title: P6c1_JIP4

description: MD229-C10 vs DBY9500


title: P6c1_ECM32

status: Public on Apr 12 2015

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: MD302-B1 vs YMD1124

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2013-08-25 Scan Time : 11:54:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name


title: 1.NB4-VEC

type: RNA

city: Boston

first: Kun Ping

last: Lu

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: NB4 cells transfected with the empty vector

hyb_protocol: Amplified, fragmented, and biotin labeled single-stranded cDNA (ss-cDNA) material was hybridized in Affymetrix GeneChip Mouse Transcription Assay 1.0

scan_protocol: Hybridized arrays were proceeding with Affymetrix GeneChip Hybridization Wash and Stain kit and then scanned.

data_processing: The data were analyzed with Affymetrix ExpressionConsole and TranscriptomeAnalysisConsole using Affymetrix default analysis settings

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NB4 cell line

label_protocol: Target preparation performed using Affymetrix (Technical Manual) WT Plus reagent kit, including labeling

growth_protocol: NB4 cells were cultured in RPMI1640 mudium with 10% fetal bovine serum (FBS) and all of the cells were cultured at 37°C in a humidified incubator containing 5% CO2

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

treatment_protocol: NB4 cells were treated with 10 uM ATRA (Sigma Aldrich) or doxycycline-induced Pin1 knockdown for 3 days. When harvesting, cells were washed with  Hank's Balanced Salt Solution(HBSS) (Invitrogen) and placed on ice in the Trizol solution (GibcoBRL).

tag: disease state

value: acute promyelocytic leukemia (APL)

tag: cell line

tag: treatment

value: transfected with the empty vector


title: WT muscle, biological rep3

first: Raul

last: Mostoslavsky

address: 185 Cambridge Street, CPZN 4100

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
The clustering figures were generated using dChip2006 Hierarchical clustering feature, and genes in each of these pathways were filtered using the dChip Software Tool Analysis.
For normalization, the normalization method included in dchip2006 (described at: http://www.hsph.harvard.edu/cli/complab/dchip/normalizing%20arrays.htm) was used.

organism: Mus musculus

source_name: muscle from WT mouse

label_protocol: Affymetrix standard protocol

extract_protocol: TriPure (Roche) extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue

value: muscle


title: P6c1_all

description: P6c1-H6 vs DBY9500, MD144-H6

scan_protocol: Pixel Size : 5 Scan Date : 2013-02-12 Scan Time : 09:24:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf


title: LSK KO replicate 1

city: New York

first: Luisa

last: Cimmino

address: 550 First Avenue

institute: NYU

description:
Sample name: LSK KO-1
Gene expression data from KO mouse LSKs

hyb_protocol: Following fragmentation/lableling, 10 ug of labeled ssDNA was added to a hybridization cocktail outlined in Affymetrix Genechip WT Terminal Labeling kit (part#900671). The cocktail-sample mixture was heated to 99°C for 5 minutes, cooled for 5 mins at 45°C, and centrifuge for 1 minute according to the protocol. The mix was injected into the array chips and hybridized for 16 hr at 45°C at 60RPM in the Genechip 645 Hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics 450 Station according to the Genechip Expression Wash, Stain, and Scan protocol (part# 7022731, revision 3).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Agilent GeneSpring 12 software. Gene level expression was summarized using ExonRMA16 algorithm and then quantile normalized.

source_name: LSK KO

label_protocol: cDNA was generated from 125ng of total RNA according to the Ambion WT Expression protocol (Life technologies, part#441974). The subsequent cDNA was fragmented and labeled according to the protocol of the Affymetrix Genechip WT Terminal Labeling kit (part#900671).

growth_protocol: Ex vivo flow sorted LSKs from 6-month old mouse bone marrow

extract_protocol: RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: LSK cells were purified from the bone marrow of 6-month old WT and Tet1 KO mice . RNA was extracted using RNeasy kit (Qiagen) and hybridized on Affymetrix microarrays.

tag: strain

value: bone marrow

tag: cell type

value: LSK hematopoietic stem cells

value: Tet1 KO


title: LSK KO replicate 3

description:
Sample name: LSK KO-3
Gene expression data from KO mouse LSKs


title: LSK KO replicate 2

description:
Sample name: LSK KO-2
Gene expression data from KO mouse LSKs


title: P6c1_chr5.6

description: MD144-A10 vs YMD1124

scan_protocol: Pixel Size : 5 Scan Date : 2012-10-04 Scan Time : 08:51:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: LSK WT replicate 3

description:
Sample name: LSK WT-3
Gene expression data from WT mouse LSKs

source_name: LSK WT

value: WT


title: P5c3_all

description: MD149-A7 vs FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-07-21 Scan Time : 13:00:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P5c3

