title: 19-22 hrs(I)

description: test-Cy5: RNA are extracted from 21-22 hr ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-24 Scan Time : 12:25:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RNA from 21-22 hr ORER embryos


title: Mid-Late Cycle 14(I)

status: Public on Mar 06 2012

type: RNA

city: Princeton

first: Bing

last: He

state: NJ

address: Washington Rd

department: Molecular Biology

country: USA

institute: Princeton University

description: test-Cy5: RNA are extracted from Cycle 14-15 ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

hyb_protocol: Temperature : 65 C Hybridization buffer : Agilent Hi-RPM hybridization buffer w/ Agilent Blocking Agent Hybridization volume : 220 uL Duration : 17 hr Rotational speed : 20 rpm Amount of extract labeled : 1000 ng

data_processing: Data were normalized using the limma package in R. Arrays were first loess normalized using NormalizeWithinArrays, and then all arrays were quantile normalized according to the reference channel using NormalizeBetweenArrays.

molecule: total RNA

organism: Drosophila melanogaster

source_name: RNA from Cycle 14-15 ORER embryos

label_protocol:
reference URL : http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90051_Two-Color_Tecan.pdf
Kit protocol : Agilent QuickAmp Labeling

extract_protocol:
Extracted molecule : polyA RNA
Extraction description : "TriZol procedure, followed by Qiagen Rneasy Kit clean up"

tag: strain name

value: Oregon R

tag: species

value: D. melanogaster

tag: developmental stage

value: embryo Mid-Late Cycle 14 (~2.5-3 hr)


title: Salivary gland (I)

type: genomic

description: DNA are extracted from fly salivary glands.

hyb_protocol: Temperature : 65 C Hybridization buffer : Agilent Hi-RPM hybridization buffer w/ Agilent Blocking Agent Hybridization volume : 220 uL Duration : 17 hr Rotational speed : 20 rpm Amount of extract labeled : 500 ng

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-24 Scan Time : 11:52:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing: For each sample, the log2 ratios were first normalized using the limma package, then renormalized by setting the median log2-ratio to 0 for known single copy euchromatic probes.

molecule: genomic DNA

source_name: Reference DNA from 0-8 hr ORER embryos

label_protocol:
Type of label : Cy3-dUTP
reference URL : http://tools.invitrogen.com/content/sfs/manuals/18094011.pdf
Kit protocol : Invitrogen BioPrime Kit

extract_protocol:
Extracted molecule : genomic DNA
Extraction description : "proteinase K digestion, followed by phenol/chloroform extraction"

value: embryo 0-8 hr

source_name: DNA from salivary glands

label_protocol:
Type of label : Cy5-dUTP
reference URL : http://tools.invitrogen.com/content/sfs/manuals/18094011.pdf
Kit protocol : Invitrogen BioPrime Kit

value: third instar larva, salivary gland


title: 130112: 2Rhet mapping

description: aCGH analysis of genomic DNA from 130112 embryos (Chr2R- embryos; from Chr2En females).

scan_protocol: Pixel Size : 5 Scan Date : 2010-07-08 Scan Time : 15:47:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing: Samples with large chromosomal deletions result in arrays containing a large number of features with very extreme red to green ratios.  Standard normalization approaches assume that on average all features will center at 0, and so are not applicable to data from samples with large deletions.  Array data were normalized using the limma package in R (Smyth and Speed, 2003). Arrays were first normalized by variance stabilization between arrays using NormalizeBetweenArrays (Huber et al., 2002).  A control array of cycle 14 wild type Oregon R embryos hybridized to the usual 0-8 hour wild type Oregon R embryo reference was the training model for variance stabilization. Following normalization between arrays, each array was normalized using NormalizeWithinArrays with all mapped probes present at normal diploid levels as control probes.  The result of this normalization was that normal diploid probes were centered to a log2 ratio equal to 0, and the log2 ratios of all other probes were normalized accordingly.  Replicate probes present on the array were collapsed with the avedups function in the limma package.

source_name: Reference DNA from ORER embryos

source_name: DNA from 130112 embryos.  C2entire female

value: embryo 3.5-8 hr


title: 0-1 hrs(I)

description: test-Cy5: RNA are extracted from 0-1 hour ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-24 Scan Time : 12:08:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RNA from 0-1 hr ORER embryos

value: embryo 0-1 hr


title: 0-1 hrs(II)

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-27 Scan Time : 12:42:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 101579: 2Rhet mapping

description: aCGH analysis of genomic DNA from 101579 embryos (Chr2R- embryos).

scan_protocol: Pixel Size : 5 Scan Date : 2010-07-07 Scan Time : 14:25:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from 101579 embryos


title: Cycle 13-early Cycle 14(I)

description: test-Cy5: RNA are extracted from Cycle 12-13 ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

source_name: RNA from Cycle 12-13 ORER embryos

value: embryo Cycle 13-Early Cycle 14 (~2-2.5 hr)


title: 114n: Xhet mapping

description: 114n: DNA is extracted from nullo embryos generated from cross between y w spl fog114/FM7/y+Ymal126 males and C(1)DX ywf females. The mutant embryos lack the X chromosome but bear a small fragment of X on Y.

scan_protocol: Pixel Size : 5 Scan Date : 2010-10-12 Scan Time : 14:00:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Reference DNA from 0-8 hour ORER embryos

source_name: DNA: nullo embryos from cross of y w spl fog114/FM7/y+Ymal126 males to C(1)DX ywf females


title: Salivary gland (II)

description: DNA extracted from salivary gland (biological repeat 2)

scan_protocol: Pixel Size : 5 Scan Date : 2010-04-01 Scan Time : 17:12:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Reference DNA from 0-8 hr ORE R embryos

source_name: DNA from salivary glands (biological repeat 2)


title: 107387: 2Rhet mapping

description: aCGH analysis of genomic DNA from 107387 embryos (Chr2R- embryos).

source_name: DNA from 107387 embryos


title: B5280: Xhet mapping

description: aCGH analysis of genomic DNA from B5280 nulloX embryos (from B5280 stock).

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-22 Scan Time : 15:09:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Reference DNA from ORER embryos.

source_name: DNA from B5280 embryos.


title: 186f: Xhet mapping

description: 186f: DNA is extracted from fog embryos generated from cross between In(1)sc8 Df(1)mal12 B/y+ Ymal males and C(1)DX ywf females. The only X chromosome that the mutant embryos bear is deficient for a region covering the fog gene.

scan_protocol: Pixel Size : 5 Scan Date : 2010-10-12 Scan Time : 13:43:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA: fog embryos from cross of In(1)sc8 Df(1)mal12 B/y+ Ymal males to C(1)DX ywf females


title: B2580: Xhet mapping

description: aCGH analysis of genomic DNA from B2580 embryos (nullo X with duplication of B2580).

scan_protocol: Pixel Size : 5 Scan Date : 2010-07-07 Scan Time : 14:09:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from B2580 embryos


title: 130093: 2Rhet mapping

description: aCGH analysis of genomic DNA from 130093 embryos (Chr2R- embryos; from Chr2En females).

source_name: DNA from 130093 embryos.  C2entire female


title: 175: Xhet mapping

description: 175: DNA is extracted from nullo embryos generated from cross between Df(1)RT645, y- / Y2 sc Y males and C(1)DX ywf females. The mutant embryos lack the X chromosome but bear a small fragment of X on Y.

scan_protocol: Pixel Size : 5 Scan Date : 2010-10-12 Scan Time : 11:41:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA: nullo embryos from cross of Df(1)RT645, y- / Y2 sc Y males to C(1)DX ywf females


title: 168: Xhet mapping

description: 168:DNA is extracted from nullo embryos generated from cross between arm YD35 / y2 Y67g males and C(1)DX ywf females. The mutant embryos lack the X chromosomes but bear a small fragment of X on Y.

source_name: DNA: nullo embryos from cross of YD35 / y2 Y67g males to C(1)DX ywf females


title: 130058: 2Rhet mapping

description: aCGH analysis of genomic DNA from 130058 embryos (Chr2R- embryos; from Chr2En females).

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-22 Scan Time : 15:25:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from 130058 embryos.  C2entire female.


title: 114f: Xhet mapping

description: 114f: DNA is extracted from fog embryos generated from cross between y w spl fog114/FM7/y+Ymal126 males and C(1)DX ywf females. The only X chromosome that the mutant embryos bear is deficient for a region covering the fog gene.

source_name: DNA: fog embryos from cross of y w spl fog114/FM7/y+Ymal126 males to C(1)DX ywf females


title: Ovary

description: DNA are extracted from fly ovaries. Stage 10 egg chambers are enriched.

source_name: Reference DNA from 0-8 hr ORER embryos

source_name: DNA from ovaries

value: adult ovary


title: 186n: Xhet mapping

description: 186n: DNA is extracted from nullo embryos generated from cross between In(1)sc8 Df(1)mal12 B/y+ Y males and C(1)DX ywf females. The mutant embryos lack the X chromosome but bear a small fragment of X on Y.

source_name: DNA: nullo embryos from cross of In(1)sc8 Df(1)mal12 B/y+ Y males to C(1)DX ywf females


title: 2219: 2Rhet mapping

description: aCGH analysis of genomic DNA from 2219 embryos (Chr2R- embryos; from Chr2En females).

source_name: DNA from 2219 embryos.  C2entire female.


title: 101988: 2Rhet mapping

description: aCGH analysis of genomic DNA from 101988 2R- embryos (from C2En female).

