patient AT

description: CC of MI oocyte from GnRH Agonist treated patient AT


title: MI, GnRH Agonist, patient AS

description: CC of MI oocyte from GnRH Agonist treated patient AS

value: AS


title: genomic DNA from microdissected human kidney10

source_name: kidney 10

value: kidney tubule


title: genomic DNA from microdissected human kidney8

source_name: kidney 8


title: MII-BL, GnRH Antagonist, patient T

description: CC of MII-BL oocyte from GnRH Antagonist treated patient T

value: T

value: GnRH Antagonist


title: MII-NF, GnRH Antagonist, patient T

description: CC of MII-NF oocyte from GnRH Antagonist treated patient T


title: genomic DNA from microdissected human kidney5

source_name: kidney 5


title: genomic DNA from microdissected human kidney9

source_name: kidney 9


title: MII-BL, GnRH Antagonist, patient P

description: CC of MII-BL oocyte from GnRH Antagonist treated patient P

value: P


title: genomic DNA from microdissected human kidney7

source_name: kidney 7


title: MII-BL, GnRH Antagonist, patient J

description: CC of MII-BL oocyte from GnRH Antagonist treated patient J

value: J


title: MII-BL, GnRH Agonist, patient L

description: CC of MII-BL oocyte from GnRH Agonist treated patient L

value: L


title: MII-BL, GnRH Antagonist, patient G

description: CC of MII-BL oocyte from GnRH Antagonist treated patient G

value: G


title: MI, GnRH Antagonist, patient J

description: CC of MI oocyte from GnRH Antagonist treated patient J


title: MI, GnRH Antagonist, patient BD

description: CC of MI oocyte from GnRH Antagonist treated patient BD

value: BD


title: genomic DNA from microdissected human kidney4

source_name: kidney 4


title: genomic DNA from microdissected human kidney3

source_name: kidney 3


title: MII-BL, GnRH Antagonist, patient BD

description: CC of MII-BL oocyte from GnRH Antagonist treated patient BD


title: MII-BL, GnRH Agonist, patient BF

description: CC of MII-BL oocyte from GnRH Agonist treated patient BF

value: GnRH Agonist


title: MI, GnRH Antagonist, patient G

description: CC of MI oocyte from GnRH Antagonist treated patient G


title: MII-NF, GnRH Agonist, patient BF (1)

description: CC of MII-NF oocyte from GnRH Agonist treated patient BF

value: MII-NF


title: MII-NF, GnRH Agonist, patient BC

description: CC of MII-NF oocyte from GnRH Agonist treated patient BC

value: BC

value: MII


title: MII-NF, GnRH Antagonist, patient P

description: CC of MII-NF oocyte from GnRH Antagonist treated patient P


title: genomic DNA from microdissected human kidney2

source_name: kidney 2


title: genomic DNA from microdissected human kidney6

source_name: kidney 6


title: MII-BL, GnRH Antagonist, patient BB

description: CC of MII-BL oocyte from GnRH Antagonist treated patient BB

value: BB


title: MII-BL, GnRH Agonist, patient BA

description: CC of MII-BL oocyte from GnRH Agonist treated patient BA

value: BA


title: MII-BL, GnRH Antagonist, patient D

description: CC of MII-BL oocyte from GnRH Antagonist treated patient D

value: D


title: genomic DNA from microdissected human kidney1

source_name: kidney 1


title: MII-NF, GnRH Antagonist, patient BB

description: CC of MII-NF oocyte from GnRH Antagonist treated patient BB


title: MII-NF, GnRH Agonist, patient BA

description: CC of MII-NF oocyte from GnRH Agonist treated patient BA


title: MI, GnRH Antagonist, patient D

description: CC of MI oocyte from GnRH Antagonist treated patient D

value: MI


title: MI, GnRH Agonist, patient L

description: CC of MI oocyte from GnRH Agonist treated patient L


title: MII-BL, GnRH Agonist, patient B

description: CC of MII-BL oocyte from GnRH Agonist treated patient B

value: B

value: MII-BL


title: MII-BL, GnRH Agonist, patient BC

description: CC of MII-BL oocyte from GnRH Agonist treated patient BC


title: MII-BL, GnRH Agonist, patient AU

description: CC of MII-BL oocyte from GnRH Agonist treated patient AU

value: AU


title: MII-NF, GnRH Agonist, patient B

description: CC of MII-NF oocyte from GnRH Agonist treated patient B


title: MII-BL, GnRH Antagonist, patient AT

description: CC of MII-BL oocyte from GnRH Antagonist treated patient AT

value: AT

value: GnRH Antagonist


title: MII-NF, GnRH Agonist, patient AU

description: CC of MII-NF oocyte from GnRH Agonist treated patient AU


title: shControl clone 1, rep2

description: gene expression data from primary fibroblasts expressing shRNA targeting KDM4C or a control constuct