description: P5c3 (aka g141_P5c1); MD143-A1

scan_protocol: Pixel Size : 5 Scan Date : 2012-06-08 Scan Time : 08:21:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P5c3_none

description: MD149-E5 vs DBY9500

scan_protocol: Pixel Size : 5 Scan Date : 2013-06-07 Scan Time : 09:13:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P5c3_FSK3

description: MD149-C12 vs DBY9500


title: P5c3_SPO23

description: MD149-F9 vs DBY9500


title: LSK WT replicate 2

description:
Sample name: LSK WT-2
Gene expression data from WT mouse LSKs


title: chrVR-Tamp 2N

description: chrV-Tamp 2N; YMD1683; chr5+ #10 zygote 2

scan_protocol: Pixel Size : 5 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: WT (FY)

source_name: ChrV-Tamp 2N


title: RT+1D11_mouse#3

first: Sandra

last: Demaria

state: New York

address: 1300 York avenue, Room A-279

department: Radiation Oncology

institute: Weill Cornell Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430.2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX software from Agilent Technologies to normalized affymetrix CEL files using Robust Multichip Average algorith. Each probe was normalized to the medium volue of the isotype control specimens.

label: Biotin

source_name: Flank tumor 22 days after 4T1 implantation

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

growth_protocol: 50,000 4T1 tumor cells were injected to the right flank of a Balb/C mice

extract_protocol: RNA was extracted and purified with Qiagen Rneasy Mini kit as described by the manufacturer.

treatment_protocol: 4T1-tumor bearing mice received i.p. injections of 1D11, a pan-isoform neutralizing TGFbeta monoclonal antobody (mAb) or its isotype control starting at day 12 post-tumor cells injection. In half of the mice of each group, tumors were treated with local RT given in 5 fractions of 6Gy starting on day 13. On day 22, tumors were harvested and kept in RNAlater at -80C until RNA extraction.

tag: gender

value: Female

value: Balb/C

value: 4T1 tumor


title: RT_mouse#3


title: Th1 cells, Tet2 wild-type, biological rep2

first: Raymond

last: Doty

department: Division of Hematology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing: Data were processed using Partek software and RMA import settings.

source_name: Th1 cells, Tet2 wild-type

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Naive T cells were isolated by sorting CD4+CD25-CD62LhighCD44low cells from spleens and lymph nodes, differentiated under several Th cell conditions, and analyzed as described. The naive T cells (5 x 10^5 cells/well) were cultured at 37oC (5% CO2) in RPMI-1640 (Invitrogen Life Technologies). The medium was supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100  g/ml streptomycin, and 50  M 2-mercaptoethanol. The cells were stimulated with the plate-bound a-CD3 (1  g/ml) and the soluble a-CD28 (1  g/ml). For Th0 differentiation, the cells were treated with 5  g/ml  -IFN-  (XMG1.2; BioXCell), 5  g/ml  -IL-4 (11B11; BioXCell) and 30 U/ml IL-2. For Th1 differentiation, the cells were treated with 10 ng/ml mIL-12 (Peprotech), 5  g/ml  -IL-4 and 30 U/ml IL-2. For Tr1 differentiation, the cells were treated with 50 ng/ml mIL-27 (R&D Systems), 2 ng/ml TGF- 1 (Peprotech) and 30 U/ml IL-2. When indicated, irradiated wild-type splenic antigen-presenting cells (APCs) were used for optimal Tr1 cell differentiation. For Th2 differentiation, the cells were treated with 10 ng/ml mIL-4 (Peprotech), 5  g/ml  -IFN- . For iTreg differentiation, the cells were treated with 1 ng/ml TGF- 1 (Peprotech), 5  g/ml  -IFN- , 5  g/ml  -IL-4 and 30 U/ml IL-2. For Th17 differentiation, the cells were treated with 0.5 ng/ml TGF- 1, 10 ng/ml IL-6 (Peprotech), 5  g/ml  -IFN- , and 5  g/ml  -IL-4. When indicated, 10 ng/ml IL-23 and 10 ng/ml IL-1  (Peprotech) were used for optimal Th17 cell differentiation.

extract_protocol: Total cellular RNA was extracted from Th1 and Th17 cells with Trizol reagent (Invitrogen) in Tet2 wild-type and Tet2 deficient mice.

