title: treated (DFO), biological rep4

city: Toronto

first: Liliana

last: Attisano

state: Ontario

address: 160 College Street

department: Biochemistry

institute: University of Toronto

description: Gene expression data from SW480 cells treated with 100 mM of DFO for 6 hours

hyb_protocol: Samples were hybridized to GeneChip® Human Gene 1.0 ST according to affymetrix protocol (GeneChip® WT Terminal  Labeling and Hybridization  User Manual). GeneChips were washed in affymetrix FS450_0007 fluidics station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: 'Log2 GC-RMA signal' data generated using Bioconductor 2.8 (www.bioconductor.org). Batch effect was removed using empirical Bayes approach. Differentially expressed genes were identified by using LIMMA (linear models for microarray data) by fitting a linear model for each spot/gene in the data.

source_name: treated (DFO), biological rep4

label_protocol: The quality of RNA samples was checked by BioAnalyzer and biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 mg total RNA (GeneChip® WT Terminal  Labeling and Hybridization  User Manual).

growth_protocol: SW480 cells were seeded in 6 well plates overnight and the next day they were lysed after 6 hours incubation with compounds.

extract_protocol: RNA was isolated using the PureLink™ Mini Kit.

treatment_protocol: Cells were incubated with 10 mM of compound (OICR623), control (DMSO) (0.1%) and two iron chelators (DFO) (100 mM) and Deferasirox (50 mM) for 6 hours.

value: Colon cancer cell

tag: agent

value: 100 mM of DFO


title: Adductor Muscle ind5 F

status: Public on Oct 16 2011

type: RNA

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

country: France

institute: Universite de caen

description: Adductor Muscle, ind5, F

hyb_protocol: Hybridization was performed using the Agilent’s Gene expression hybridization kit as described by the purchaser with 1.65μg of aRNA samples labeled with Cy3. Subsequently, slides were washed with Gene expression wash buffer kit (Agilent Technologies), dried and stablilized in Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 6.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A matrix of gene expression levels was generated, where each row corresponds to a different gene and each column to one sample. The expression level of each gene was then logarithmically transformed, centered, and reduced, so that relative variations rather than absolute values were used for interpretation.

molecule: total RNA

organism: Magallana gigas

source_name: Adductor Muscle, ind5, F

label_protocol: 200 ng of total RNA was indirectly labeled with Cy3 using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Qiagen's RNeasy mini spin columns were used for purifying amplified RNA (aRNA) samples. After purification, aRNA amplification and dye incorporation rates were controlled using a ND-1000 spectrophotometer (Nanodrop Technologies) and were comprised respectively between 200 and 500 ng/μL (concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation).

extract_protocol: Total RNA was extracted from the tissues with Tri-Reagent kit (Sigma) and subsequently cleaned with nucleospin RNA Clean-up (Macherev Nagel) isolation columns. After homogenisation of the N2 grinding powder in Tri-reagent and the first centrifugation, the aqueous phase was extracted to directly isolate the tota RNA on the column as described by the provide. RNA concentrations were measured using an ND-1000 spectrophotometer (Nanodrop Technologies) and RNA integrity was controlled on the Agilent bioanalyser using RNA 6000 nano kit (Agilent Technologies)

treatment_protocol: Oysters were sampled in july 2010 in Locamriaquer (brittany, France) and their tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80 degrees celcius for total RNA extraction

tag: individual

tag: gender

value: F

tag: tissue

value: Adductor muscle

tag: array


title: iPS cell abrogated iHAC2 F-E4

city: Yonago

first: Masaharu

last: Hiratsuka

state: Tottori

address: Nishicho 86

department: Molecular and Cellular Biology

country: Japan

institute: Tottori university, Faculty of Medicine

hyb_protocol: Cy3-labeled cRNA 1.65 g was combined with spiked in control probes specific for targets on the arrays and hybridized for 17 hours at 65 deg C to Agilent Mouse Whole Genome 44K Oligo Microarrays (Agilent Technologies, Palo Alto, CA). The arrays were washed with Agilent Gene Expression Washing Buffer 1 at room temperature and Agilent Gene Expression Washing Buffer 2 at 37 deg C. The slides were then air-dried.

scan_protocol: Arrays were scanned at a 5um resolution using an Agilent Microarray Scanner, G2505C.

data_processing: Signals were processed by 75% Percentile Shift Normalization in GeneSpring GX11.

organism: Mus musculus

source_name: mouse iPS

label_protocol: total RNA 500 ng was labeled with Cy3 using Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) according to manufacturer’s instructions. Qiagen RNeasy columns (Qiagen Valencia, CA) were used to purify the labeled cRNA.

extract_protocol: For each array sample, the RNA was prepared by using the RNeasy Midi Kit (Qiagen, Valencia, CA). Quality and quantity of the total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell type

value: mouse induced pluripotent stem cells abrogated iHAC2 vector after generation using iHAC2 vector

tag: genetic background


title: treated (Deferasirox), biological rep3

country: Canada

description: Gene expression data from SW480 cells treated with 50 mM of Deferasirox for 6 hours

label: biotin

organism: Homo sapiens

source_name: treated (Deferasirox), biological rep3

tag: cell line

value: 50 mM of Deferasirox


title: Labial Palps ind1 M

description: Labial Palps, ind1, M

source_name: Labial Palps, ind1, M

value: M

value: Labial palps


title: treated (Deferasirox), biological rep2

source_name: treated (Deferasirox), biological rep2


title: iPS cell iHAC2 2-E

value: mouse induced pluripotent stem cells generated by iHAC2 vector

tag: vector

value: iHAC2 with p53 KD and 2 more copies of Oct4 in addition to the construct of iHAC1


title: Mantle ind3 F

description: Mantle, ind3, F

source_name: Mantle, ind3, F

value: Mantle


title: Mantle ind2 F

description: Mantle, ind2, F

source_name: Mantle, ind2, F


title: Mock-transduced mouse CD8+ T cells, pooled sample#4

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-Thy1.1, pooled sample derived from four mice, sample #4

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data from .CEL files were imported into Partek Genomincs Suite using the RMA method. For gene level analyses, probeset level data were merged using the median probeset expression level.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: CD8+ T cells

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: On day zero, transgenic mouse Pmel-1 CD8+ cells expressing a TCR specific for gp100, were enriched with a MACS negative selection kit (Miltenyi Biotech). Cells were activated on plates coated with 2 g/ml anti-CD3 antibody and 1 g/ml of soluble anti-CD28 antibody in culture medium containing 10 ng/ml of IL-2 (Chiron Corporation).

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

treatment_protocol: Twenty four hours after activation, cells were transduced with pMSGV1-ID32aThy1.1 (ID3-transduced group) or pMSGV1-Thy1.1 (mock-transduced group) retrovirus following standard protocol. On day 5, 3e5 cells were transferred into C57BL/6 mice in conjunction with 2E7 pfu rvvhgp100 virus. Five days later, Thy1.1+CD8+ cells were sorted out from CD8+ enriched splenocytes and analyzed using microarrays.

tag: treatment

value: Mock-transduced

tag: batch

value: Array batch 1

tag: strain


title: Adductor Muscle ind1 M

description: Adductor Muscle, ind1, M

source_name: Adductor Muscle, ind1, M


title: treated (DFO), biological rep3

source_name: treated (DFO), biological rep3


title: treated (OICR623), biological rep2

description: Gene expression data from SW480 cells treated with 10 mM of (OICR623) for 6 hours

source_name: treated (OICR623), biological rep2

value: 10 mM of (OICR623)


title: control (DMSO), biological rep4

description: Gene expression data from SW480 cells treated with 0.1% DMSO for 6 hours

source_name: control (DMSO), biological rep4

value: 0.1% DMSO


title: iPS cell iHAC2 2-N


title: Mantle ind1 M

description: Mantle, ind1, M

source_name: Mantle, ind1, M


title: Adductor Muscle ind6 F

description: Adductor Muscle, ind6, F

source_name: Adductor Muscle, ind6, F


title: iPS cell iHAC2 2-C6


title: Adductor Muscle ind2 F

description: Adductor Muscle, ind2, F

source_name: Adductor Muscle, ind2, F


title: Digestive Gland ind3 F

description: Digestive Gland, ind3, F

source_name: Digestive Gland, ind3, F

value: Digestive Gland


title: iPS cell iHAC1 1-C3

value: mouse induced pluripotent stem cells generated by iHAC1 vector

value: iHAC1 with 2 copies of each 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: Digestive Gland ind1 M