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-22 Scan Time : 14:53:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from 101988 embryos.  C2entire female.


title: 101042 (ChrX euchromatin-)

description: aCGH analysis of genomic DNA from 101042 nulloX embryos (from attached X female).

source_name: Reference DNA from ORER embryos

source_name: DNA from 101042 embryos

value: 101042 (ChrX euchromatin-)


title: ChrX-

description: aCGH analysis of DNA from ChrX- embryos, repeat hybridization of samples labeled by Bing He on 9/1/2009

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-19 Scan Time : 12:37:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

tag: genotype/variation

value: wild type

source_name: DNA from ChrX- embryos

tag: genotype/variation name


title: WT (Cycle14 ORE R)

description: DNA samples are extracted from ORER cycle 14 embryos.

scan_protocol: Pixel Size : 5 Scan Date : 2009-11-25 Scan Time : 15:45:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from ORER cycle 14 embryos

value: embryo 2.5-3.5 hr


title: 130186 (Chr2L euchromatin-)

description: aCGH analysis of genomic DNA from 130186 2L- embryos (from C2En female).

source_name: DNA from 130186 embryos, C2entire female

value: 130186 (Chr2L euchromatin-)


title: 102004 (Chr3L euchromatin-)

description: aCGH analysis of genomic DNA from 102004 3L- embryos (from C3En female).

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-22 Scan Time : 13:44:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from 102004 embryos. C3entire females

value: 102004 (Chr3L euchromatin-)


title: Chr3entire-

description: DNA extracted from embryos missing the entire third chromosome (from C3En stock).

scan_protocol: Pixel Size : 5 Scan Date : 2010-07-21 Scan Time : 13:16:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Chr3 entire- embryos

value: C(3)EN, 3entire-


title: ChrXY-

description: aCGH analysis of DNA from ChrXY- embryos, repeat hybridization of samples labeled by Bing He on 9/1/2009

source_name: DNA from ChrXY- embryos

value: attached-XY, XY-


title: Chr3R-

description: aCGH analysis of DNA from Chr3R- embryos, repeat hybridization of samples labeled by Bing He on 9/1/2009

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-19 Scan Time : 12:20:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DNA from Chr3R- embryos


title: cultivar: IR24 - strain: PXO99AME2 - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: IR24 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0001053 3 leaf fully expanded (Development Stage); 14 days (Age); peat/perlite/soil (Growth Media).

hyb_protocol: standard Affymetrix Protocol

scan_protocol: standard Affymetrix Protocol

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

label: biotin

molecule: polyA RNA

organism: Oryza sativa

source_name: leaf (cultivar: IR24 - strain: PXO99AME2)

label_protocol: Affymetrix (AGRF)

extract_protocol: TRIZOL RNA extraction

tag: cultivar

tag: infection

value: Xanthomonas oryzae  PXO99AME2

tag: tissue

value: leaf

tag: age


title: cultivar: IR24 - strain: PXO99AME2 - rep3


title: Control sample 9

city: Philadelphia

first: Nadir

last: Yehya

state: PA

address: 390 Towne Bldg, U Penn

department: Bioengineering

institute: University of Pennsylvania

description: Each array was hybridized with each sample labeled with Hy5 against a Common Reference (labeled Hy3). Common Reference is an equal (same ng of RNA) mix of all sample groupings (Control, 1hr stretch, 6hr stretch) from each of the 12 individual samples pooled together.

hyb_protocol: Mix dyed samples with warmed hyb buffer; denature 95C x 3min; snap cool on ice 2-15min; centrifuge max 1min; apply sample to Agilent coverslip and slide, and assemble hyb apparatus; hyb 56C x 16hr rotation speed 4; wash 3x with buffers A, B, C 2min each, rinse with water, dry by centriguge 800rpm x 3min

scan_protocol: Images acquired at 635 and 532 nm using GenePix 4000B, analyzed genePix pro 6.0.1.27

data_processing: The software was Partek Genomics Suite (version 6.4) where background subtracted intensities were extracted, any background intensity below 1 was changed to 1, and loess normalization was applied.

organism: Rattus norvegicus

source_name: Control

label_protocol: Adjust RNA and volume to 0.25ug to 1ug in 2ul of nuclease free water; add CIP buffer, enzyme, and spike-in RNA at 37C x 30min; quench 95C x 5min; snap cool on ice 2-15min; mix with Labeling buffer, enzyme, dye, and DMSO 16C x 1hr; quench 65C x 15min, cool to 4C; hybridization within 1 hour

extract_protocol: Quiagen miRNAeasy Kit per protocol; quality control with Agilent 2100 bioanalyzer

treatment_protocol: Isolated type II cells from whole lung, grown for 5 days in MEM + 0.1x FBS until cells attain type I characteristics

tag: cell type

value: Primary alveolar epithelial cell

tag: strain

value: Sprague Dawley

tag: gender

value: male

tag: weight


title: cultivar: IR24 - strain: PXO99AME1 - rep3

source_name: leaf (cultivar: IR24 - strain: PXO99AME1)

value: Xanthomonas oryzae  PXO99AME1


title: cultivar: IR24 - strain: PXO99A-2 - rep2

source_name: leaf (cultivar: IR24 - strain: PXO99A-2)

value: Xanthomonas oryzae  PXO99A-2


title: cultivar: IR24 - strain: PXO99A-2 - rep1


title: cultivar: IR24 - strain: PXO99A-2 - rep3


title: Chr2L-

description: DNA samples are extracted from C2V halo embryos.

scan_protocol: Pixel Size : 5 Scan Date : 2009-11-25 Scan Time : 16:01:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: D. melanogaster

value: Oregon R

value: embryo 0-8 hr

source_name: DNA from C2V halo (2L-) embryos

value: embryo 3.5-8 hr


title: cultivar: IR24 - strain: PXO99AME1 - rep2


title: Stretch 1 hour sample 8

source_name: Stretch 1 hour


title: Control sample 8


title: Stretch 1 hour sample 9


title: Stretch 6 hours sample 9

source_name: Stretch 6 hours


title: Stretch 6 hours sample 8


title: cultivar: IR24 - strain: PXO99AME1 - rep1


title: Chr2entire-

description: aCGH analysis of DNA from Chr2 entire - (2794 halo) embryos, repeat hybridization of samples labeled by Bing He on approximately 5/15/2009 (original data are in Amy's archive, experiment 111584)

scan_protocol: Pixel Size : 5 Scan Date : 2010-03-19 Scan Time : 12:53:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: wild type

source_name: DNA from Chr2entire- embryos

value: C(2)EN, 2entire-


title: cultivar: IR24 - strain: BLS303 - rep3

source_name: leaf (cultivar: IR24 - strain: BLS303)

value: Xanthomonas oryzae  BLS303


title: cultivar: IR24 - strain: PXO99AME2 - rep1


title: Chr2R-

description: aCGH analysis of DNA from Chr2R- embryos, repeat hybridization of samples labeled by Bing He on approximately 5/15/2009 (original data are in Amy's archive, experiment 111583)

source_name: Reference DNA from ORER embryos

source_name: DNA from Chr2R- embryos


title: Chr4entire-

description: aCGH analysis of genomic DNA from Chr4En(-) embryos (~22-26 hr old).

source_name: DNA from Chr4- embryos

value: C(4)RM, 4entire-

value: embryo 23-24 hr


title: Stretch 6 hours sample 7


title: Control sample 7


title: cultivar: IR24 - strain: PXO86 - rep2

source_name: leaf (cultivar: IR24 - strain: PXO86)

value: Xanthomonas oryzae  PXO86


title: cultivar: IR24 - strain: BLS303 - rep2


title: Stretch 1 hour sample 7


title: cultivar: IR24 - strain: PXO86 - rep1


title: cultivar: IR24 - strain: T7174 - rep3

source_name: leaf (cultivar: IR24 - strain: T7174)

value: Xanthomonas oryzae  T7174


title: cultivar: IR24 - strain: BLS303 - rep1

value: leaf


title: Control sample 6

value: Primary alveolar epithelial cell


title: Stretch 6 hours sample 6

value: Sprague Dawley


title: cultivar: IR24 - strain: T7174 - rep2


title: cultivar: IR24 - strain: PXO86 - rep3


title: cultivar: IR24 - strain: T7174 - rep1


title: cultivar: IR24 - strain: NO TREATMENT - rep3

source_name: leaf (cultivar: IR24 - strain: NO TREATMENT)

value: untreated


title: cultivar: IR24 - strain: NO TREATMENT - rep2


title: cultivar: IR24 - strain: PXO99AME5 - rep2

source_name: leaf (cultivar: IR24 - strain: PXO99AME5)

value: Xanthomonas oryzae  PXO99AME5


title: cultivar: IR24 - strain: MOCK - rep3

source_name: leaf (cultivar: IR24 - strain: MOCK)

value: mock


title: Chr3L-

description: aCGH analysis of DNA from Chr3L- embryos, repeat hybridization of samples labeled by Bing He on 9/1/2009

value: D. melanogaster

source_name: DNA from Chr3L- embryos


title: Stretch 1 hour sample 6

value: male


title: cultivar: IR24 - strain: MOCK - rep1


title: RD19

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description: retina free of retinal pigment epithelium (RPE)

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: GCRMA

organism: Homo sapiens

source_name: retina

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

extract_protocol: Retinal tissue was dissected free of retinal pigment epithelium (RPE) and placed in guanidine HCL.  The samples were subsequently disrupted and homogenized using a rotor–stator  (Polytron PT2100).  Total RNA used for microarray studies was purified  from a caesium chloride gradient produced by high-speed  ultra-centrifugation.

treatment_protocol: Retina samples were collected from patients with or without rhegmatogenous retinal detachment (RD)

tag: retinal detachment

value: yes

tag: patient identifier

tag: total rd duration

value: 4 months


title: cultivar: IR24 - strain: MOCK - rep2


title: cultivar: IR24 - strain: NO TREATMENT - rep1


title: RD16

value: 3 months


title: cultivar: IR24 - strain: PXO99A - rep3

source_name: leaf (cultivar: IR24 - strain: PXO99A)

value: Xanthomonas oryzae  PXO99A


title: cultivar: IR24 - strain: PXO99AME7 - rep2

source_name: leaf (cultivar: IR24 - strain: PXO99AME7)

value: Xanthomonas oryzae  PXO99AME7


title: RD15

value: 2 months


title: RD17

value: 1 week


title: RD18

value: 1 month


title: cultivar: IR24 - strain: PXO99AME7 - rep1


title: cultivar: IR24 - strain: PXO99AME5 - rep1


title: cultivar: IR24 - strain: PXO99A - rep2


title: RD14


title: RD13

value: 6 months


title: cultivar: IR24 - strain: PXO99AME5 - rep3

value: leaf


title: RD12


title: cultivar: IR24 - strain: PXO99AME7 - rep3


title: RD11


title: (pre)adipocytes, 3 days of differentiation, donor 2

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

country: Germany

institute: Miltenyi Biotec GmbH

description: female, 37 y, BMI 21.67, subcutaneous thighs

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

label_protocol: 1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Subcutaneous human preadipocytes were incubated in basal growth medium (Cambrex) containing 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml penicilline and 100 µg/ml streptomycine (= culture medium).