value: spleen and lymph node

value: CD4+ T cell

value: wild-type


title: Th1 cells, Tet2 wild-type, biological rep1


title: LSK WT replicate 1

description:
Sample name: LSK WT-1
Gene expression data from WT mouse LSKs


title: RT+1D11_mouse#1


title: Th1 cells, Tet2-/-, biological rep2

source_name: Th1 cells, Tet2-/-


title: Th17 cells, Tet2-/-, biological rep2

source_name: Th17 cells, Tet2-/-


title: RT+1D11_mouse#2


title: Th17 cells, Tet2-/-, biological rep1


title: Th17 cells, Tet2 wild-type, biological rep1

source_name: Th17 cells, Tet2 wild-type


title: Th1 cells, Tet2-/-, biological rep1


title: 1D11_mouse#3


title: Isotype control_mouse#3


title: MA-10_siRNA MEF2_rep1

city: Quebec

first: Caroline

last: Daems

state: Qc

address: 2705, boulevard Laurier

department: Obstetrics, Gynecology, and Reproduction

country: Canada

institute: CRCHUQ-ULAVAL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. The cDNAss hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 17±1 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G and Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files.

data_processing: Analysis was performed using Partek® software, version 6.6 update 6.13.0621 (Partek Inc., St. Louis, MO). Robust Multiarray Analysis (RMA) background correction and a logarithmic transformation were applied to data arrays.

source_name: MA-10 Leydig cells_MEF2_siRNA

label_protocol: Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol

growth_protocol: Cells were grown in DMEM-F12 supplemented with 15% horse serum and penicillin/streptomycin (P/S) at 37°C, 5% CO2 prior to treatment.

extract_protocol: Total RNA was extracted using the TRIZOL reagent, as per the manufacturer's instructions.

treatment_protocol: Cells were treated with siRNA MEF2 or siRNA Ctrl for 48h.

value: Tumour MA-10 Leydig cells


title: RT_mouse#1


title: MA-10_siRNA MEF2_rep3


title: chrIIR-Tamp 1N

description: S6_transformant_#1, ACB461

scan_protocol: Pixel Size : 5 Scan Date : 2012-02-14 Scan Time : 12:33:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: RT_mouse#2


title: 1D11_mouse#1


title: Isotype control_mouse#2


title: 1D11_mouse#2


title: MA-10_siRNA MEF2_rep2


title: MA-10_siRNA Ctrl_rep3

source_name: MA-10 Leydig cells_control_siRNA


title: Th17 cells, Tet2 wild-type, biological rep2


title: YOR050C_Tamp

description: CFV Clone, Plate 3 well F8; MD330-8F

scan_protocol: Pixel Size : 5 Scan Date : 2013-10-13 Scan Time : 11:03:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: YPR198W_Tamp

description: CFV Clone, Plate 4 well B10; MD331-10B

scan_protocol: Pixel Size : 5 Scan Date : 2013-10-13 Scan Time : 10:55:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: YNR027W_Tamp

description: CFV Clone, Plate 4 well D8; MD331-8D


title: YMR130W_Tamp

description: CFV Clone, Plate 4 well A10; MD331-10A


title: Isotype control_mouse#1


title: YLR339C_Tamp

description: CFV Clone, Plate 3 well B7; MD330-7B


title: WT Th17, biological rep1

description: Gene expression data from wild-type Th17 cells.

hyb_protocol: The samples were hybridized according to Affymetrix protocol. The chips were washed and stained using fluidics protocol FS450_0007.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G Scanner.

data_processing:
Images were processed into CEL files with the Affymetrix GCOS software.
Raw CEL intensity data was RMA-normalized using the Expression Console from Affymetrix.

source_name: Tet2(f/f) mice, Th17 cells

label_protocol: The samples were fragmented and biotin labeled using the WT Terminal Labeling Kit (Affymetrix).


title: KO Th17, biological rep1

description: Gene expression data from Tet2-defficient Th17 cells.

source_name: CD2(Cre)Tet2(f/f) mice, Th17 cells


title: MA-10_siRNA Ctrl_rep1


title: KO Th17, biological rep2


title: KO Th1, biological rep2

description: Gene expression data from Tet2-defficient Th1 cells.

source_name: CD2(Cre)Tet2(f/f) mice, Th1 cells


title: YLR042C_Tamp

description: CFV Clone, Plate 3 well H12; MD330-12H


title: YJR003C_Tamp

description: CFV Clone, Plate 3 well H5; MD330-5H


title: MA-10_siRNA Ctrl_rep2


title: YEL072W_Tamp

description: CFV Clone, Plate 3 well D9; MD330-9D


title: YGR238C_Tamp

description: CFV Clone, Plate 3 well E12; MD330-12E


title: YDR100W_Tamp

description: CFV Clone, Plate 4 well E1; MD331-2E; (original name: CFV Clone, Plate 4 well E1)


title: YCR088W_Tamp

description: CFV Clone, Plate 4 well G3; MD331-3G


title: YDR496C_Tamp

description: CFV Clone, Plate 3 well D5; MD330-5D


title: YFL005W_Tamp

description: CFV Clone, Plate 3 well F2; MD330-2F


title: P5c3_chr6.16

description: MD292-A2 vs YMD1124

scan_protocol: Pixel Size : 5 Scan Date : 2013-07-21 Scan Time : 12:53:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P5c3_POB3

description: MD292-A4 vs YMD1124


title: YLR007W_Tamp

description: CFV Clone, Plate 4 well D4; MD331-4D


title: WT Th1, biological rep2

description: Gene expression data from wild-type Th1 cells.