description: Digestive Gland, ind1, M

source_name: Digestive Gland, ind1, M


title: iPS cell iHAC2 2-B1


title: Digestive Gland ind6 F

description: Digestive Gland, ind6, F

source_name: Digestive Gland, ind6, F


title: Mantle ind6 F

description: Mantle, ind6, F

source_name: Mantle, ind6, F


title: control (DMSO), biological rep3

source_name: control (DMSO), biological rep3

value: Colon cancer cell


title: Gonad ind1 M

description: Gonad, ind1, M

source_name: Gonad, ind1, M

value: Gonad


title: Digestive Gland ind5 F

description: Digestive Gland, ind5, F

source_name: Digestive Gland, ind5, F

value: F


title: Gonad ind4 M

description: Gonad, ind8, M

source_name: Gonad, ind4, M


title: iPS cell iHAC1 1-D6

source_name: mouse iPS


title: Gonad ind7 M

description: Gonad, ind7, M

source_name: Gonad, ind7, M


title: Gonad ind6 F

description: Gonad, ind6, F

source_name: Gonad, ind6, F


title: treated (DFO), biological rep2

source_name: treated (DFO), biological rep2

value: 100 mM of DFO


title: Gonad ind2 F

description: Gonad, ind2, F

source_name: Gonad, ind2, F


title: iPS cell iHAC1 1-A3


title: treated (Deferasirox), biological rep1

source_name: treated (Deferasirox), biological rep1

value: 50 mM of Deferasirox


title: Gills ind6 F

description: Gills, ind6, F

source_name: Gills, ind6, F

value: Gills


title: Gills ind1 M

description: Gills, ind1, M

source_name: Gills, ind1, M

value: M


title: control (DMSO), biological rep2

source_name: control (DMSO), biological rep2


title: Gills ind5 F

description: Gills, ind5, F

source_name: Gills, ind5, F


title: embryonic stem cell TT2

source_name: mouse ES

value: mouse embryonic stem cells from C57BL/6 x CBA F1 mice

value: C57BL/6 x CBA


title: Gonad ind5 F

description: Gonad, ind5, F

source_name: Gonad, ind5, F


title: iPS cell 20D17

value: mouse induced pluripotent stem cells generated by retrovirus vectors

value: C57BL/6 x DBA

value: retrovirus vectors


title: embryonic fibroblast MEF

source_name: fibroblast

value: mouse embryonic fibroblasts from C57BL/6 mice


title: embryonic stem cell B6 ES

value: mouse embryonic stem cells from C57BL/6 mice


title: Gills ind3 F

description: Gills, ind3, F

source_name: Gills, ind3, F


title: Renal medulla of hypertensive, m68

status: Public on Oct 15 2011

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

description: Gene expression from male hypertensive patient.

hyb_protocol: After fragmentation, ssDNA was hybridized to GeneChip Human Gene 1.0 ST Arrays for 17 hr at 45°C. Chips were washed and stained in the Affymetrix GeneChip Fluidics Stations 450. For all of these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to manufacturer’s recommendations (GeneChip Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip Scanner 3000 7G 4C (Affymetrix) according to the manufacturer’s recommendations (GeneChip Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) in the R application (version 2.11.1). Differentially expressed genes were identified using the moderated two-sample t-test in the Limma package.

source_name: Renal medulla of hypertensive male

label_protocol: 100ng of total RNA was prepared for hybridization according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

growth_protocol: Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery.

extract_protocol: The RNeasy kit (Qiagen) was used for extraction of total RNA according to the manufacturer's instructions. Medulla and cortex were separated and individual RNA was obtained for each of them.

treatment_protocol: Tissue was transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction.

value: male

value: renal medulla

tag: blood pressure

value: hypertensive


title: Renal medulla of hypertensive, m61


title: Renal medulla of hypertensive, m44


title: control (DMSO), biological rep1

source_name: control (DMSO), biological rep1

value: Colon cancer cell

value: 0.1% DMSO


title: Hemocytes Poolc

description: Hemocytes, Poolc

source_name: Hemocytes, Poolc

value: c

value: Hemocytes


title: iPS cell iHAC1 1-B

source_name: mouse iPS

value: mouse induced pluripotent stem cells generated by iHAC1 vector

value: iHAC1 with 2 copies of each 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: Renal medulla of hypertensive, m32


title: Renal medulla of hypertensive, m34


title: Renal medulla of hypertensive, m70


title: Renal medulla of normotensive, m66

description: Gene expression from male normotensive patient.

source_name: Renal medulla of normotensive male

value: normotensive


title: Renal medulla of hypertensive, m29


title: treated (DFO), biological rep1

source_name: treated (DFO), biological rep1

value: 100 mM of DFO


title: Renal medulla of hypertensive, m42


title: Renal medulla of hypertensive, m31


title: Renal medulla of normotensive, m38


title: Renal cortex of hypertensive, c32D

source_name: Renal cortex of hypertensive male

value: renal cortex


title: Renal cortex of hypertensive, c42D


title: Renal medulla of normotensive, m36


title: Renal medulla of normotensive, m16


title: Renal cortex of hypertensive, c31D


title: Renal cortex of normotensive, c38D

source_name: Renal cortex of normotensive male


title: 1078-A12

type: other

city: Rochester

first: Christopher

middle: Taylor

last: Barry

state: NY

address: 601 Elmwood Avenue

department: Transplant Surgery

country: USA

institute: University of Rochester

description: Micro RNA expression from liver transplant patients with HCC

hyb_protocol: Labeled samples were hybridized to Affymetrix micro RNA 1.0 microarrays per the manufacturer's instructions.

scan_protocol: Hybridized arrays were scanned with an Affymetrix GenChip Scanner 7G Plus.

data_processing: CEL files were generated using the miRNA-1_0_2X gain library file. Hybridization quality metrics were assessed using the AffyMir miRNA QCTool program using RMA normalization.

molecule: other

source_name: HCC from explanted liver at time of transplant

label_protocol: MiRNA samples were labeled with the Genisphere FlashTag Biotin labeling kit per the manufacturer's instructions.

extract_protocol: Micro RNA extraction from FFPE tissue blocks using the Roche High Pure miRNA Isolation kit per the manufacturer's instructions.

treatment_protocol: Patients received liver transplants for HCC. Recurrent HCC within 3 years of transplant and Milan criteria status at time of transplant were noted for each patient.

value: hepatocellular carcinoma

tag: recurrence status

value: Recurrence

tag: milan criteria

value: Outside


title: 1048-A5


title: Renal cortex of normotensive, c18D


title: Renal cortex of hypertensive, c44D


title: 1174-B12


title: 1078-A5


title: 1174-B7


title: 1048-A8


title: Renal cortex of normotensive, c16D


title: 1048-A4


title: 882-A7

value: Within


title: 865-A5


title: 865-A6


title: 865-A3


title: 1048-A7


title: 869-D7


title: Renal medulla of normotensive, m18


title: 1174-B10


title: 869-D9


title: 702-A3


title: 882-A3


title: 869-D10


title: 155


title: 1013


title: 941


title: 702-A7


title: 755


title: BMDC-Curdlan100/GMCSF-1

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented cRNAs were hybridized to the standard arrays for 16 hours at 45°C, the arrays were then washed and stained using the fluidics station according to genechip array manufacturer's protocol.

scan_protocol: The genechips were scanned using GeneChip Scanner 3000 according to genechip array manufacturer's protocol.

data_processing: Data was RMA corrected, probes averged using median polish.  Arrays were then quantile normalized. The quantile normalized data was generated using R version 2.13.2.

source_name: CD11b+ FLT3L-derived BM DC

label_protocol: Total RNA samples were amplified and biotinylated according to the Ambion MessageAMP III protocol.

growth_protocol: FLT3L-derived BM DCs were generated by incubating freshly prepared bone marrow (BM) cells for 8 days in IMDM medium supplemented with 100 ng/ml FLT3L, respectively. CD11b+ cells were then purified by magnetic separation.

extract_protocol: Total RNA was extracted following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up . RNA purity was assessed by spectrophotometer (Nanodrop)procedure and total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: CD11b+ fraction of FLT3L generated BM DCs (3-4 x106) were stimulated for 4 hours with 100 or 1 μg/ml curdlan in presence or absence of 5 ng/ml GM-CSF.