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: Differentiation into adipocytes was initiated by addition of 10 µg/ml insulin, 1 µM dexamethasone, 200 µM indomethacin and 500 µM isobutylmethylxanthine (Cambrex) to the culture medium.

value: preadipocytes

tag: time

value: 3 days of differentiation

tag: individual

value: donor 2


title: cultivar: IR24 - strain: PXO99A - rep1


title: cultivar: Nipponbare - strain: PXO99A-2 - rep3

description: Nipponbare (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0001053 3 leaf fully expanded (Development Stage); 14 days (Age); peat/perlite/soil (Growth Media).

source_name: leaf (cultivar: Nipponbare - strain: PXO99A-2)

value: Nipponbare

value: Xanthomonas oryzae  PXO99A-2


title: preadipocytes, no differentiation, donor 2

value: 0 days of differentiation


title: cultivar: Nipponbare - strain: PXO99AME2 - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO99AME2)

value: Xanthomonas oryzae  PXO99AME2


title: (pre)adipocytes, 3 days of differentiation, donor 1

description: female, 33 y, BMI 21.56, subcutaneous thighs

value: donor 1


title: (pre)adipocytes, 7 days of differentiation, donor 3

description: female, 34 y, BMI 22.24, subcutaneous abdomen

value: 7 days of differentiation

value: donor 3


title: cultivar: Nipponbare - strain: PXO99AME2 - rep2


title: RD8

value: yes

value: 7 months


title: RD9

value: 2 months


title: RD7

value: 1 year


title: cultivar: Nipponbare - strain: PXO99AME1 - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO99AME1)

value: Xanthomonas oryzae  PXO99AME1


title: (pre)adipocytes, 3 days of differentiation, donor 3


title: cultivar: Nipponbare - strain: PXO99AME1 - rep2


title: cultivar: Nipponbare - strain: PXO99A-2 - rep2


title: cultivar: Nipponbare - strain: PXO99AME1 - rep1


title: RD5

value: 1 month


title: cultivar: Nipponbare - strain: PXO99A-2 - rep1

value: leaf


title: (pre)adipocytes, 7 days of differentiation, donor 1

value: preadipocytes


title: RD10


title: cultivar: Nipponbare - strain: BLS303 - rep2

source_name: leaf (cultivar: Nipponbare - strain: BLS303)

value: Xanthomonas oryzae  BLS303


title: cultivar: Nipponbare - strain: PXO86 - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO86)

value: Xanthomonas oryzae  PXO86


title: cultivar: Nipponbare - strain: PXO86 - rep2

value: Nipponbare


title: cultivar: Nipponbare - strain: BLS303 - rep3


title: preadipocytes, no differentiation, donor 3


title: RD4

value: 6 months


title: (pre)adipocytes, 7 days of differentiation, donor 2

value: donor 2


title: E2 treatment 48h rep2

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: MCF7 BCa cells

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

growth_protocol: MCF7/Runx2dox cells were maintained in DMEM supplemented with 10% FBS and 50µg of Hygromycin

extract_protocol: RNA was extracted with Bio-Rad Aurum Total RNA mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel analysis.

treatment_protocol: MCF7/Runx2dox cells were treated with 0.5µg/ml doxycycline or 10nM estradiol and/or both for 48h

tag: cell name

value: MCF7/Rx2dox cells

tag: cell line

tag: transgene

value: Runx2 expression upon doxycycline treatment

tag: treatment


title: cultivar: Nipponbare - strain: PXO99AME2 - rep1

tag: cultivar

value: Xanthomonas oryzae  PXO99AME2


title: RD3

value: > 3 months


title: Dox and E2 treatment 48h rep2

value: Dox + E2


title: RD6

value: yes

value: 3 weeks


title: cultivar: Nipponbare - strain: T7174 - rep3

source_name: leaf (cultivar: Nipponbare - strain: T7174)

tag: infection

value: Xanthomonas oryzae  T7174


title: RD2

value: 1 year


title: Dox and E2 treatment 48h rep1


title: E2 treatment 48h rep1


title: cultivar: Nipponbare - strain: PXO86 - rep1

tag: tissue


title: RD1

value: 2 months


title: Ethanol treatment 48h rep3

description: Control

value: Control


title: Control-ko-b

city: shanghai

first: Luan

last: Yang

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

country: China

institute: Shanghai Institute of Medicine of Chinese Academy of Medical Sciences

description:
Gene expression for Dicer1 KO mouse
In the present study, Alb promoter-driven Cre recombinase transgenic mice (Albumin-Cre mice) and mice carrying the floxed allele of Dicer1 (Dicer1loxP/loxP mice) were crossed to obtain hepatocyte-specific Dicer1 knockout mice (Albumin-Cre;Dicer1loxP/loxP mice). Dicer1loxP/loxP littermates were used as controls throughout the experiment.

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60 ℃ for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F(Platform GPL4134) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent's Feature Extraction v.10.5.1.Data were analyzed with GeneSpring GX 10.0. Normalization method by quantile.

organism: Mus musculus

source_name: Liver Dicer1 KO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The recommendations set forth by our Institutional Animal Care and Use Committee for the handling, maintenance, treatment, and sacrifice of animals were followed. Dicer1 KO are gift from Chinese Academy of Sciences. Six-month-old female mice were injected intraperitoneally with a single dose of 120 mg/kg body weight ENU (CAS# 759–73–9, Sigma, St. Louis, MO) or the vehicle dimethylsulfoxide (DMSO, Sigma) in a volume of 2 ml/kg body weight.

extract_protocol: RNA was prepared using RNeasy Plus Mini Kit (Qiagen,German) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The tissues were isolated and frozen at -80°C. The liver samples were used for this study. All animal experiments were conducted by following the recommendations set forth by our Institutional Animal Care and Use Committee.

tag: genotype/variation

value: Dicer1 KO

tag: agent

value: control

value: Liver


title: cultivar: Nipponbare - strain: T7174 - rep1

value: Nipponbare

value: leaf

tag: age


title: preadipocytes, no differentiation, donor 1

tag: cell type

value: preadipocytes

value: 0 days of differentiation

value: donor 1


title: Control-wt-b

description:
Gene expression for wild type  mouse
In the present study, Alb promoter-driven Cre recombinase transgenic mice (Albumin-Cre mice) and mice carrying the floxed allele of Dicer1 (Dicer1loxP/loxP mice) were crossed to obtain hepatocyte-specific Dicer1 knockout mice (Albumin-Cre;Dicer1loxP/loxP mice). Dicer1loxP/loxP littermates were used as controls throughout the experiment.

source_name: Liver wild type

tag: strain

value: wild type


title: cultivar: Nipponbare - strain: T7174 - rep2


title: CTR19

tag: retinal detachment

value: no

value: 0 weeks


title: Control-ko-a


title: F1-3DAS-2

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

country: Australia

institute: CSIRO

description: Gene expression in whole plants at 3 DAS

hyb_protocol: A total of 5ug of labelled cDNA was then hybridised to the GeneChip® Arabidopsis Tiling  1.0R Array GeneChip (Millenium Sciences cat no. 900594) by preparing a probe cocktail (labelled cDNA @ 0.025ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO.A total hybridisation volume of 220ul is prepared for each sample and 200ul loaded into a GeneChip® Arabidopsis Tiling 1.0R Array GeneChip.  The chip is hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.

scan_protocol: After hybridisation the chip is washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.  Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating the subsequent CEL file for analysis.
Data was quantile normalised using the affy Bioconductor package in R and log2 values for each probe and sample are reported in .txt files.

organism: Arabidopsis thaliana

source_name: whole plants at 3 DAS

label_protocol: Arabidopsis total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 3ug was labelled using the Affymetrix GeneChip® WT Double-Stranded cDNA Synthesis Kit (Millenium Sciences cat no. 900813).  The subsequent cRNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cRNA the next step was to incorporate dUTP into the second cycle first strand cDNA synthesis step.  The presence of the dUTP was used to facilitate fragmentation using the APE1 and UDG enzymes that specifically recognised dUTP.  The fragmented cDNA was quality checked using the Agilent Bioanalyser 2100 using the NanoChip protocol.The fragmented single stranded cDNA was end-labelled using terminal deoxynucleotidyl transferase enzyme and the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Millenium Sciences cat no. 900812).

growth_protocol: Controlled enviromental condition (22C) under fluorescent lights and a 16h/8h (day/light) photoperiod.

extract_protocol: Total RNA was isolated from whole plants using SV Total RNA Isolation system (Promega)

value: Seedlings

tag: strain/line

value: Col x C24 F1 hybrids


title: Dox treatment 48h rep3

description: Dox

value: MCF7/Rx2dox cells

value: Runx2 expression upon doxycycline treatment

value: Dox


title: cultivar: Nipponbare - strain: NO TREATMENT - rep2

source_name: leaf (cultivar: Nipponbare - strain: NO TREATMENT)

value: untreated


title: CTR17

tag: patient identifier

tag: total rd duration


title: Control-wt-a


title: cultivar: Nipponbare - strain: NO TREATMENT - rep1


title: Dox treatment 48h rep2

description: Dox


title: Drug-ko-b

description:
Gene expression after ENU-treated for Dicer1 KO mouse
In the present study, Alb promoter-driven Cre recombinase transgenic mice (Albumin-Cre mice) and mice carrying the floxed allele of Dicer1 (Dicer1loxP/loxP mice) were crossed to obtain hepatocyte-specific Dicer1 knockout mice (Albumin-Cre;Dicer1loxP/loxP mice). Dicer1loxP/loxP littermates were used as controls throughout the experiment.