source_name: primary fibroblasts expressing a control shRNA construct, clone 1

value: neonatal foreskin

value: primary dermal fibroblasts

value: Control construct


title: MII-NF, GnRH Antagonist, patient AT

description: CC of MII-NF oocyte from GnRH Antagonist treated patient AT


title: MII-NF, GnRH Agonist, patient AS

description: CC of MII-NF oocyte from GnRH Agonist treated patient AS

value: AS


title: MII-BL, GnRH Agonist, patient AS

description: CC of MII-BL oocyte from GnRH Agonist treated patient AS

value: GnRH Agonist


title: MII-NF, GnRH Antagonist, patient AO

description: CC of MII-NF oocyte from GnRH Antagonist treated patient AO

value: AO

value: MII-NF


title: MII-BL, GnRH Agonist, patient AH

description: CC of MII-BL oocyte from GnRH Agonist treated patient AH

value: AH

value: MII


title: MII-BL, GnRH Antagonist, patient AO

description: CC of MII-BL oocyte from GnRH Antagonist treated patient AO


title: MII-BL, GnRH Antagonist, patient A

description: CC of MII-BL oocyte from GnRH Antagonist treated patient A

value: A


title: MII-BL, GnRH Agonist, patient AL

description: CC of MII-BL oocyte from GnRH Agonist treated patient AL

value: AL


title: MI, GnRH Agonist, patient AL

description: CC of MI oocyte from GnRH Agonist treated patient AL

value: MI


title: MII-BL, GnRH Agonist, patient AM

description: CC of MII-BL oocyte from GnRH Agonist treated patient AM

value: AM


title: MII-NF, GnRH Agonist, patient AH

description: CC of MII-NF oocyte from GnRH Agonist treated patient AH


title: MII-NF, GnRH Agonist, patient AM

description: CC of MII-NF oocyte from GnRH Agonist treated patient AM


title: MII-NF, GnRH Antagonist, patient A

description: CC of MII-NF oocyte from GnRH Antagonist treated patient A


title: S41-T-BetKO Stat5ca d54

city: MARSEILLE

first: Nathalie

last: AUPHAN-ANEZIN

address: Parc Scientifique de Luminy

country: France

institute: CIML

description: S41-T-BetKO Stat5ca d54

hyb_protocol: Affy-169 : 125.0 ng at 45 degree_C during 17 hours

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Expression console data processing

source_name: S41-T-BetKO Stat5ca d54

label_protocol:
Affy-FS450-0007
AMBION WT Expression kit-Affy

extract_protocol: standard Affymetrix protocol

value: Spleen and lymph nodes

tag: amount in (ug)

tag: origin

value: purified CD8 T lymphocytes

tag: genotype

value: T-BetKO

tag: strain

tag: developmental stage

value: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d54)

tag: rin number

tag: genetic background

value: memory CD8 T-BetKO lymphocytes expressing an active form of the transcription factor Stat5


title: S39-T-BetKO Stat5ca d14

description: S39-T-BetKO Stat5ca d14

source_name: S39-T-BetKO Stat5ca d14

tag: tissue

value: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d14)

tag: cell type


title: S40-T-BetKO Stat5ca d14

description: S40-T-BetKO Stat5ca d14

source_name: S40-T-BetKO Stat5ca d14


title: naive peripheral CD8 T lymphocytes S36

label_protocol:
standard Affymetrix protocol
AMBION WT Expression kit-Affy

value: naive peripheral CD8 T lymphocytes

value: TCRP1A transgenic Rag-1-/-


title: naive peripheral CD8 T lymphocytes S35


title: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d20) S12

description: S12-TCRP1A Stat5ca d20

source_name: S12-TCRP1A Stat5ca d20


title: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d20) S11

description: S11-TCRP1A Stat5ca d20

source_name: S11-TCRP1A Stat5ca d20


title: Genomic DNA from peripheral blood sample 8

city: New York

first: Andrew

last: Sharp

address: Hess CSM Building Floor Floor 8 Room 116

department: Genetics and Genomics

institute: Icahn School of Medicine at Mount Sinai

description: Case 5

hyb_protocol: Genome-wide measurement of CpG methylation levels was performed by hybridization of bisulfite-converted DNA from each case to Infinium HumanMethylation450 BeadChips, according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