tag: protocol

value: Curdlan 100 μg/GMCSF

value: Bone Marrow

value: dendritic cell


title: 718


title: 745


title: BMDC-Curdlan100-2

value: Curdlan 100 μg/ml


title: BMDC-Curdlan100-3


title: BMDC-Curdlan100-1


title: 74-IN-2

value: Non-Recurrence


title: BMDC-Curdlan1/GMCSF-2

value: Curdlan 1 μg/ml/GMCSF


title: 335


title: Renal cortex of hypertensive, c29D

value: male

value: hypertensive


title: BMDC-Curdlan1-3

value: Curdlan 1 μg/ml


title: BMDC-Curdlan100/GMCSF-2


title: BMDC-Curdlan1/GMCSF-1


title: 499


title: BMDC-Curdlan1-2


title: BMDC-Curdlan1-1


title: 351


title: BMDC-Curdlan100/GMCSF-3


title: 274-IE


title: BMDC-Curdlan1/GMCSF-3


title: BMDC-GMCSF-3

value: GMCSF


title: 329


title: 1065


title: BMDC-GMCSF-2


title: treated (OICR623), biological rep1

source_name: treated (OICR623), biological rep1

value: Colon cancer cell

value: 10 mM of (OICR623)


title: 1052


title: 296


title: 688


title: BMDC-GMCSF-1


title: BMDC-Unstimulated-3

value: Unstimulated


title: 854

value: hepatocellular carcinoma


title: 494


title: 484


title: 604


title: 1217-A6

value: Recurrence


title: BMDC-Unstimulated-2


title: 835


title: BMDC-Unstimulated-1


title: 551

value: Outside


title: 297


title: 1205-A6


title: 1177-A5


title: 1205-A7


title: 1177-A6


title: 1177-A8


title: 1217-A12


title: 919-A3

value: Within


title: 879-B16


title: 1094


title: 1205-A12


title: 910-A5


title: 850(15)


title: 910-A6


title: 983


title: 827-A7


title: 855-A5


title: 843-A4


title: 794-A3


title: 827-A4


title: 838-A4


title: 813-A14


title: 1078-A3


title: 813-A18


title: 791-A4


title: 791-A3


title: 785-A4


title: 879-B3


title: 773


title: 775


title: 711


title: 672-A6


title: 672-A5


title: 717-A4


title: 670


title: 585-A4


title: 579-I


title: 692


title: 585-A5


title: 568


title: 646-A7


title: 619


title: 615


title: 540-D


title: Renal medulla miRNA expression of hypertensive, m44D miR

description: miRNA expression from male hypertensive patient.

hyb_protocol: After fragmentation, samples were hybridized to Agilent Human miRNA Microarrays (V3, release 12.0) for 20 hr at 55°C. Chips were washed and stained in the Agilent Microarray Hybridization Chamber SureHyb. The Agilent’s miRNA Complete Labeling and Hyb Kit was used according to Agilent's manual.

scan_protocol: The chips were scanned on an Agilent G2565BA scanner.

data_processing: The samples were between-array normalized so that expression intensities were similar across all arrays using the quantile method, in the R application (version 2.11.1). Differentially expressed miRNAs were identified using the moderated two-sample t-test in the Limma package.

label_protocol: 100ng of total RNA was prepared for hybridization according to the standard Agilent protocol (microRNA Labeling & Hybridization Kit Manual, Agilent, Version 1.7, October 2009).

value: renal medulla


title: 717-A6


title: 577-G


title: 549


title: 446


title: 555


title: Renal medulla miRNA expression of hypertensive, m29D miR


title: Renal medulla miRNA expression of hypertensive, m42D miR


title: Renal medulla miRNA expression of hypertensive, m32D miR


title: 666


title: 481


title: Renal medulla miRNA expression of normotensive, m38D miR

description: miRNA expression from male normotensive patient.

value: normotensive


title: Renal medulla miRNA expression of normotensive, m18D miR


title: 735


title: Renal medulla miRNA expression of normotensive, m16D miR


title: Renal cortex miRNA expression of hypertensive, c44D miR

hyb_protocol: After fragmentation, samples were hybridized to Agilent Human miRNA Microarrays (V3, release 12.0) for 20 hr at 55°C . Chips were washed and stained in the Agilent Microarray Hybridization Chamber SureHyb. The Agilent’s miRNA Complete Labeling and Hyb Kit was used according to Agilent's manual.

value: renal cortex


title: Renal cortex miRNA expression of hypertensive, c32D miR


title: Renal cortex miRNA expression of hypertensive, c31D miR


title: Renal cortex miRNA expression of normotensive, c18D miR


title: Renal cortex miRNA expression of hypertensive, c42D miR


title: Renal cortex miRNA expression of hypertensive, c29D miR


title: Renal cortex miRNA expression of normotensive, c38D miR


title: Renal cortex miRNA expression of normotensive, c16D miR


title: 579-H


title: 540-F


title: 414


title: 12 h post Ara-C treatment

city: Beijing

first: Lv

last: Yi

address: Haidian District,Tsinghua University

department: School Of Medicine

country: China

institute: Tsinghua University

hyb_protocol: standard CapitalBio Methods

scan_protocol: Arrays scanned using a confocal scanner LuxScanTM 10K/A (CapitalBio), and the data of obtained images were extracted with the LuxScan3.0 software (CapitalBio).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (both above 2.0-fold) in both microarray were selected as differentially expressed genes

source_name: NB4 treated with Ara-C for 12 h

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: The NB4 cell line was obtained from Peking Union Medical College. The cells were maintained in RPMI 1640 media (Gibco/Invitrogen, Grand Island, NY) supplemented with 10% (v/v) FBS (fetal bovine serum; PAA, Pasching, Austria), and 1% (v/v) penicillin/streptomycin (Invitrogen). The cells were grown at 37C with 5% CO2.

extract_protocol: Total RNAs were isolated using the Trizol method (Invitrogen).

treatment_protocol: Ara-C was purchased from Sigma-Aldrich (St. Louis, MO). To induce apoptosis, the NB4 cells at a density of 3×10^5 cells/mL were treated with Ara-C at a final concentration of 10-5 M.The incubation period included four time points: 2, 4, 6 and 12 h.

value: NB4 cell (acute promyelocytic leukemia)

source_name: NB4 in log phase of growth_control


title: 2 h post Ara-C treatment

source_name: NB4 treated with Ara-C for 2 h


title: recombinant myxoma virus/ovine BM-DC - II_MOI1_8h

city: Toulouse cedex 03

first: Gilles

last: FOUCRAS

address: 23, chemin des Capelles

institute: INRA

description: cells: BM-DC were infected in vitro with SG33-GFP, an attenuated myxoma virus strain expressing GFP.

hyb_protocol: One ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol. One ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into GeneSpring GX11. Then probe data were filtered on the value and the distribution of their intensity. A total of 6303 probes out of the 15008 probes were retained for further analysis.

organism: Ovis aries

source_name: Mammary epithelial cells (MEC)

label_protocol: The Low RNA input Fluorescent Linear amplification kit (Agilent Technologies) was used to generate Cy3- and Cy5-labelled cRNA. The concentration and the amount of dye hence incorporated were measured using the ND-1000 spectrophotometer (Nanodrop Technologies). After purification of the labelled cRNA, a reference sample that resulted from the pool of 500 ng of each of the samples was done. After fragmentation, 500 ng of cRNA of each samples were hybridized with 500 ng of the reference sample to the ovine oligo-array 019921 Agilent slide (Agilent Technologies), according to a reference design without dye swap, following the manufacturer's protocol.

extract_protocol: Total RNA was extracted from BM-DC  using an extraction method with  RNeasy. Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 8,5 was measured for all samples. Five hundred ng of RNA were converted to double-stranded cDNA and amplified with the Quick amp Labelling kit, two colors  (Ref : 5190-0424, Agilent's technologies).

tag: time

tag: moi

tag: animal id

tag: infection

value: attenuated myxoma virus

source_name: common reference

tag: sample type

value: pool of all samples

value: pool of all Ovine bone marrow-derived dendritic cells infected


title: recombinant myxoma virus/ovine BM-DC - I_MOI1_3h

value: Ovine bone marrow-derived dendritic cells infected


title: recombinant myxoma virus/ovine BM-DC - II_MOI1_0h


title: recombinant myxoma virus/ovine BM-DC - I_MOI1_0h


title: recombinant myxoma virus/ovine BM-DC - II_MOI1_3h


title: E. coli K12_ybjN_OVER-EXPRESSION_M9_rep3

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

hyb_protocol: Prepare hybridization samples 1. Add 20 μl water to dissolve the dried labeled-cDNA (600ng). 2. Add 5 μl 10 × Blocking Agent 3. Add 25 μl 2 × GE × Hybridization Buffer H1-RPM. Mix well by pipetting to reduce bubble formation. Spin for 1 min and place on ice.  Prepare the hybridization assembly 1. Load a clean gasket slide into the Agilent Suretlyb chamber base with the label facing up. 2. Slowly dispense 40 μl hybridization samples onto the gasket well. To minimize bubble formation. 3. Slowly place an array “active side (Agilent facing down)” onto the gasket slide. 4. Place the SureHyb chamber clamp cover on the sandwiched slides and slide the clamp assembly onto both pieces. 5. Hand-tighten the clamp on to the chamber. Rotate the gasket slide when tightening. 6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 7. Place assembled slide chamber in a hybridization oven set to 65°C, 15 rpm. 8. Hybridize at 65°C for 17 h.  Washing This step is performed under dark conditions. 1. Add triton into the X-102 to Gene Expression washing buffer 1 and 2. 2. Pre-warm gene expression wash buffer 2 in a 37°C water bath O/N 3. Dessemble the hybridization chamber, put gaskets and slide into Washing Buffer 1. Use a tweezer to separate the slide from the cover slide. 4. Put the slide into the washing container and array side facing out. Wash for 1 min 5. Transfer the slide into another container containing Washing Buffet 2 and wash for another min. 6. Remove the slide slowly to minimize the attachment of water. Put the slide into a 50 ml tubes in dark places.