value: Dicer1 KO

value: N-ethyl-N-nitrosourea (ENU)


title: CTR15


title: Ethanol treatment 48h rep2

description: Control

value: Control


title: Drug-wt-b

description:
Gene expression after ENU-treated for wild type mouse
In the present study, Alb promoter-driven Cre recombinase transgenic mice (Albumin-Cre mice) and mice carrying the floxed allele of Dicer1 (Dicer1loxP/loxP mice) were crossed to obtain hepatocyte-specific Dicer1 knockout mice (Albumin-Cre;Dicer1loxP/loxP mice). Dicer1loxP/loxP littermates were used as controls throughout the experiment.

value: Liver


title: Drug-wt-a


title: CTR16


title: F1-3DAS-1


title: Ethanol treatment 48h rep1

description: Control


title: Dox treatment 48h rep1

description: Dox


title: C24-3DAS-2

source_name: whole plants at 4 DAS


title: cultivar: Nipponbare - strain: MOCK - rep3

source_name: leaf (cultivar: Nipponbare - strain: MOCK)

value: Nipponbare

value: mock

value: leaf


title: cultivar: Nipponbare - strain: MOCK - rep1


title: C24-3DAS-1


title: Drug-ko-a


title: CTR13


title: Col-3DAS-2

value: Col


title: CTR14


title: Col-3DAS-1


title: LSK CONTROL, rep1

city: Madrid

first: Antonio

middle: Herrera

last: Merchan

address: Melchor Fernández Almagro, 3

department: Regenerative Cardiology

country: Spain

institute: CNIC

hyb_protocol: Microarray: Mouse Gene Expression G3 8x60K (Agilent microarray design ID 028005, P/N G4852A). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: ~190-250 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 40 hours.

scan_protocol: Scanned on a G2505C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Raw data from hybridized microarray images were backgound subtracted with Agilent Feature Extraction (FE) Software. Raw data signals are thresholded to 1, and replicated probe signals are summarized by computing their geometric mean. Log base2 transformation is then performed and followed by an intra-array shift to 75th percentile. Optionally, a final inter-array baseline transformation to the median of all samples is applied. These manipulations are done with GeneSpring GX11.5 software.

source_name: LSK cells, control

label_protocol:
Amount of nucleic acid labeled: 250ng. Commercial Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) version 3.2 kit was used. Recommendations from Sigma-Aldrich for the integration of TransPlex WTA with the Agilent microarray workflow were followed, such as the omission of Cot-1 DNA.
Briefly, cDNA is non-enzymatically labeled with ULS technology (Kreatech), in which a platinum dye complexed with either Cy3 or Cy5 fluorophores couples preferentially with guanine molecules of the sample. Labeled samples are purified with gel filtration columns.

extract_protocol: Trizol extraction of total RNA. RNA Integrity Numbers (RINs) were in the range 9 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Available RNA amounts in the range of 0.1-5 ng were subjected to a preliminary amplification step with a TransPlex Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich). Optimal cycle number was set at 16-16-19-18, respectively, by proceeding 2-3 cycles beyond the amplification “plateau” as observed with real-time qPCR.

value: LSK


title: IGR37

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description: Human Cancer Cell Line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Golden Gate Methylation Cancer Panel  I Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: Lymph node metastasis melanoma

label_protocol: Standard Illumina labelling protocol

growth_protocol: DMEM media, 10% FBS, Pen/Str, 37ºC, 5% CO2

extract_protocol: Total DNA was isolated by standard procedures

value: Lymph node metastasis melanoma


title: LSK CONTROL, rep2


title: LSK KO EZH1, rep2

source_name: LSK cells, EZH1 KO

tag: genotype

value: EZH1 knockout


title: cultivar: Nipponbare - strain: PXO99AME5 - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO99AME5)

value: Xanthomonas oryzae  PXO99AME5


title: LSK KO EZH1, rep1


title: IGR39

description: Human Cancer Cell Line

source_name: Primary melanoma

value: Primary melanoma


title: cultivar: Nipponbare - strain: PXO99AME5 - rep1


title: cultivar: Nipponbare - strain: PXO99AME5 - rep2


title: CTR12

source_name: retina

value: no

value: 0 weeks


title: CTR11


title: SIHN011B

description: Human Cancer Cell Line

source_name: Lymph node metastasis head and neck

value: Lymph node metastasis head and neck


title: cultivar: Nipponbare - strain: PXO99AME7 - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO99AME7)

value: Xanthomonas oryzae  PXO99AME7


title: cultivar: Nipponbare - strain: PXO99AME7 - rep2


title: CTR7


title: CTR10


title: cultivar: Nipponbare - strain: PXO99AME7 - rep1


title: CTR9


title: cultivar: Nipponbare - strain: BLS303 - rep1

source_name: leaf (cultivar: Nipponbare - strain: BLS303)

value: Xanthomonas oryzae  BLS303


title: cultivar: Nipponbare - strain: PXO99A - rep3

source_name: leaf (cultivar: Nipponbare - strain: PXO99A)

value: Xanthomonas oryzae  PXO99A


title: CTR8


title: prdm-Rosi, biological rep2

city: San Francisco

first: Kosaku

last: Shinoda

address: 35 Medical Center Way

department: UCSF Diabetes Center and Department of Cell and Tissue Biology

institute: University of California, San Francisco

hyb_protocol: The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45C.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer (dChip). The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

source_name: SV cells isolated from inguinal White adipose tissue

label_protocol: cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

extract_protocol: Total RNA was isolated from cells or tissues using Trizol (Invitrogen).

tag: Sex

value: male

tag: expression

value: rosiglitazone at 1uM


title: SIHN011A

description: Human Cancer Cell Line

source_name: Primary head and neck

tag: cell line

value: Primary head and neck


title: prdm-Rosi, biological rep1


title: cultivar: Nipponbare - strain: PXO99A - rep1

value: Nipponbare


title: prdm-control, biological rep2


title: cultivar: Nipponbare - strain: PXO99A - rep2

value: leaf


title: CTR5


title: prdm-control, biological rep1


title: CTR4


title: Dual Tag Rap1:Myc Control ChIP Rep 3

status: Public on Mar 05 2012

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hal, CB#3280

department: Biology

institute: UNC-Chapel Hill

hyb_protocol: Samples For Ch1 and Ch2 were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Hybridizations were carried out overnight at 65 C.

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: The normalized median log2 ratios (ch2/ch1) were download from UNC microarray database, dye swapped experiments were inverted

organism: Saccharomyces cerevisiae

source_name: Myc IP Rap1:Myc ChIP-chip

label_protocol: IP and/or Input DNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) kit (WGA2-50RXN, Sigma) and then reamplified using GenomePlex WGA Reamplification Kit (WGA3-50RXN, Sigma) using provided protocols. 1 µg of amplified DNA was labeled with either dUTP Cy5 (PA55022, GE Healthcare) or Cy3 (PA53022, GE Healthcare). DNA was purified using Zymo columns according to the manufacturer's instructions (Zymo Research).

growth_protocol: Yeast were grown to log phase (O.D. 0.6-0.8 in YPD (Yeast Extract 1%, Peptone 2%, Dextrose 2%)

extract_protocol: 1/20 of WCE for IP used as Input

tag: fraction

value: Input DNA

tag: growth conditions

value: Log Phase YPD(1 % Yeast Extract 2% Peptone 2% Dextrose)

extract_protocol: IP DNA isoloated from 1mg protein from WCE by immunoprecipitation (Lieb et al 2001, Nature Genetics)

value: Rap1-Myc IP

tag: antibody

value: anti-Myc 9E10 (Millipore, Catalog # 05-419, Lot # JBC1395508)


title: CTR18


title: CTR3


title: CTR1


title: Dual Tag Rap1:Myc Control ChIP Rep 2


title: Dual Tag Rap1:Myc Control ChIP Rep 1


title: MDSC_BM_WT_rep2

city: Indianapolis

first: Hong

last: Du

state: OH

address: 635 Barnhill Drive

department: Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

description: Myeloid derived Suppresive Cells from the Bone Marrow of WT Mice

hyb_protocol: Biotinylated sense strand fragments were hybridized to Affymetrix Mouse Gene 1.0 ST GeneChips using the Hybridisation Control and Hybridisation Wash and Stain kits at 45° C for 18 hrs. Affymetrix GeneChip Scanner 3000 7G was used to scan the stained array

data_processing: The data were analysed with GeneChip Operating Software 1.1(GCOS 1.1) using Affymetrix default analysis settings and all global scaling to the same target intensity value

source_name: cells (MDSC) isolated from Wild type Bone marrow

label_protocol: Biotinylated cRNA was prepared using the WT Terminal labelling kit according to standard affymetrix protocol. The Ovation Pico WTA System (Nugen) is used to prepare target cDNA. Finally the Encore Biotin Module (NuGEN) chemically fragments and labels the target sense cDNA

extract_protocol: Total RNA was extracted from the purified MDSC isolated from the Bone Marrow using  the Qiagen total RNA purification kit.

value: CD11b +ve Gr-1 +ve cells

tag: tissue

value: bone marrow

value: 5 months

value: 10 generation back-cross on FVB/N

value: WT


title: MDSC_BM_LALKO_rep2

description: Gene profile of Myeloid derived Suppresive Cells from the Bone Marrow of Lysosomal Acid Lipase Knock-out Mice