scan_protocol: Scanning was performed using an Illumina HiScan Bead Array scanner according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

data_processing: Array data were processed using the Methylation Module of GenomeStudio v1.8 software using default parameters.

label_protocol: Labelling was performed according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

extract_protocol: Genomic DNA was isolated from peripheral blood samples from each individual, extracted using a custom salt/ethanol precipitation method.

tag: gender

value: female

value: peripheral blood

tag: disease state

value: menstruated at 16 years

value: unbalanced X;14 translocation, 46,X,der(X)t(X;14)(q13;q24)[27]/45,X[3]


title: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d20) S13

description: S13-TCRP1A Stat5ca d20

source_name: S13-TCRP1A Stat5ca d20


title: activated CD8 T lymphocytes transferred in congenic hosts (d120) S32

description: S32-TCRP1A eTL d120

source_name: S32-TCRP1A eTL d120


title: activated (72h) CD8 T lymphocytes transduced to express Stat5ca  S10

description: S10-TCRP1A Stat5ca GFP+ eTL 72h

source_name: S10-TCRP1A Stat5ca GFP+ eTL 72h


title: activated (72h) CD8 T lymphocytes S1

description: S1-TCRP1A eTL 72h

source_name: S1-TCRP1A eTL 72h

value: activated (72h) CD8 T lymphocytes


title: Genomic DNA from peripheral blood sample 4

description: Case 2

source_name: t(X;7)_Case 2

value: premature ovarian failure, secondary amennorhea

value: unbalanced X;7 translocation, 46,X,der(X)t(X;7)(q27;q31)


title: activated CD8 T lymphocytes transferred in congenic hosts (d18) S30

description: S30-TCRP1A eTL d18

source_name: S30-TCRP1A eTL d18


title: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d20) S14

description: S14-TCRP1A Stat5ca d20

source_name: S14-TCRP1A Stat5ca d20


title: Genomic DNA from peripheral blood sample 2

description:
Case 3A
Niece of case 3B.

source_name: t(X;10)_Case 3A

value: developmental delay, secondary amenorrhea

value: unbalanced X;10 translocation, 46,X,der(X)t(X;10)(q26.3;q23.3)


title: activated (72h) CD8 T lymphocytes S2

description: S2-TCRP1A eTL 72h

source_name: S2-TCRP1A eTL 72h


title: Genomic DNA from peripheral blood sample 3

description:
Case 3B
Aunt of case 3A.

source_name: t(X;10)_Case 3B

value: primary amenorrhea


title: Genomic DNA from peripheral blood sample 5

description: Case 1

source_name: t(X;3)_Case 1

value: developmental delay, menstruated at 21 years

value: unbalanced X;3 translocation, 46,X,der(X)t(X;3)(q27.3;p26.2)


title: activated (72h) CD8 T lymphocytes S3

description: S3-TCRP1A eTL 72h

source_name: S3-TCRP1A eTL 72h

value: purified CD8 T lymphocytes


title: sMPNST_JQ1_2day_rep2

first: Ping

last: Chi

address: 417 East 68th Street

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, 15 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 400.

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

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 100.

source_name: sMPNST cells treated with 500 nM JQ1

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: cells grown in DMEM (high glucose, 10% FBS, 1% Pen-strep, 1% Sodium Pyruvate, 1% L-glutamine) medium in 37oC incuabtor

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

treatment_protocol: Cells were plated in the evening. Next day, 1ug/mL  doxycycline was added to induce shRNA expression or JQ1 to final concentration of 500 nM was added

tag: genotype/variation

value: Derived from Nf1-/- P53-/- SKPs

value: spindle cell malignant peripheral nerve sheath tumor cell (SMPNST)

tag: treatment

value: JQ1 treated


title: sMPNST_JQ1_2day_rep3