scan_protocol: Slides were scanned using an Agilent Scanner (Agilent technologies, Santa Clara, CA, USA) at 5-µm resolution. All slides were scanned using 100% laser power; PMT voltages were automatically adjusted using the Genepix Pro 6.0 software acquisition system to obtain maximal signal intensities with <0.02% probe saturation. The resulting 16 bit images were processed using the GenePix Pro 6.0 image analysis software (v6.0.1.26).

data_processing:
Microarray data normalization
Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method.
1. library(maanova)
go to the directory:
setwd("C:\\Documents and Settings\\Wang\\Desktop\\Erwinia in vivo\\rcsC MBMA")
2. Read data:
Data = read.madata("NormInput.txt", designfile="Designfile1.txt", header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6)
3. Log transformation:
LogData = createData(Data, n.rep=1, log.trans=TRUE)
4. Normalization by Glowess method:
NormalData=transform.madata(LogData, method=c("glowess"))
5. Save the plot files
postscript(file="PlotRawData.ps")
riplot(LogData, onScreen=FALSE)
postscript(file="PlotGLOWESS.ps")
riplot(NormalData, onScreen=FALSE)
6. close the graph:
graphics.off()
norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data)
7. output:
write.table(norm.temp, file="Normal_Data.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE)

Data selection
Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5. Gene functions were assigned using data from EcoCyc (http://ecocyc.org/).

label: Alexa Fluor 555

organism: Escherichia coli

source_name: E. coli K12 ybjN over-expression cells, M9, 8 h

label_protocol:
cDNA labeling was carried out using the FairPlay III Microarray Labeling Kit from Agilent.

Reverse transcription
10 μ g total RNA was used to generate cDNA. Add 1 μl of 500 ng/ μl random primers into the 10 μg total RNA which is dissolved in 12 μl RNase free water. Incubate at 70°C for 10 min in a PCR machine. Cool samples immediately on ice until ready for use. Combine the following components in a sterile, RNase and DNase free tube: 2 μl 10 × AffinityScript RT Buffer; 1 μl 20 × dNTP mix; 1.5 μl 0.1 M DTT; 0.5 μl 40 U/ul RNase Block. Add the annealed primers and RNA into the mixture. Add 3 μl of AffinityScript RT and incubate at 42°C for 60 min. Add 10 μl of 1 M NaOH and incubate at 70°C for 10 min to hydrolyzed RNA. Cool to room temperature and add 10 μl 1 M HCL to neutralize the solution.

cDNA purification
Add 4 μl of 3 M sodium acetate pH 5.5 to the reaction. Add 1 μl of 20 mg/ml glycogen to the reaction. Add 100 μl ice cold 100% ethanol and incubate at -20°C overnight. Spin the reaction at 13.2 rpm for 15 min at 4°C and decant the supernatant (You should see some white pellet at the bottom of the tube). Wash with 200 μl ice cold 70% ethanol and spin 5 min. Decant supernatant carefully and allow for air dry for about 30 min to eliminate ethanol.

cDNA labeling with a reaction fluorescence dye
Prepare the amine-modified cDNA. Thoroughly dissolve the amine-modified DNA in 5 μl of nuclease-free water, warm in a 42°C water bath for 5 min. Prepare labeling buffer: 2.5 g sodium bicarbonate in 100 ml water. Add 3 μl labeling buffer to the amine-labeled cDNA. Dissolve one vial of dye in 2 μl of high quality DMSO, vortex for 10 s. Add the 8 ul amine-modified cDNA into the dissolved dye. Incubate the reaction in dark for 1 h.

Purification of dye-labeled cDNA using QIAquick PCR Purification column
Add 8 μl of nuclease-free water and 2 μl 3 M sodium acetate pH 5.5 to the reaction mixture. Add 100 μl buffer PB to the mixture. Apply the sample to the QIAquick column and centrifuge for 60 s. Discard flow-through and place the QIAquick column back into the same tube. To wash, add 0.75 ml buffer PE to the column and centrifuge for 60 s. Centrifuge in a 2 ml collection tube for 1 min. Place QIAquick column in a clean 1.5 ml tube. Add 50 μl buffer EB and centrifuge for 1 min.

extract_protocol:
Total RNA isolation was performed using the RNeasy Protect Bacteria system from Qiagen.

Sample collection from M9 medium
Grow bacteria overnight in LB medium, reinoculate in M9 minimal medium at an initial OD600 of 0.005. After eight hours growth at 34°C in M9 medium, 2 mL of RNA Protect Reagent (Qiagen) was added to 1 ml bacterial cultures (at OD600 of about 0.5-0.8) to stabilize RNA. Centrifuge for 10 min at 4000 g. Decant the supernatant.

Bacterial lysis
Add 100 μl 1 mg/ml lysozyme buffer (TE buffer: 10 mM Tris-HCL, 1 mM EDTA pH=8.0 containing 1 mg/ml lysozyme). Vortex for 10 s and incubate at RT for at least 15 min. Add 350 μl Buffer RLT and vortex vigorously. Add 250 μl 100% ethanol, mix by pipetting.

Column purification
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C.

tag: genotype

value: ybjN over-expression

tag: growing condition

value: M9 minimal medium

tag: Stage

value: logarithm phase


title: recombinant myxoma virus/ovine BM-DC - III_MOI1_8h

tag: cell type


title: recombinant myxoma virus/ovine BM-DC - III_MOI1_0h


title: 4 h post Ara-C treatment

source_name: NB4 treated with Ara-C for 4 h


title: 6 h post Ara-C treatment

source_name: NB4 treated with Ara-C for 6 h


title: recombinant myxoma virus/ovine BM-DC - III_MOI1_3h


title: E. coli K12_ybjN_MUTANT_M9_rep2

source_name: E. coli K12 ybjN mutant cells, M9, 8 h

value: ybjN mutant


title: E. coli K12_ybjN_MUTANT_M9_rep1


title: recombinant myxoma virus/ovine BM-DC - I_MOI1_8h


title: E. coli K12_ybjN_OVER-EXPRESSION_M9_rep1


title: E. coli K12_ybjN_MUTANT_M9_rep3


title: E. coli K12_ybjN_OVER-EXPRESSION_M9_rep2


title: Sample # 9

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Partek GS 6.4 software (St. Louis, MO) using GCRMA normalization algorithm

source_name: MCF7 cell line

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: Qiagen RNA extraction kit used according to the manufacturer's protocol

treatment_protocol: MCF7 cultured cells with or without retrovirus carrying a constitutivly active RAF1 full length cDNA and xenografts from nude mice.

tag: genotype/variation

value: RAF1 transfected MCF7


title: Sample # 3

value: Wild type


title: Sample # 8


title: Sample # 10

value: Visceral metastases


title: Sample # 7

value: Lung metastases


title: Sample # 5

value: RAF1 transfected first generation


title: Sample # 4


title: Sample # 11


title: Sample # 6


title: Sample # 2

value: First generation


title: E. coli K12_WT_M9_rep2

source_name: E. coli K12 cells, M9, 8 h

value: wild type


title: Kc_48hrs-20HE_CP190-RNAi_rep2

status: Public on Oct 14 2011

city: Atlanta

first: Ashley

middle: M

last: Wood

state: GA

address: 1510 Clifton Rd. RRC 1071B

institute: Emory University

description: This sample is of Kc cells treated with 20HE for 48 hours and RNAi targeting the insulator protein CP190.  This is the second of two biological replicates.

hyb_protocol: Hybridization was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

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

organism: Drosophila melanogaster

label_protocol: Labeling was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: RNA was purified from Kc cell and Mbn2 cells with RNeasy kit (Qiagen) and cDNA synthesis was performed with High-Capacity cDNA Reverse Transctipion kit (Applied Biosystems). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: RNAi target

tag: ecdysone treatment

value: 48 hours


title: Kc_0hrs-20HE_CP190-RNAi_rep2

description: This sample is of Kc cells treated with RNAi targeting the insulator protein CP190.  This is the second of two biological replicates.