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the stained array

source_name: cells (MDSC) isolated from LALKO Bone marrow

tag: genotype/variation

value: LALKO


title: scr-control, biological rep1

value: sh-scr

tag: agent


title: CTR2

value: no

value: 0 weeks


title: Dual Tag Rap1:Flag Control ChIP Rep 3

source_name: Flag IP Rap1:Flag ChIP-chip

value: Rap1-Flag IP

value: anti-Flag M2 (Sigma, Catalog # F1804-1MG, Lot # 035K6196)


title: Dual Tag Rap1:Flag Control ChIP Rep 4


title: scr-Rosi, biological rep2

value: male

value: rosiglitazone at 1uM


title: Expression Turnover T=60 Rep 2

type: mixed

source_name: Rap1 Turnover Strain Time Course T=60 Expression

label_protocol: Total RNA (30 micrograms) was reverse-transcribed using SuperScript II Reverse Transcriptase (Invitrogen) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy Dye (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

growth_protocol: Yeast were grown overnight in YPD (Yeast Extract 1%, Peptone 2%, Dextrose 2%) and used to inoculate 800 ml of YPR (Yeast Extract 1%, Peptone 2%, Raffinose 2%) to an OD600 of 0.2 (Genesys 20 Spectrophotometer) in a 4 L Erlenmeyer flask. These cells were grown for approximately 4 hours to an OD600 of 0.4 and subsequently arrested using 5 µM alpha-factor (400 µL of 10 mM, GenScript) until 95% of the yeast cells were unbudded (~3hrs). Cells were then induced by adding 40% galactose directly to the growing yeast to a final galactose concentration of 2%. At this time additional alpha factor was added (400 µL of 10 mM, GenScript). At time points 0, 10, 20, 30, 40, 50, 60, 90, 120, 150, 180, 210, 240 minutes following galactose induction, 35ml of culture was taken at each time point and added immediately to 37% formaldehyde to a final concentration of 1% for 20 minutes of crosslinking. 13 ml were taken and washed once in sterile ice cold water, pelleted, and frozen in liquid nitrogen for subsequent RNA preparation.

extract_protocol: Total RNA was isolated from frozen samples using hot acid-phenol as previously described (Ausubel 1997).

value: Total RNA

value: 100 µm alpha-factor YPR(1 % Yeast Extract 2% Peptone 2% Raffinose) + 2% Galactose

label_protocol: Purified genomic DNA (4 micrograms) was labeled with Klenow (NEB) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy Dye (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

growth_protocol: Rap1 Turnover Strain CLy013 was grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8.

extract_protocol: 100 ml of vegetative cells (OD600 0.6-0.8) were pelleted and resuspended in 2 ml lysis buffer (10 mM Tris-Cl pH 8.0, 100 mM NaCl, 1 mM EDTA, 1% SDS, 2% Triton X-100). The cells were split into 4 tubes (500 ul each) and an equal volume of phenol:chloroform:isoamyl-alcohol was added to each tube. The cells were then lysed with glass beads. The samples were spun down for 5 minutes at top speed and the aqueous layers was transfered to fresh tubes. Nucleic acids were precipitated with 1 ml of 95% ethanol and resuspended in 200 ul of 1X TE + 30 ug RNAse and incubated at 30 C for 30 minutes. 5 M NaCl was added to a final concentration of 500 mM and the samples were precipitated with isopropanol. Pellets were washed 2X with 70% ethanol and dried at room temperature for 30 minutes. The resulting genomic DNA was resuspended in 10 mM Tris-Cl pH 7.4 and pooled and the concentration was determined with a spectrophotometer.

value: Genomic DNA from Rap1 Turnover Strain


title: Dual Tag Rap1:Flag Control ChIP Rep 2

value: Input DNA

value: Log Phase YPD(1 % Yeast Extract 2% Peptone 2% Dextrose)


title: scr-Rosi, biological rep1


title: MDSC_BM_WT_rep1

value: CD11b +ve Gr-1 +ve cells

value: bone marrow

tag: age


title: Dual Tag Rap1:Flag Control ChIP Rep 1


title: Expression Turnover T=60 Rep 1

source_name: Genomic DNA from Rap1 Turnover Strain


title: scr-control, biological rep2


title: T=210_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=210 ChIP-chip

value: Rap1-Myc IP

value: anti-Myc 9E10 (Millipore, Catalog # 05-419, Lot # JBC1395508)


title: Rap1 Occupancy 60 min Rep 2

source_name: Rap1 Turnover Strain Time Course T=60 ChIP-chip

value: Rap1 IP

value: anti-Rap1 Y-300 (Santa Cruz, Catalog # sc-20167, Lot # A3003)

value: 100 µm alpha-factor YPR(1 % Yeast Extract 2% Peptone 2% Raffinose)


title: Rap1 Occupancy 60 min Rep 1


title: Rap1 Occupancy 0 min Rep 2

source_name: Rap1 Turnover Strain Time Course T=0 ChIP-chip


title: MDSC_BM_LALKO_rep1

description: Myeloid derived Suppresive Cells from the Bone Marrow of Lysosomal Acid Lipase Knock-out Mice

tag: cell type

value: 5 months

value: 10 generation back-cross on FVB/N

value: LALKO


title: Expression Turnover T=0 Rep 1

source_name: Rap1 Turnover Strain Time Course T=0 Expression


title: Rap1 Occupancy 0 min Rep 1


title: T=240_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=240 ChIP-chip

value: Rap1-Flag IP

value: anti-Flag M2 (Sigma, Catalog # F1804-1MG, Lot # 035K6196)


title: Expression Turnover T=0 Rep 2

value: Total RNA


title: T=30_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=30 ChIP-chip


title: cultivar: Nipponbare - strain: MOCK - rep2

source_name: leaf (cultivar: Nipponbare - strain: MOCK)

tag: cultivar

value: Nipponbare

tag: infection

value: mock

value: leaf


title: T=10_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T= 10 ChIP-chip


title: T=20_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=20 ChIP-chip


title: CTR6

source_name: retina

tag: retinal detachment

value: no

value: 0 weeks


title: T=240_Rap1_Turnover_Rep1_Myc/Flag

value: 100 µm alpha-factor YPR(1 % Yeast Extract 2% Peptone 2% Raffinose) + 2% Galactose


title: T=40_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=40 ChIP-chip

value: Rap1-Myc IP


title: T=60_Rap1_Turnover_Rep2_Myc/Flag

value: anti-Myc 9E10 (Millipore, Catalog # 05-419, Lot # JBC1395508)


title: T=150_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=150 ChIP-chip


title: T=50_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=50 ChIP-chip


title: T=90_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T= 90 ChIP-chip


title: T=180_Rap1_Turnover_Rep1_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=180 ChIP-chip


title: T=120_Rap1_Turnover_Rep2_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=120 ChIP-chip


title: T=150_Rap1_Turnover_Rep1_Myc/Flag


title: T=120_Rap1_Turnover_Rep1_Myc/Flag


title: T=30_Rap1_Turnover_Rep1_Myc/Flag


title: T=20_Rap1_Turnover_Rep1_Myc/Flag


title: T=0_Rap1_Turnover_Rep1_Myc/Flag

hyb_protocol: Samples For Ch1 and Ch2 were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Hybridizations were carried out overnight at 65 C


title: T=10_Rap1_Turnover_Rep1_Myc/Flag


title: T=210_Rap1_Turnover_Rep1_Myc/Flag


title: T=180_Rap1_Turnover_Rep2_Myc/Flag


title: T=0_Rap1_Turnover_Rep2_Myc/Flag


title: T=50_Rap1_Turnover_Rep1_Myc/Flag


title: T=40_Rap1_Turnover_Rep1_Myc/Flag


title: adipose tissue from subject#18 at day 14, biological replicate 13

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description: TA 18B

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2,0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: human adipose tissue after 14 days of  high fat diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

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

tag: subject

tag: bmi

value: Lean

tag: protocol

value: high fat diet

tag: time

value: after 14 days

value: adipose tissue


title: adipose tissue from subject#17 at day 56, biological replicate 12

description: TA 17C

source_name: human adipose tissue after 56 days of  high fat diet

value: after 56 days


title: adipose tissue from subject#18 at day 56, biological replicate 13

description: TA 18C


title: adipose tissue from subject#17 at day 0, biological replicate 12

description: TA 17A

source_name: human adipose tissue before the diet

value: before the diet


title: adipose tissue from subject#16 at day 14, biological replicate 11

description: TA 16B

value: Overweight


title: adipose tissue from subject#18 at day 0, biological replicate 13

description: TA 18A


title: adipose tissue from subject#16 at day 0, biological replicate 11

description: TA 16A


title: T=90_Rap1_Turnover_Rep1_Myc/Flag

value: Rap1-Flag IP

value: anti-Flag M2 (Sigma, Catalog # F1804-1MG, Lot # 035K6196)


title: T=60_Rap1_Turnover_Rep1_Myc/Flag

source_name: Rap1 Turnover Strain Time Course T=60 ChIP-chip


title: adipose tissue from subject#17 at day 14, biological replicate 12

description: TA 17B


title: adipose tissue from subject#15 at day 0, biological replicate 10

description: TA 15A


title: adipose tissue from subject#16 at day 56, biological replicate 11

description: TA 16C


title: adipose tissue from subject#12 at day 56, biological replicate 9

description: TA 12C


title: adipose tissue from subject#9 at day 14, biological replicate 7

description: TA 9B


title: adipose tissue from subject#12 at day 14, biological replicate 9

description: TA 12B


title: adipose tissue from subject#12 at day 0, biological replicate 9

description: TA 12A


title: adipose tissue from subject#11 at day 56, biological replicate 8

description: TA 11C


title: adipose tissue from subject#15 at day 14, biological replicate 10

description: TA 15B


title: adipose tissue from subject#9 at day 56, biological replicate 7

description: TA 9C


title: adipose tissue from subject#8 at day 0, biological replicate 6

description: TA 8A


title: adipose tissue from subject#8 at day 56, biological replicate 6

description: TA 8C


title: adipose tissue from subject#11 at day 14, biological replicate 8

description: TA 11B


title: adipose tissue from subject#9 at day 0, biological replicate 7

description: TA 9A


title: adipose tissue from subject#7 at day 14, biological replicate 5

description: TA 7B


title: adipose tissue from subject#8 at day 14, biological replicate 6

description: TA 8B


title: adipose tissue from subject#7 at day 56, biological replicate 5

description: TA 7C


title: HT-29 siCDK8-1 replicate 3

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

description: Biological replicate 3 of 3. siCDK8-1 treated for 3 days

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried, and then scanned.

scan_protocol: Scanned on an Agilent scanner; images were processed using Agilent Feature Extraction software version 9.5.

data_processing: Agilent Feature Extraction software version 9.5 was used for background subtraction and LOWESS normalization.

source_name: HT-29 human colon cancer cells + siCDK8-1

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).

growth_protocol: HT-29 cells were grown for 3 days after siRNA transfection.

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol, including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.

treatment_protocol: HT-29 cells were transfected with siNTC, siCDK8-1, or siCDK8-2 with Lipofectamine RNAiMAX.

tag: knockdown

source_name: Stratagene universal human reference RNA

tag: sample type

value: Mixture of multiple human cell lines


title: HT-29 siCDK8-1 replicate 2

description: Biological replicate 2 of 3. siCDK8-1 treated for 3 days

tag: cell line

value: Stratagene universal human reference RNA


title: HT-29 siCDK8-1 replicate 1

description: Biological replicate 1 of 3. siCDK8-1 treated for 3 days


title: HT-29 siCDK8-2 replicate 2

description: Biological replicate 2 of 3. siCDK8-2 treated for 3 days

source_name: HT-29 human colon cancer cells + siCDK8-2


title: HT-29 siCDK8-2 replicate 3

description: Biological replicate 3 of 3. siCDK8-2 treated for 3 days


title: adipose tissue from subject#11 at day 0, biological replicate 8

description: TA 11A


title: HT-29 siCDK8-2 replicate 1

description: Biological replicate 1 of 3. siCDK8-2 treated for 3 days


title: adipose tissue from subject#5 at day 56, biological replicate 3

description: TA 5C


title: adipose tissue from subject#7 at day 0, biological replicate 5

description: TA 7A


title: adipose tissue from subject#6 at day 56, biological replicate 4

description: TA 6C


title: adipose tissue from subject#6 at day 0, biological replicate 4

description: TA 6A


title: HT-29 siNTC replicate 3

description: Biological replicate 3 of 3. siNTC treated for 3 days

source_name: HT-29 human colon cancer cells + siNTC

value: siNTC


title: adipose tissue from subject#5 at day 14, biological replicate 3

description: TA 5B


title: adipose tissue from subject#6 at day 14, biological replicate 4

description: TA 6B


title: adipose tissue from subject#3 at day 56, biological replicate 2

description: TA 3C


title: adipose tissue from subject#3 at day 14, biological replicate 2

description: TA 3B


title: DGM-01602 [gene_expr]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: smoking status

value: NS


title: adipose tissue from subject#3 at day 0, biological replicate 2

description: TA 3A

tag: tissue


title: HT-29 siNTC replicate 1

description: Biological replicate 1 of 3. siNTC treated for 3 days


title: adipose tissue from subject#1 at day 14, biological replicate 1

description: TA 1B


title: adipose tissue from subject#1 at day 0, biological replicate 1

description: TA 1A


title: adipose tissue from subject#5 at day 0, biological replicate 3

description: TA 5A


title: sham-injected+high fat diet-fed+lung 3

city: Chuncheon

first: Eun Ji

last: Kim

address: 1 Hallymdaehak-gil

country: South Korea

institute: Hallym University

description: SAMPLE 18

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized to the Illumina MouseWG-6   Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis were performed using Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

source_name: Mouse lung tissue

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep   RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Three-week-old female BALB/c mice were acclimatized to the laboratory conditions while providing free access to a standard non-purified rodent diet and water. The mice were acclimated for 1 wk prior to use and maintained throughout the study in a controlled environment: 24 ± 2°C, 50 ± 10% relative humidity and a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted using Trizol reagent and purified using Qiagen RNeasy columns according to the manufacturer’s instructions. For quality control, RNA purity and integrity were evaluated by using denaturing gel electrophoresis and the absorbance ratio at 260 nm vs 280 nm

treatment_protocol: Mice were randomly divided into four groups: sham-injected + control diet (CD)-fed (SC), sham-injected + high fat dier (HFD)-fed (SH), 4T1 cell-injected + CD-fed (TC), and 4T1 cell-injected + HFD-fed (TH). Following 16 weeks of the CD or HFD, 4T1 cells were injected into the mammary fat pads of TC and TH groups and all mice were continuously fed identical diets. Fourteen days post-injection, the mice were sacrificed.

value: lung

tag: strain

value: Balb/c

value: 22 weeks

tag: treatment

value: sham-injected


title: DGM-01682 [gene_expr]


title: DGM-01774 [gene_expr]


title: DGM-01505 [gene_expr]


title: 4T1 cell-injected+high fat diet-fed+lung 1

description: SAMPLE 22

tag: age

value: 4T1 cell-injected


title: 4T1 cell-injected+high fat diet-fed+lung 2

description: SAMPLE 23


title: 4T1 cell-injected+control diet-fed+lung 3

description: SAMPLE 21


title: 4T1 cell-injected+control diet-fed+lung 2

description: SAMPLE 20


title: 4T1 cell-injected+high fat diet-fed+lung 3

description: SAMPLE 24


title: 4T1 cell-injected+control diet-fed+lung 1

description: SAMPLE 19


title: adipose tissue from subject#1 at day 56, biological replicate 1

description: TA 1C

value: Lean

value: high fat diet


title: sham-injected+high fat diet-fed+lung 2

description: SAMPLE 17


title: HT-29 siNTC replicate 2

description: Biological replicate 2 of 3. siNTC treated for 3 days


title: sham-injected+high fat diet-fed+lung 1

description: SAMPLE 16


title: sham-injected+control diet-fed+lung 3

description: SAMPLE 15


title: R1 shMed12-2 replicate 3 - 13 days

description: Biological replicate 3 of 3. shMed12-2 treated for 13 days

scan_protocol: Scanned on an Agilent scanner; images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.

source_name: R1 mouse ES cells + shMed12-2, 13 days

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: R1 cells were grown for 8 days or 13 days after shRNA infection.

treatment_protocol: R1 cells were infected with shNTC, shCdk8-1, shCdk8-2, shMed12-1, or shMed12-2 using lentivirus.

value: 13 days

source_name: Stratagene universal mouse reference RNA

value: Mixture of multiple mouse cell lines


title: R1 shMed12-2 replicate 2 - 13 days

description: Biological replicate 2 of 3. shMed12-2 treated for 13 days

value: Stratagene universal mouse reference RNA


title: 4T1 cell-injected+high fat diet-fed+liver 1

description: SAMPLE 10

source_name: Mouse liver tissue

value: liver


title: 4T1 cell-injected+high fat diet-fed+liver 2

description: SAMPLE 11


title: sham-injected+control diet-fed+lung 2

description: SAMPLE 14


title: R1 shCdk8-1 replicate 3 - 13 days

description: Biological replicate 3 of 3. shCdk8-1 treated for 13 days

source_name: R1 mouse ES cells + shCdk8-1, 13 days


title: R1 shMed12-2 replicate 1 - 13 days

description: Biological replicate 1 of 3. shMed12-2 treated for 13 days


title: 4T1 cell-injected+high fat diet-fed+liver 3

description: SAMPLE 12


title: R1 shMed12-1 replicate 1 - 13 days

description: Biological replicate 1 of 3. shMed12-1 treated for 13 days

source_name: R1 mouse ES cells + shMed12-1, 13 days


title: sham-injected+control diet-fed+lung 1

description: SAMPLE 13


title: R1 shMed12-1 replicate 2 - 13 days

description: Biological replicate 2 of 3. shMed12-1 treated for 13 days


title: 4T1 cell-injected+control diet-fed+liver 2

description: SAMPLE 8


title: sham-injected+high fat diet-fed+liver 2

description: SAMPLE 5


title: 4T1 cell-injected+control diet-fed+liver 3

description: SAMPLE 9


title: sham-injected+high fat diet-fed+liver 3

description: SAMPLE 6


title: R1 shCdk8-2 replicate 2 - 13 days

description: Biological replicate 2 of 3. shCdk8-2 treated for 13 days

source_name: R1 mouse ES cells + shCdk8-2, 13 days


title: sham-injected+high fat diet-fed+liver 1

description: SAMPLE 4


title: R1 shCdk8-2 replicate 3 - 13 days

description: Biological replicate 3 of 3. shCdk8-2 treated for 13 days


title: sham-injected+control diet-fed+liver 3

description: SAMPLE 3


title: R1 shCdk8-1 replicate 2 - 13 days

description: Biological replicate 2 of 3. shCdk8-1 treated for 13 days


title: R1 shCdk8-2 replicate 1 - 13 days

description: Biological replicate 1 of 3. shCdk8-2 treated for 13 days


title: Myc/Flag 0 min Rep2

description: 46641 A12

hyb_protocol: Samples were hybridized by Roche-Nimblegen, Inc. Madison Wisconsin according to internal protocols.

scan_protocol: Samples were scanned by Roche-Nimblegen, Inc. Madison Wisconsin according to internal protocols.

data_processing: Data was scaled subtracting the biweight mean from the log2 ratio for each probe.

source_name: Myc ChIP DNA 0 min

label_protocol: IP and/or Input DNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) kit (WGA2-50RXN, Sigma) and then reamplified using GenomePlex WGA Reamplification Kit (WGA3-50RXN, Sigma) using provided protocols. DNA was purified using Zymo columns according to the manufacturer's instructions (Zymo Research).

growth_protocol: Yeast were grown overnight in YPD (Yeast Extract 1%, Peptone 2%, Dextrose 2%) and used to inoculate 800 ml of YPR (Yeast Extract 1%, Peptone 2%, Raffinose 2%) to an OD600 of 0.2 (Genesys 20 Spectrophotometer) in a 4 L Erlenmeyer flask. These cells were grown for approximately 4 hours to an OD600 of 0.4 and subsequently arrested using 5 µM alpha-factor (400 µL of 10 mM, GenScript) until 95% of the yeast cells were unbudded (~3hrs). Cells were then induced by adding 40% galactose directly to the growing yeast to a final galactose concentration of 2%. At this time additional alpha factor was added (400 µL of 10 mM, GenScript). At time points 0, 10, 20, 30, 40, 50, 60, 90, 120, 150 minutes following galactose induction, 35ml of culture was taken at each time point and added immediately to 37% formaldehyde to a final concentration of 1% for 20 minutes of crosslinking. 13 ml were taken and washed once in sterile ice cold water, pelleted, and frozen in liquid nitrogen for subsequent RNA preparation.