source_name: D.melanogaster Kc cells_CP190-RNAi_


title: Kc_0hrs-20HE_control-RNAi_rep2

description: This sample is of Kc cells treated with RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the second of two biological replicates.

source_name: D.melanogaster Kc cells_control-RNAi

value: control (Bgal)


title: Kc_48hrs-20HE_control-RNAi_rep2

description: This sample is of Kc cells treated with 20HE for 48 hours and RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the second of two biological replicates.


title: Kc_48hrs-20HE_CP190-RNAi_rep1

description: This sample is of Kc cells treated with 20HE for 48 hours and RNAi targeting the insulator protein CP190.  This is the first of two biological replicates.


title: Kc_0hrs-20HE_CP190-RNAi_rep1

description: This sample is of Kc cells treated with RNAi targeting the insulator protein CP190.  This is the first of two biological replicates.

source_name: D.melanogaster Kc cells_CP190-RNAi


title: E. coli K12_WT_M9_rep1

tag: strain


title: Kc_3hrs-20HE_CP190-RNAi_rep2

description: This sample is of Kc cells treated with 20HE for 3 hours and RNAi targeting the insulator protein CP190.  This is the second of two biological replicates.

value: 3 hours


title: Kc_3hrs-20HE_CP190-RNAi_rep1

description: This sample is of Kc cells treated with 20HE for 3 hours and RNAi targeting the insulator protein CP190.  This is the first of two biological replicates.


title: Kc_48hrs-20HE_control-RNAi_rep1

description: This sample is of Kc cells treated with 20HE for 48 hours and RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the first of two biological replicates.


title: Sample # 1


title: Kc_0hrs-20HE_control-RNAi_rep1

description: This sample is of Kc cells treated with RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the first of two biological replicates.


title: Kc_3hrs-20HE_control-RNAi_rep2

description: This sample is of Kc cells treated with 20HE for 3 hours and RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the second of two biological replicates.


title: Kc_3hrs-20HE_control-RNAi_rep1

description: This sample is of Kc cells treated with 20HE for 3 hours and RNAi targeting beta-galactosidase that was used as a control knockdown.  This is the first of two biological replicates.


title: PC-3 cell transfection with miR-520c, sample 12 [Set 3]

city: Tokyo

first: Kumiko

last: Ui-Tei

address: 2-11-16 Yayoi Bunkyo-ku

department: Biophysics and Biochemistry, Graduate School of Science

institute: The University of Tokyo

description: RNA extraction at 24 hours after transfection with miR-520c, sample12

hyb_protocol: The cRNA was hybridized against the Agilent Whole Human Genome Microarray (4 × 44 K multipack format) at 65°C for 17 hours, then washed with Gene Expression Wash Buffer 1 and Wash Buffer 2 (Agilent) in 0.005% Triton X-102.

scan_protocol: The microarray slide was scanned using the DNA Microarray Scanner (Agilent) and quantified using Feature Extraction Software (Agilent).

data_processing: Data was analyzed with Agilent Feature Extraction and GeneSpring GX v11.5 software. Quantile normalization and data elimination (removed probes with flag 'M' ) were performed on GeneSpring GX.

label_protocol: After cDNA was synthesized with the Agilent One Color Spike Mix Kit, cRNA was prepared using the Quick Amp Labeling Kit (Agilent), labeled with Cy-3, and purified with the RNeasy Mini Kit (Qiagen).

growth_protocol: Human prostate cancer-derived PC-3 cells were cultured in RPMI-1640 medium (Wako Pure Chemical Industries Industries, Ltd.) with 10% fetal bovine serum (FBS,SigmaIGMA) at 37ºC.

extract_protocol: At 24 hours after transfection,the total RNA was extracted using the RNeasy Mini Kit (Qiagen). As a control, mock transfected cells treated with transfection reagent without siRNA and miRNA were used.Transfection was carried out four times independently, and the RNA quality was examined using Bioanalyzer (Agilent). Mixed RNA samples (150 ng total) of four experiments were used for the microarray analysis.

treatment_protocol: Chemically synthesized dsEcad640, miR-302a, miR-372, miR-373, miR-520c, and miR-520f duplexes were transfected into PC-3 cells.

tag: cell line

value: prostate cancer cell line PC-3

tag: transfection


title: PC-3 cell transfection with mock, sample 9 [Set 3]

description: RNA extraction at 24 hours after transfection with mock, sample9

source_name: mock

value: mock


title: PC-3 cell transfection with miR-373, sample 7 [Set 2]

description: RNA extraction at 24 hours after transfection with miR-373, sample7


title: PC-3 cell transfection with miR-530f, sample 6 [Set 2]

description: RNA extraction at 24 hours after transfection with miR-520f, sample6


title: PC-3 cell transfection with mock, sample 11 [Set 3]

description: RNA extraction at 24 hours after transfection with mock, sample11


title: PC-3 cell transfection with mock, sample 8 [Set 2]

description: RNA extraction at 24 hours after transfection with mock, sample8


title: PC-3 cell transfection with miR-302a, sample 3 [Set 1]

description: RNA extraction at 24 hours after transfection with miR-302a, sample3


title: PC-3 cell transfection with miR-372, sample 10 [Set 3]

description: RNA extraction at 24 hours after transfection with miR-372, sample10


title: PC-3 cell transfection with mock, sample 1 [Set 1]

description: RNA extraction at 24 hours after transfection with mock, sample 1


title: PC-3 cell transfection with miR-372, sample 4 [Set 1]

description: RNA extraction at 24 hours after transfection with miR-372, sample4


title: FUR- mutant vs. WT (dye swap-2)

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

address: 720 4th Ave S

department: Biology

institute: St. Cloud State University

description: no additional information

hyb_protocol: The slides were washed at increasing stringencies (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature).

scan_protocol: the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, MA). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot.

data_processing:
The signal intensity at each spot from the FNR mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing 2.5-fold change.
VALUE column reports log2 (mutant/wt) ratios.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: FUR null mutant

label_protocol: The labelling of the total RNA was performed using indirect labelling with AA-dUTP and subsequent coupling.

growth_protocol: OD600=0.3, anaerobic, LB medium, 20 mM Xylose

extract_protocol: Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by using agarose gel electrophoresis.

source_name: WT


title: PC-3 cell transfection with dsEcad-640, sample 2 [Set 1]

description: RNA extraction at 24 hours after transfection with dsEcad-640, sample2


title: CLL_Peripheral_Blood_GED149 HG_U133plus2 II

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

source_name: peripheral_blood_mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Peripheral blood mononuclear cells from patients with chronic lymphocytic leukaemia (CLL)

tag: FISH (del 13q14)

tag: FISH (del 13q14 single)

tag: FISH (del 17p13)

tag: FISH (trisomy 12)

tag: FISH (no del 13q14, no del 11q22-23, no del 17p13, no trisomy 12)

value: peripheral blood mononuclear cell

tag: disease state

value: CLL


title: CLL_Peripheral_Blood_GED156 HG_U133plus2 II


title: FUR- mutant vs. WT (dye swap-1)

description: no additional information


title: Renal medulla miRNA expression of hypertensive, m31D miR

description: miRNA expression from male hypertensive patient.

source_name: Renal medulla of hypertensive male

tag: gender

value: male

tag: tissue

value: renal medulla

tag: blood pressure

value: hypertensive


title: FUR- mutant vs. WT (dye swap-3)

description: no additional information


title: CLL_Peripheral_Blood_GED143 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED154 HG_U133plus2 II


title: FUR- mutant vs. WT (3)

description: no additional information


title: CLL_Peripheral_Blood_GED146 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED151 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED147 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED148 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED153 HG_U133plus2 II


title: FUR- mutant vs. WT

description: no additional information

extract_protocol: Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by using agarose gel electrophoresis


title: FUR- mutant vs. WT (2)

description: no additional information


title: CLL_Peripheral_Blood_GED139 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED134 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED138 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED129 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED135 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED132 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED133 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED137 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED130 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED124 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED126 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED125 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED119 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED140 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED120 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED121 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED114 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED136 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED115 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED118 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED117 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED123 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED112 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED109 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED113 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED107 HG_U133plus2 II


title: C. elegans ground control, technical rep3

city: Bandar Tun Razak,

first: Sue-Mian

last: Then

state: Kuala Lumpur

address: Jalan Yaacob Latif,

department: UKM Medical Molecular Biology Institute (UMBI)

country: Malaysia

institute: Universiti Kebangsaan Malaysia (UKM)

description: Gene expression data from C. elegans ground control

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operation Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Caenorhabditis elegans

source_name: C. elegans ground control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ng - 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: The worms were cultured in C. elegans maintenance medium; CeMM provided by Bioserve Space Technology, University of Colorado, USA.