tag: ip

value: Rap1-myc IP

tag: antibody

value: anti-Myc 9E10 (Millipore, Catalog # 05-419, Lot # JBC1395508)

source_name: Flag ChIP DNA

value: Rap1-flag IP


title: R1 shCdk8-1 replicate 1 - 13 days

description: Biological replicate 1 of 3. shCdk8-1 treated for 13 days


title: sham-injected+control diet-fed+liver 2

description: SAMPLE 2


title: 4T1 cell-injected+control diet-fed+liver 1

description: SAMPLE 7


title: R1 shNTC replicate 3 - 13 days

description: Biological replicate 3 of 3. shNTC treated for 13 days

source_name: R1 mouse ES cells + shNTC, 13 days

value: shNTC


title: Myc/Flag 50 min Rep2

description: 46641 A09

source_name: Myc ChIP DNA 50 min

value: anti-Flag M2 (Sigma, Catalog # F1804-1MG, Lot # 035K6196)


title: R1 shNTC replicate 2 - 13 days

description: Biological replicate 2 of 3. shNTC treated for 13 days


title: Myc/Flag 40 min Rep2

description: 46641 A07

source_name: Myc ChIP DNA 40 min


title: R1 shCdk8-2 replicate 3 - 8 days

description: Biological replicate 3 of 3. shCdk8-2 treated for 8 days

source_name: R1 mouse ES cells + shCdk8-2, 8 days

value: 8 days


title: R1 shNTC replicate 1 - 13 days

description: Biological replicate 1 of 3. shNTC treated for 13 days


title: Myc/Flag 20 min Rep2

description: 46641 A08

source_name: Myc ChIP DNA 20 min


title: Myc/Flag 60 min Rep2

description: 46641 A06

source_name: Myc ChIP DNA 60 min


title: Myc/Flag 30 min Rep2

description: 46641 A10

source_name: Myc ChIP DNA 30 min


title: Myc/Flag 10 min Rep2

description: 46641 A11

source_name: Myc ChIP DNA 10 min


title: V205G C

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

description: Replicate 3

data_processing: Data were quantile normalized and background was subtracted with IlluminaGUI

label_protocol: Standard Illumina label protocol

growth_protocol: G1ME cells were cultured in 1% TPO supernatant (v/v)

extract_protocol: RNeasy column (Qiagen)

treatment_protocol: Retroviral supernatant was added to the cells at 1e6 cells per ml, and the culture was centrifuged at 3200rpm for 90min. The cells were incuabted in the virus for an additional 4h, and then the virus was removed. The cells were gorwn in growth media  for 68hours.  GFP-positive cells were sorted on a Moflo cell sorter.  The cells were allowed to recover for 4h in growth media, and then RNA was extracted.

tag: cell type

value: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential

value: Cells grown in TPO supernatant (10% v/v)

tag: retrovirus

tag: cell subtype

value: Sorted GFP-postive cells


title: sham-injected+control diet-fed+liver 1

description: SAMPLE 1

value: Balb/c

value: 22 weeks

value: sham-injected


title: R1 shMed12-1 replicate 3 - 13 days

description: Biological replicate 3 of 3. shMed12-1 treated for 13 days


title: R1 shCdk8-2 replicate 2 - 8 days

description: Biological replicate 2 of 3. shCdk8-2 treated for 8 days


title: R1 shCdk8-2 replicate 1 - 8 days

description: Biological replicate 1 of 3. shCdk8-2 treated for 8 days


title: GATA1 B

description: Replicate 2


title: V205G B

description: Replicate 2


title: GATA1 C

description: Replicate 3


title: V205G A

description: Replicate 1


title: R1 shCdk8-1 replicate 3 - 8 days

description: Biological replicate 3 of 3. shCdk8-1 treated for 8 days

source_name: R1 mouse ES cells + shCdk8-1, 8 days


title: Total Rap1/Input 0 min Rep2

description: 46641 A04

source_name: Total Rap1 ChIP DNA 0 min

value: Total Rap1 IP

value: anti-Rap1 Y-300 (Santa Cruz, Catalog # sc-20167, Lot # A3003)

source_name: Genomic Input DNA

value: Input DNA


title: Ball-milled aspen rep3 53944602_532

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) applied

organism: Gelatoporia subvermispora

source_name: mycelium

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C

growth_protocol: Five days growth in shaking flasks at room temperature.

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

value: RP-B

tag: substrate

value: Ball-milled aspen


title: MIGR1 B

description: Replicate 2

tag: protocol


title: Ball-milled aspen rep2 53952102_532


title: R1 shCdk8-1 replicate 2 - 8 days

description: Biological replicate 2 of 3. shCdk8-1 treated for 8 days

tag: time

source_name: Stratagene universal mouse reference RNA

value: Mixture of multiple mouse cell lines


title: MIGR1 A

description: Replicate 1


title: R1 shCdk8-1 replicate 1 - 8 days

description: Biological replicate 1 of 3. shCdk8-1 treated for 8 days

tag: knockdown

value: Stratagene universal mouse reference RNA


title: Glucose rep3 53945602_532

value: Glucose


title: Total Rap1/Input 60 min Rep2

description: 46641 A01

source_name: Total Rap1 ChIP DNA 60 min


title: R1 shNTC replicate 3 - 8 days

description: Biological replicate 3 of 3. shNTC treated for 8 days

source_name: R1 mouse ES cells + shNTC, 8 days

value: shNTC

tag: sample type


title: Ball-milled aspen rep1 54050602_532


title: R1 shNTC replicate 2 - 8 days

description: Biological replicate 2 of 3. shNTC treated for 8 days

tag: cell line


title: Glucose rep1 53933602_532


title: Myc/Flag 0 min Rep1

description: 46674 A09

source_name: Flag ChIP DNA 0 min

value: Rap1-flag IP

value: anti-Flag M2 (Sigma, Catalog # F1804-1MG, Lot # 035K6196)

source_name: Myc ChIP DNA 0 min

value: Rap1-myc IP

value: anti-Myc 9E10 (Millipore, Catalog # 05-419, Lot # JBC1395508)


title: Myc/Flag 90 min Rep2

description: 46641 A05

source_name: Myc ChIP DNA 90 min

source_name: Flag ChIP DNA


title: Myc/Flag 120 min Rep2

description: 46641 A03

source_name: Myc ChIP DNA 120 min


title: R1 shNTC replicate 1 - 8 days

description: Biological replicate 1 of 3. shNTC treated for 8 days

value: 8 days


title: GATA1 A

description: Replicate 1

value: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential

value: Cells grown in TPO supernatant (10% v/v)

value: Sorted GFP-postive cells


title: Myc/Flag 30 min Rep1

description: 46674 A11

source_name: Flag ChIP DNA 30 min


title: Myc/Flag 150 min Rep2

description: 46641 A02

source_name: Myc ChIP DNA 150 min


title: Cellulose rep3 53930302_532

value: Cellulose


title: Myc/Flag 90 min Rep1

description: 46674 A12

source_name: Flag ChIP DNA 90 min


title: Myc/Flag 20 min Rep1

description: 46674 A07

source_name: Flag ChIP DNA 20 min

source_name: Myc ChIP DNA 20 min


title: Cellulose rep1 53925602_532


title: Cellulose rep2 53933702_532


title: Myc/Flag 50 min Rep1

description: 46674 A08

source_name: Flag ChIP DNA 50 min

source_name: Myc ChIP DNA 50 min


title: HC3

status: Public on Mar 04 2012

city: Tampa

first: Kathleen

last: Scott

state: FL

address: 4202 E Fowler Ave

institute: University of South Florida

hyb_protocol: Following fragmentation, labeled RNA was hybridized to the Combimatrix array according to protocol provided by manufacturer (Combimatrix, Mulkilteo, WA)

scan_protocol: Arrays were washed and imaged per Combimatrix Custom Array 12K microarray: hybridization and imaging protocol (Combimatrix, Mulkilteo, WA)

data_processing:
Spot intensities were normalized so each array would have the same average signal (Combimatrix, Mulkilteo, WA)
Globally normalized signal, (Global normalizing was used for all six arrays (three low-DIC, and three high-DIC) to compensate for between-array variation in overall signal strength.

organism: Hydrogenovibrio crunogenus

source_name: high-DIC cells: 50 mM DIC, 0.8 mM (NH4)2SO4, 3.1 mM PO4-x, sparged with 5% CO2, balance O2

label_protocol: 1 µg total RNA was directly labeled with cy5 using the LabelIT kit (Mirus Bio, Madison, WI)

extract_protocol: Total RNA was extracted via the Ribopure System (Ambion, Austin, TX). Further purification was carried out with the RNeasy Minelute Kit (Qiaen, Germantown, MD)

value: high-DIC


title: LC2

source_name: low-DIC cells: 0.1 mM DIC, 13 mM (NH4)2SO4, 3.1 mM PO4-x, sparged with pure O2

value: low-DIC


title: HC2


title: Myc/Flag 10 min Rep1

description: 46674 A10

source_name: Flag ChIP DNA 10 min

source_name: Myc ChIP DNA 10 min


title: LC1


title: Myc/Flag 40 min Rep1

description: 46674 A06

source_name: Flag ChIP DNA 40 min

source_name: Myc ChIP DNA 40 min


title: male to female worm 1

city: Shanghai

first: Yanxun

last: Xia

address: 3 Lane 345,Shilong Road

institute: Shanghai Institute of Domestic Animal Parasitology,Chinese Academy of Agricultural Sciences

description:
The cDNA from female and male worms RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluorescein, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs , 2uL of Superscript II reverse transcriptase, and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65°C  for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from male worms were labeled with Cy5-dCTP and those from females with Cy3-dCTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.
The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42°Cfor 6hr.  Fluorescent probe mixtures were denatured at 95°Cfor 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42°C for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature.

data_processing: Fluorescent array images were collected with a ScanArray 5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. Image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3 and Cy5, Ratios of Cy5/Cy3 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the  value of  ratios was >2 or <0.5.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.

organism: Schistosoma japonicum

source_name: male worms

tag: Male worms were homogenized in TRIzol respectively.  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.

source_name: female worms

tag: Female worms were homogenized in TRIzol respectively.  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.


title: Glucose rep2 53925902_532

source_name: mycelium

value: RP-B


title: Total Rap1/Input 0 min Rep1

description: 46674 A05

source_name: Input DNA 0 min

value: Input DNA

source_name: Rap1 ChIP DNA 0 min

value: Total Rap1 IP

value: anti-Rap1 Y-300 (Santa Cruz, Catalog # sc-20167, Lot # A3003)


title: male to female worm 2

tag: Male  worms were  homogenized in TRIzol respectively.  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.

tag: !Sample_description = The cDNA from female and male worms RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluorescein, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs , 2uL of Superscript II reverse transcriptase, and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65°C  for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from male worms were labeled with Cy5-dCTP and those from females with Cy3-dCTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.

tag: !Sample_description = The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42°Cfor 6hr.  Fluorescent probe mixtures were denatured at 95°Cfor 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42°C for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature.

tag: Female worms were  homogenized in TRIzol respectively.  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.


title: Myc/Flag 150 min Rep1

description: 46674 A03

source_name: Flag ChIP DNA 150 min

tag: ip

source_name: Myc ChIP DNA 150 min


title: HC1


title: Myc/Flag 120 min Rep1

description: 46674 A04

source_name: Flag ChIP DNA 120 min

tag: antibody

source_name: Myc ChIP DNA 120 min


title: LC3


title: female to male worm 2

description:
The cDNA from female and male worms RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluorescein, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs , 2uL of Superscript II reverse transcriptase, and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65°C  for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from male worms were labeled with Cy3-dCTP and those from females with Cy5-dCTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.
!Sample_description = The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42°Cfor 6hr.  Fluorescent probe mixtures were denatured at 95°Cfor 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42°C for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature.

tag: Male worms were  homogenized in TRIzol respectively.  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.


title: Total Rap1/Input 60 min Rep1

description: 46674 A02

source_name: Input DNA 60 min

source_name: Rap1 ChIP DNA 60 min


title: MIGR1 C

description: Replicate 3

tag: strain

tag: cell type

tag: retrovirus


title: Myc/Flag 60 min Rep1

description: 46674 A01

source_name: Flag ChIP DNA 60 min

source_name: Myc ChIP DNA 60 min


title: female to male worm 1


title: CD4-145-C

status: Public on Mar 03 2012

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: cRNA was hybridized to the Illumina Whole Genome 6 (version 3) BeadChip (Illumina, San Diego, non-RA inflammatory arthritisA), following the manufacturer’s protocol.

scan_protocol: Each BeadChip measured the expression of 48,804 genes (annotation file at http://www.illumina.com/support/annotation_files.ilmn) and was imaged using the Illumina BeadArray Reader.

data_processing:
Phases 1 and 2 of the study were independently normalized in 2 steps: each probe measurement was first divided by the 50th percentile of all measurements in its array, before being centred around its own median expression measurement accross all samples in the phase. The within-phase batch-effect related to RNA labelling was corrected in the R statistical computing environment (http://www.r-project.org/) using the empirical Bayes method of Johnston et al. (2007) before phases were combined.  Phases were then combined and residual between-phase batch effect corrected by the same method.

Non-normalized data is available in 'GSE20098_non-normalized.txt', which is linked to the Series GSE20098 record as a supplementary file.

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA inflammatory arthritis

label_protocol: 250ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 1300hrs and 1630hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

tag: tissue

value: peripheral blood

value: CD4+ T-cells

tag: outcome

value: C

tag: classification

value: training

tag: phase batch

tag: labelling batch


title: CD4-149-C

value: UA


title: NORMAL_SCLD_12Day

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description:
NORMAL_SCLD_12Day
pool of 3 animals

hyb_protocol: The obtained labeled copy RNA samples were hybridized 17 h at 65°C to a SurePrint G3 Rat GE 8x60K (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Slides were scanned using an Agilent C Scanner

data_processing: The raw data were processed using Feature Extraction software version 10.5. The initial analysis and normalization to the median were performed using GeneSpring GX software (Agilent). Differentially expressed mRNAs with signal intensities higher than two-fold over the background standard deviation were filtered by t-test with p<0.05. Only the statistically significant data (p<0.05) were used to calculate gene expression ratios in the samples.

source_name: Spinal cord left dorsal quarter of lumber enlargement, 12 days post-injection

label_protocol: Samples of total RNA (50 ng) were labeled using a LowInput QuickAmp Labeling Kit and Cy3-CTP (Agilent Technologies).

extract_protocol: Total RNA was extracted from sciatic nerves, DRG and spinal cords (SC) using TRIzol reagent and purified using the RNeasy columns (Qiagen). The RNA purity was estimated by measuring the OD260/280 and the 260/230 ratios. The integrity of the RNA samples was validated using an Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Rats were obtained from Harlan Labs. Sprague-Dawley rats (N=144, 200-225 g adult females) and athymic nude rats (rnu-/-, Hsd:RH-Foxn1rnu, N=6)  8-week-old females were housed at 22°C under a 12 h light/dark cycle with food and water ad libitum. A rodent anesthesia cocktail containing Nembutal (50 mg/ml; Abbott Labs) and diazepam (5 mg/ml, Steris Labs, Phoenix, AZ) in 0.9% saline (Steris Labs) was used for anesthesia. The common sciatic nerve was exposed unilaterally at the mid-thigh level and four loosely constrictive ligatures were tied around to produce CCI [Bennett, G.J. and Y.K. Xie. Pain, 1988. 33(1): p. 87-107]. In a separate group of animals, the exposed naïve sciatic nerves received the intra-sciatic injection of MBP84-104 peptide (50 µg) in 5 µl PBS, or equal volume of PBS as a vehicle using a 33-gauge-needle on a Hamilton syringe. For a sham-operated control, the sciatic nerve is exposed but otherwise not affected in any way. SB-3CT was injected i.p. (10 mg/kg body weigh in 10% dimethyl sulfoxide) twice: first, at the initiation of CCI and then in 24 h. Solvent alone was used as a vehicle. Animals were sacrificed by an overdose of a Nembutal/diazepam rodent anesthesia cocktail, followed by a lethal injection i.p. of Beuthanasia (100-150 mg/ml, Schering-Plough Animal Health). The sciatic nerve, lumbar (L) 4 and 5 DRG and the spinal cord at the lumbar enlargement specimens were collected for the follow-up analyses. Animals were handled according to the NIH Guide for the Care and Use of Laboratory Animals and the protocols approved by the VA San Diego Institutional Animal Care and Use Committee.

value: Sprague-Dawley

tag: gender

value: female

tag: age

value: adults (8 weeks)


title: NORMAL_LDRG_12Day

description:
NORMAL_LDRG_12Day
pool of 3 animals

source_name: Left dorsal root ganglia, 12 days post-injection

value: left dorsal root ganglia


title: NORMAL_RDRG_12Day_control

description:
NORMAL_RDRG_12Day
pool of 3 animals

source_name: Right dorsal root ganglia control, 12 days post-injection

value: right dorsal root ganglia


title: NUDE_SCCF_7Day_control

description:
NUDE_SCCF_7Day
pool of 3 animals

source_name: Spinal cord left dorsal quarter of cord above lumber enlargement control, 7 days post-injection

value: athymic nude rats

tag: genotype/variation

value: Spinal cord left dorsal quarter of cord above lumber enlargement for control


title: NORMAL_SCCF_12Day_control

description:
NORMAL_SCCF_12Day
pool of 3 animals

source_name: Spinal cord left dorsal quarter of cord above lumber enlargement control, 12 days post-injection


title: CD4-144-C


title: NORMAL_LN_12Day

description:
NORMAL_LN_12Day
pool of 3 animals

source_name: Left sciatic nerve (MBP84-104 injection site), 12 days post-injection

value: left sciatic nerve


title: NUDE_LDRG_7Day

description:
NUDE_LDRG_7Day
pool of 3 animals

source_name: Left dorsal root ganglia, 7 days post-injection


title: NUDE_RN_7Day_control

description:
NUDE_RN_7Day
pool of 3 animals

source_name: Right sciatic nerve control (PBS injection site), 7 days post-injection

value: right sciatic nerve


title: NUDE_SCLD_7Day

description:
NUDE_SCLD_7Day
pool of 3 animals

source_name: Spinal cord left dorsal quarter of lumber enlargement, 7 days post-injection


title: NORMAL_RN_12Day_control

description:
NORMAL_RN_12Day
pool of 3 animals

source_name: Right sciatic nerve control (PBS injection site), 12 days post-injection


title: CD4-133-B

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA+ RA

value: B


title: CD4-134-C


title: CD4-141-D

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA/non-inflammatory arthritis

value: D


title: NUDE_RDRG_7Day_control

description:
NUDE_RDRG_7Day
pool of 3 animals

source_name: Right dorsal root ganglia control, 7 days post-injection


title: NUDE_LN_7Day

description:
NUDE_LN_7Day
pool of 3 animals

source_name: Left sciatic nerve (MBP84-104 injection site), 7 days post-injection


title: CD4-135-C


title: CD4-136-C


title: CD4-132-C


title: MDAH2774 rhSTIP1 2

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with MAS5 by Affymetrix Expression Console Ver 1.1

source_name: MDAH2774 cell with rhSTIP treatment-2

label_protocol: Standard Affymetrix protocol

extract_protocol: Cellular RNA Extraction with TRIZOL

tag: cell line

tag: treatment

value: 0.4 uM recombinant STIP1


title: MDAH2774 control 2

source_name: MDAH2774 cell without rhSTIP treatment-2

value: control


title: CD4-120-A

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA- RA

value: peripheral blood

value: CD4+ T-cells

value: A


title: CD4-125-C

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA inflammatory arthritis

value: C

value: UA


title: MDAH2774 control 1

label: Biotin

source_name: MDAH2774 cell without rhSTIP treatment