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

treatment_protocol: The asynchronous stages of C. elegans were grown through multi-generation (up to +10 generations) on the International Space Station (ISS). The worms were automatically transferred from one chamber to another chamber with fresh CeMM at approximately 1-month intervals. The ground sample was passaged synchronously to the flight sample at the same time.


title: C. elegans ground control, technical rep2


title: C. elegans exposed to space condition, technical rep1

description: Gene expression data from C. elegans exposed to space radiation and microgravity

source_name: C. elegans exposed to space conditions


title: CLL_Peripheral_Blood_GED152 HG_U133B II


title: CLL_Peripheral_Blood_GED111 HG_U133plus2 II


title: C. elegans exposed to space condition, technical rep2


title: CLL_Peripheral_Blood_GED106 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED110 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED150 HG_U133B II


title: C. elegans ground control, technical rep1


title: CLL_Peripheral_Blood_GED102 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED100 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED104 HG_U133plus2 II


title: C. elegans exposed to space condition, technical rep3


title: CLL_Peripheral_Blood_GED103 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED145 HG_U133B II


title: CLL_Peripheral_Blood_GED105 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED144 HG_U133B II


title: CLL_Peripheral_Blood_GED099 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED098 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED092 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED142 HG_U133B II


title: CLL_Peripheral_Blood_GED095 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED088 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED093 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED096 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED094 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED090 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED081 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED141 HG_U133B II


title: CLL_Peripheral_Blood_GED131 HG_U133B II


title: CLL_Peripheral_Blood_GED089 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED084 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED116 HG_U133B II


title: CLL_Peripheral_Blood_GED082 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED087 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED097 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED108 HG_U133B II


title: CLL_Peripheral_Blood_GED128 HG_U133B II


title: CLL_Peripheral_Blood_GED080 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED101 HG_U133B II


title: CLL_Peripheral_Blood_GED079 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED077 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED122 HG_U133B II


title: CLL_Peripheral_Blood_GED074 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED127 HG_U133B II


title: CLL_Peripheral_Blood_GED072 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED075 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED076 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED086 HG_U133B II


title: CLL_Peripheral_Blood_GED071 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED085 HG_U133B II


title: CLL_Peripheral_Blood_GED057 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED056 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED068 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED060 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED078 HG_U133B II


title: CLL_Peripheral_Blood_GED083 HG_U133B II


title: CLL_Peripheral_Blood_GED061 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED070 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED055 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED062 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED063 HG_U133B II


title: CLL_Peripheral_Blood_GED067 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED051 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED047 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED064 HG_U133B II


title: CLL_Peripheral_Blood_GED058 HG_U133B II


title: CLL_Peripheral_Blood_GED048 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED066 HG_U133B II


title: CLL_Peripheral_Blood_GED054 HG_U133B II


title: CLL_Peripheral_Blood_GED053 HG_U133B II


title: CLL_Peripheral_Blood_GED069 HG_U133B II


title: CLL_Peripheral_Blood_GED065 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED049 HG_U133B II


title: CLL_Peripheral_Blood_GED043 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED046 HG_U133B II


title: CLL_Peripheral_Blood_GED059 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED039 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED034 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED045 HG_U133B II


title: CLL_Peripheral_Blood_GED050 HG_U133B II


title: CLL_Peripheral_Blood_GED029 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED026 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED019 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED052 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED028 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED032 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED025 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED040 HG_U133B II


title: CLL_Peripheral_Blood_GED044 HG_U133B II


title: CLL_Peripheral_Blood_GED024 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED023 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED031 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED038 HG_U133B II


title: CLL_Peripheral_Blood_GED012 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED020 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED015 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED035 HG_U133B II


title: CLL_Peripheral_Blood_GED009 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED018 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED016 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED010 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED021 HG_U133B II


title: CLL_Peripheral_Blood_GED008 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED002 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED013 HG_U133B II


title: CLL_Peripheral_Blood_GED022 HG_U133B II


title: CLL_Peripheral_Blood_GED006 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED027 HG_U133B II


title: CLL_Peripheral_Blood_GED036 HG_U133B II


title: CLL_Peripheral_Blood_GED004 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED005 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED033 HG_U133B II


title: CLL_Peripheral_Blood_GED030 HG_U133B II


title: CLL_Peripheral_Blood_GED014 HG_U133B II


title: CLL_Peripheral_Blood_GED017 HG_U133B II


title: CLL_Peripheral_Blood_GED007 HG_U133B II


title: CLL_Peripheral_Blood_GED011 HG_U133B II


title: CLL_Peripheral_Blood_GED150 HGU133B

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization. The 44 HG-U133 A, B chips and the 107 HG-U133 Plus 2.0 chips were normalized separately by the Robust Multichip Average (RMA) method as described by Irizarry et al 2003. Only the 44754 probe sets present on A, B chips and the 2.0 chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method. This data was used in the statistical analysis. Finally we separated the normalized data for publication in GEO again. This separated normalized data is provided in the VALUE column.

tag: life status (censoring day)

tag: overall survival (days)

tag: treatment status (censoring day)

tag: time to treatment (days)

value: Chronic lymphocytic leukemia


title: CLL_Peripheral_Blood_GED145 HGU133B

tag: cell type


title: CLL_Peripheral_Blood_GED001 HG_U133B II


title: CLL_Peripheral_Blood_GED141 HGU133B


title: CLL_Peripheral_Blood_GED003 HG_U133B II


title: CLL_Peripheral_Blood_GED128 HGU133B


title: CLL_Peripheral_Blood_GED131 HGU133B


title: CLL_Peripheral_Blood_GED152 HGU133B


title: CLL_Peripheral_Blood_GED122 HGU133B


title: CLL_Peripheral_Blood_GED127 HGU133B


title: CLL_Peripheral_Blood_GED108 HGU133B


title: CLL_Peripheral_Blood_GED142 HGU133B


title: CLL_Peripheral_Blood_GED066 HGU133B


title: CLL_Peripheral_Blood_GED069 HGU133B


title: CLL_Peripheral_Blood_GED086 HGU133B


title: CLL_Peripheral_Blood_GED064 HGU133B


title: CLL_Peripheral_Blood_GED144 HGU133B


title: CLL_Peripheral_Blood_GED101 HGU133B


title: CLL_Peripheral_Blood_GED085 HGU133B


title: CLL_Peripheral_Blood_GED078 HGU133B


title: CLL_Peripheral_Blood_GED152 HGU133A


title: CLL_Peripheral_Blood_GED116 HGU133B


title: CLL_Peripheral_Blood_GED144 HGU133A


title: CLL_Peripheral_Blood_GED145 HGU133A


title: CLL_Peripheral_Blood_GED063 HGU133B


title: CLL_Peripheral_Blood_GED142 HGU133A


title: CLL_Peripheral_Blood_GED150 HGU133A


title: CLL_Peripheral_Blood_GED058 HGU133B


title: CLL_Peripheral_Blood_GED141 HGU133A


title: CLL_Peripheral_Blood_GED053 HGU133B


title: CLL_Peripheral_Blood_GED131 HGU133A


title: CLL_Peripheral_Blood_GED108 HGU133A


title: CLL_Peripheral_Blood_GED050 HGU133B


title: CLL_Peripheral_Blood_GED046 HGU133B


title: CLL_Peripheral_Blood_GED127 HGU133A


title: CLL_Peripheral_Blood_GED045 HGU133B


title: CLL_Peripheral_Blood_GED116 HGU133A


title: CLL_Peripheral_Blood_GED038 HGU133B


title: CLL_Peripheral_Blood_GED086 HGU133A


title: CLL_Peripheral_Blood_GED128 HGU133A


title: CLL_Peripheral_Blood_GED040 HGU133B


title: CLL_Peripheral_Blood_GED027 HGU133B


title: CLL_Peripheral_Blood_GED101 HGU133A


title: CLL_Peripheral_Blood_GED036 HGU133B


title: CLL_Peripheral_Blood_GED063 HGU133A


title: CLL_Peripheral_Blood_GED058 HGU133A


title: CLL_Peripheral_Blood_GED033 HGU133B


title: CLL_Peripheral_Blood_GED049 HGU133B


title: CLL_Peripheral_Blood_GED078 HGU133A


title: CLL_Peripheral_Blood_GED064 HGU133A


title: CLL_Peripheral_Blood_GED122 HGU133A


title: CLL_Peripheral_Blood_GED044 HGU133B


title: CLL_Peripheral_Blood_GED035 HGU133B


title: CLL_Peripheral_Blood_GED030 HGU133B


title: CLL_Peripheral_Blood_GED085 HGU133A


title: CLL_Peripheral_Blood_GED066 HGU133A


title: CLL_Peripheral_Blood_GED054 HGU133A


title: CLL_Peripheral_Blood_GED053 HGU133A


title: CLL_Peripheral_Blood_GED022 HGU133B


title: CLL_Peripheral_Blood_GED021 HGU133B


title: CLL_Peripheral_Blood_GED050 HGU133A


title: CLL_Peripheral_Blood_GED014 HGU133B


title: CLL_Peripheral_Blood_GED013 HGU133B


title: CLL_Peripheral_Blood_GED069 HGU133A


title: CLL_Peripheral_Blood_GED045 HGU133A


title: CLL_Peripheral_Blood_GED054 HGU133B


title: CLL_Peripheral_Blood_GED011 HGU133B


title: CLL_Peripheral_Blood_GED046 HGU133A


title: CLL_Peripheral_Blood_GED044 HGU133A


title: CLL_Peripheral_Blood_GED049 HGU133A


title: CLL_Peripheral_Blood_GED040 HGU133A


title: 20x Infected Macrophages rep5

city: Cincinnati

first: George

middle: Samuel

last: Deepe

state: Ohio

address: 231 Albert Sabin Way

department: Dept. of Medicine/Division of Infectious Diseases

institute: University of Cincinnati College of Medicine

scan_protocol: 40 cycles; 10 minute hot start at 95 degrees C then each cycle is 95 degrees C followed by 60 degrees C for 1 minute

data_processing: The data were analyzed using the software program provided by SA biosciences on their website. The real time PCR was performed on a Applied Biosystems real time PCR instrument-7500 fast. The software with that instrument calculates the cycle of amplification. That data is then plugged into the program on the website and it calculates the delta CT and delta delta CT. We normalized the data to one of the housekeeping genes, beta actin. AVG Delta(Ct) = (Ct(GOI) - Ave Ct(HKG)). [Further-processed data is available as Series supplementary files.]

label: SYBR green

source_name: 20x Infected Macrophages

label_protocol: 0.5 micrograms of RNA was used to synthesize cDNA using the kit provided by SA Biosciences.

extract_protocol: The RNA was isolated using the Qiagen RNAeasy kit. The RNA was DNase treated and then quantified

tag: strain

value: Bone marrow derived macrophage

tag: infection agent

value: Histoplasma capsulatum


title: CLL_Peripheral_Blood_GED007 HGU133B


title: 5x Infected Macrophages rep5

source_name: 5x Infected Macrophages


title: Uninfected macrophages rep5

source_name: Uninfected macrophages


title: CLL_Peripheral_Blood_GED038 HGU133A


title: CLL_Peripheral_Blood_GED035 HGU133A


title: 5x Infected Macrophages rep4


title: CLL_Peripheral_Blood_GED030 HGU133A


title: 20x Infected Macrophages rep4


title: CLL_Peripheral_Blood_GED003 HGU133B


title: Uninfected macrophages rep4


title: CLL_Peripheral_Blood_GED033 HGU133A


title: CLL_Peripheral_Blood_GED017 HGU133B


title: SMRTmRID E18.5 lungs with PTU, technical replicate 2

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: technical replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: E18.5 lung

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: SMRTmRID in c57Bl6/J bkg

tag: age

value: E18.5 embryos

value: lung

tag: diet


title: CLL_Peripheral_Blood_GED001 HGU133B


title: CLL_Peripheral_Blood_GED036 HGU133A


title: 5x Infected Macrophages rep3


title: Uninfected macrophages rep3


title: CLL_Peripheral_Blood_GED027 HGU133A


title: CLL_Peripheral_Blood_GED022 HGU133A


title: 20x Infected Macrophages rep2


title: CLL_Peripheral_Blood_GED021 HGU133A


title: normal wild-type E18.5 lungs with PTU, technical replicate 1

description: technical replicate 1


title: 20x Infected Macrophages rep3


title: normal wild-type E18.5 lungs with PTU, technical replicate 2

description: technical replicate 2


title: SMRTmRID E18.5 lungs, technical replicate 2

description: technical replicate 2

value: control chow


title: SMRTmRID E18.5 lungs with PTU, technical replicate 1

description: technical replicate 1


title: 5x Infected Macrophages rep2


title: Uninfected macrophages rep1


title: CLL_Peripheral_Blood_GED017 HGU133A


title: SMRTmRID E18.5 lungs, technical replicate 1

description: technical replicate 1


title: normal wild-type E18.5 lungs, technical replicate 2

description: technical replicate 2


title: 20x Infected Macrophages rep1


title: Uninfected macrophages rep2


title: GS115_methanol_6 hr

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Agilent Feature Extraction File:
US83000164_252508810001_S01_GE1_105_Dec08_1_1.txt
Gene expression profile of WT(GS115) cultured in YNBMethanol medium for 6 hr.

hyb_protocol: 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software V 10.5 of Agilent and Normalized using  75th Percentile shift normalization Agilent GeneSpring GX v11 software.

organism: Komagataella pastoris

source_name: GS115 cultured in YNBMethanol for 6 hr

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was isolated from P. pastoris cells by the hot-phenol method (Schmitt et al., Nucleic Acids Res. [1990]18:3091-3092).

tag: genotype/variation

value: wild type

tag: cultured in

value: YNBMethanol

tag: time


title: 5x Infected Macrophages rep1


title: ∆ROP_methanol_24 hr

description:
Agilent Feature Extraction File:
US83000164_252508810001_S01_GE1_105_Dec08_1_4.txt
Gene expression profile of ΔROP cultured in YNBMethanol medium for 24 hr.

source_name: ∆ROP cultured in YNBMethanol for 24 hr

value: ∆ROP


title: CLL_Peripheral_Blood_GED014 HGU133A


title: ∆ROP_methanol_6 hr

description:
Agilent Feature Extraction File:
US83000164_252508810001_S01_GE1_105_Dec08_1_2.txt
Gene expression profile of ΔROP cultured in YNBMethanol medium for 6 hr.

source_name: ∆ROP cultured in YNBMethanol for 6 hr


title: CLL_Peripheral_Blood_GED011 HGU133A


title: normal wild-type E18.5 lungs, technical replicate 1

description: technical replicate 1


title: GS115_methanol_24 hr

description:
Agilent Feature Extraction File:
US83000164_252508810001_S01_GE1_105_Dec08_1_3.txt
Gene expression profile of WT(GS115) cultured in YNBMethanol medium for 24 hr.

source_name: GS115 cultured in YNBMethanol for 24 hr


title: CLL_Peripheral_Blood_GED003 HGU133A


title: CLL_Peripheral_Blood_GED007 HGU133A


title: expt.373 extraction4_array1

status: Public on Oct 13 2011

type: genomic

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

molecule: genomic DNA

source_name: expt.373 extraction4_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: Sex

value: Male


title: expt.645 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;

source_name: expt.645 extraction3_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

tag: tissue


title: expt.1919 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.1919 extraction6_array1 channel_1


title: expt.1160 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(var)3-9-Q2598;target name: Su(var)3-9;host: Rabbit;antigen: AA's 320-419;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2598;short description: Affinity purified antibodies from 80mL rabbit antisera;

source_name: expt.1160 extraction1_array1 channel_1


title: expt.1004 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1004 extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: 3rd Instar Larvae

tag: genotype


title: expt.1527 extraction4_array1

source_name: expt.1527 extraction4_array1 channel_1


title: expt.814 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction4_array1 channel_1


title: expt.1166 extraction1_array1

source_name: expt.1166 extraction1_array1 channel_1


title: expt.1159 extraction3_array1

source_name: expt.1159 extraction3_array1 channel_1


title: expt.1481 extraction3_array1

source_name: expt.1481 extraction3_array1 channel_1


title: expt.1930 extraction5_array1

source_name: expt.1930 extraction5_array1 channel_1


title: expt.453 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.453 extraction2_array1 channel_1


title: expt.1003 extraction7_array1

description: channel ch1 is input DNA;

source_name: expt.1003 extraction7_array1 channel_1


title: expt.815 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.815 extraction2_array1 channel_1


title: expt.1531 extraction5_array1

description: channel ch1 is input DNA;

source_name: expt.1531 extraction5_array1 channel_1


title: CLL_Peripheral_Blood_GED001 HGU133A

source_name: peripheral_blood_mononuclear cells

tag: life status (censoring day)

value: peripheral blood mononuclear cell

tag: disease state


title: expt.644 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.644 extraction4_array1 channel_1


title: expt.675 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Pho;target name: Pho;host: Rabbit;clonal: Unknown;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal rabbit antibody raised against recombinant Pleiohomeotic protein.  Serum used for ChIP (50ul).;

source_name: expt.675 extraction3_array1 channel_1


title: expt.148 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.148 extraction2_array1 channel_1


title: expt.1515 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1515 extraction2_array1 channel_1

extract_protocol:
The template for the dsRNA synthesis was PCR amplified from Drosophila genomic DNA using specific primers extended with 5? T7-promoter tails. The sequence of the T7-promoter tails is as follows: 5?- CTAATACGACTCACTATAGGGAG-3?. The amplicon was selected such that it is contained within single exon. Following PCR the template was purified using PCR purification Kit from Qiagen. 2.5ug of purified template was used to synthesize dsRNA with Ribomax T7 RNA transcription kit from Promega. The dsRNA was precipitated with ethanol, dissolved in 300ul of pure water, denatured by heating to 65C for 30min and re-annealed by slow cooling to room temperature.2x10^6cells were treated with 50ug of dsRNA in 25cm2 T-flask for 1 hour in serum-free Schneider?s media. They were further brought up 6ml of Schneider?s media supplemented with 10% FBS and grown to confluence (~4 days). The cells were passaged to a 75cm2 T-flask and treated the second time with 200ug of dsRNA as described above. Following the treatment the cells were grown to confluence in 15ml Schneider?s media. 1ml of resulted culture was taken for preparation of nuclear and cytoplasmic protein extracts and the rest was in vivo crosslinked with formaldehyde. The protocol typically yields about 7x10^7 crosslinked cells, which is enough for about 7 ChIPs. And the RNAi treated cells were treated with formaldehyde as in normal cultured cell.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).


title: expt.1391 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1391 extraction4_array1 channel_1


title: expt.1609 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1 wa191;target name: HP1a;host: Rabbit;antigen: CYAVEKIIDRRVRKGKVEYYLKWKG;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin;short description: Rabbit polyclonal;

source_name: expt.1609 extraction3_array1 channel_1


title: expt.152 extraction1_array1

source_name: expt.152 extraction1_array1 channel_1


title: expt.1165 extraction6_array1

source_name: expt.1165 extraction6_array1 channel_1


title: expt.939 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.939 extraction4_array1 channel_1


title: expt.646 extraction1_array1

source_name: expt.646 extraction1_array1 channel_1


title: expt.1184 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1184 extraction2_array1 channel_1


title: expt.1179 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2-Ab2 (new lot);target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal to histone H3 di-methyl K9 chIP grade;

source_name: expt.1179 extraction3_array1 channel_1


title: expt.1144 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.1144 extraction6_array1 channel_1


title: expt.1086 extraction5_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K23ac;target name: H3K23ac;host: Rabbit;antigen: Ovalbumin-conjugated synthetic peptide (KQLASAcKAARK-C) corresponding to amino acids 18-27 of yeast histone H3 acetylated on lysine 23 with a C-terminal cysteine added for conjugation purposes;clonal: Polyclonal;purified: Crude;company: Upstate;catalog: 07-355;reference: http://www.millipore.com/catalogue/item/07-355;short description: rabbit polyclonal against a synthetic peptide corresponding to aa 18-27 of yeast histone 3 with K23 acetylated;

source_name: expt.1086 extraction5_array1 channel_1


title: expt.149 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: ZW5;target name: ZW5;host: Rabbit;antigen: GST fusion of aa 5-110 of ZW5 protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Vincent Pirrotta;short description: Rabbit antibody raised against GST fusion protein containing Zeste white 5 sequence.;

source_name: expt.149 extraction1_array1 channel_1


title: expt.897 extraction1_array1

source_name: expt.897 extraction1_array1 channel_1


title: expt.902 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.902 extraction4_array1 channel_1


title: expt.1513 extraction1_array1

source_name: expt.1513 extraction1_array1 channel_1


title: expt.125 extraction3_array1

source_name: expt.125 extraction3_array1 channel_1


title: expt.896 extraction3_array1

source_name: expt.896 extraction3_array1 channel_1


title: expt.116 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.116 extraction4_array1 channel_1


title: expt.1185 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1185 extraction4_array1 channel_1


title: expt.1152 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1152 extraction2_array1 channel_1


title: expt.1785 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1785 extraction4_array1 channel_1


title: expt.903 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.903 extraction2_array1 channel_1


title: expt.1523 extraction5_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: RNA Pol II (abcam);target name: PolII;host: Mouse;antigen: Synthetic peptide: YSPTSpPS (Human). The sequence is repeated multiple times in the C-terminal domain of RNA polymerase II.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab5408;reference: http://www.abcam.com/RNA-polymerase-II-CTD-repeat-YSPTSPS-antibody-4H8-ChIP-Grade-ab5408.html;short description: Mouse Monoclonal (4H8) to RNA polymerase II CTD repeat YSPTSPS (ChIP grade);

source_name: expt.1523 extraction5_array1 channel_1


title: expt.1879 extraction1_array1

source_name: expt.1879 extraction1_array1 channel_1


title: expt.1699 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Smc3 Q2580;target name: Smc3;host: Rabbit;antigen: aa 321-420;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2580;short description: Smc3/Cap (CG9802) aa 321-420;

source_name: expt.1699 extraction3_array1 channel_1


title: expt.1782 extraction3_array1

source_name: expt.1782 extraction3_array1 channel_1


title: expt.1700 extraction1_array1

source_name: expt.1700 extraction1_array1 channel_1


title: expt.1776 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction4_array1 channel_1


title: expt.1793 extraction3_array1

source_name: expt.1793 extraction3_array1 channel_1


title: expt.1531 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.1531 extraction6_array1 channel_1


title: expt.1524 extraction1_array1

source_name: expt.1524 extraction1_array1 channel_1


title: expt.1532 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1532 extraction2_array1 channel_1


title: expt.1756 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1756 extraction4_array1 channel_1


title: expt.1490 extraction1_array1

source_name: expt.1490 extraction1_array1 channel_1


title: expt.1750 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction2_array1 channel_1


title: expt.1761 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Psc;target name: Psc;host: Rabbit;antigen: GST-fusion of aa 819-926 of PSC protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Vincent Pirrotta;short description: Polyclonal rabbit antibody raised against recombinant PSC protein. Eight ug/ul (3ul total) was used for ChIP experiments.;

source_name: expt.1761 extraction3_array1 channel_1


title: expt.1775 extraction1_array1

source_name: expt.1775 extraction1_array1 channel_1


title: expt.1341 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1341 extraction4_array1 channel_1


title: expt.960 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.960 extraction2_array1 channel_1


title: expt.1361 extraction3_array1

source_name: expt.1361 extraction3_array1 channel_1


title: expt.1671 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1671 extraction4_array1 channel_1


title: expt.1672 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: PCL Q3412;target name: PCL;host: Rabbit;antigen: Peptide based on the aa 681-780 of the PCL protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3412;short description: Rabbit polyclonal Ab raised against the PCL protein;

source_name: expt.1672 extraction3_array1 channel_1


title: expt.1075 extraction1_array1

source_name: expt.1075 extraction1_array1 channel_1


title: expt.1871 extraction1_array1

source_name: expt.1871 extraction1_array1 channel_1


title: expt.1750 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction4_array1 channel_1


title: expt.1670 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Pc;target name: Pc;host: Rabbit;antigen: directed against amino acids 191-354 of PC;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal Rabbit antibody against Polycomb protein.;

source_name: expt.1670 extraction1_array1 channel_1


title: expt.1114 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1114 extraction2_array1 channel_1


title: expt.1875 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: mod2.2-VC;target name: MOD(MDG4)67.2;host: Rat;antigen: Polypeptide encoded by exons 5 and 6 of the corresponding mRNA isoform (Mongelard et al. 2002);clonal: Monoclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Antibody against MOD(MDG4)67.2 protein;

source_name: expt.1875 extraction3_array1 channel_1


title: expt.1113 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1113 extraction4_array1 channel_1


title: expt.1586 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: NURF301 Q2602;target name: NURF301;host: Rabbit;antigen: Amino Acids 1155-1254;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2602;short description: Accession Number : AAN11431

source_name: expt.1586 extraction1_array1 channel_1


title: expt.1753 extraction3_array1

source_name: expt.1753 extraction3_array1 channel_1


title: expt.1585 extraction3_array1

source_name: expt.1585 extraction3_array1 channel_1


title: expt.1776 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction2_array1 channel_1