source_name: Tet2(f/f) mice, Th1 cells


title: chrII Tamp pool: YBR297W

description: SUL1_pilot_499c5_redo; ACB545

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-23 Scan Time : 10:52:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P5c3_chr13

description: MD291-C3 vs YMD1124

scan_protocol: Pixel Size : 5 Scan Date : 2013-07-13 Scan Time : 16:09:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: chrII Tamp pool: YBR296C

description: SUL1_pilot_498c20; ACB592

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-21 Scan Time : 15:59:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: chrII Tamp pool: YBR301W

description: SUL1_pilot_508c2; ACB554


title: YBL107C_Tamp

description: CFV Clone, Plate 4 well C10; MD331-10C


title: chrII Tamp pool: YBR291C

description: SUL1_pilot_495c1_redo; ACB543


title: P6c1_NRK1

description: MD231-B6 vs YMD1124

scan_protocol: Pixel Size : 5 Scan Date : 2013-05-17 Scan Time : 10:44:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: YGR010W_Tamp

description: CFV Clone, Plate 4 well D5; MD331-5D


title: KO Th1, biological rep1


title: chrII Tamp pool: YBR288C

description: SUL1_pilot_505c4; ACB587


title: chrII Tamp pool: YBR284W

description: SUL1_pilot_491c4; ACB536

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-16 Scan Time : 14:04:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: chrII Tamp pool: YBR292C

description: SUL1_pilot_496c10; ACB585


title: chrII Tamp pool: YBR285W

description: SUL1_pilot_492c1; ACB538


title: WT Th17, biological rep2


title: chrII Tamp pool: YBR289W

description: SUL1_pilot_506c6; ACB551

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-16 Scan Time : 13:56:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: chrII Tamp pool: YBR298C_Tamp

description: SUL1_pilot_500c19; ACB586


title: chrII Tamp pool: YBR293W

description: SUL1_pilot_510c2; ACB556

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-21 Scan Time : 16:07:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: chrII Tamp pool: YBR286W

description: SUL1_pilot_493c1; ACB540


title: chrII Tamp pool: YBR290W

description: SUL1_pilot_494c1; ACB542


title: chrII Tamp pool: YBR287W

description: SUL1_pilot_504c3_redo; ACB549


title: VentralHorn, Individual 3

city: Toledo

first: Daniel

last: Garcia-Ovejero

state: Toledo

address: Finca La Peraleda s/n

department: Neurología Experimental

country: Spain

institute: Hospital Nacional de Parapléjicos (SESCAM)

description:
Reference Region
SAMPLE 7

data_processing:
Automatic detection of Ct was used to establish the threshold of amplification for each gene. Cts shown in the MAtrix non normalized template correspond to the average of Cts from technical duplicates or cuadrupilcates. Cts>36 were considered as non-amplified. We calculated ΔCt, the difference between the Ct of each gene and the Ct of the endogenous gene (18S) for all the genes in the samples. A fixed very low value was assigned as ΔCt to genes considered unamplified in the RT-PCR for further statistical comparisons. This value was ΔCt= 22, to surpass the detection limit of the apparatus (Ct=40) in the most abundant sample (18S Ct=19). ΔCt values were used for statistical comparisons. Only genes expressed in at least three out of four samples were considered as consistently expressed in that region (central canal or ventral gray matter) and included in the final analysis. With those genes, we determined genes enriched in the ependymal region, defining  enrichment as a higher and statistically significant expression in that region vs gray matter (Student t-test, p<0.05, with multiple testing correction by Benjamini-Hochberg (Benjamini et al., 2001). To obtain folds of enrichment, we obtained ΔΔCt of each gene, subtracting the average value of expression in the ependymal region by the average value of expression in the gray matter. Fold of enrichment is shown by the Relative Quantity (RQ= 2^- ΔΔCt). For RQs < 1, the inverse was performed to show folds of empoverishment in ependymal region vs ventral horn.
Normalized values (ΔCt), are ΔCt = Ct_Target − Ct_18S; Normalize value for a sample which expression was beyond our established threshold of reliable detection (Ct>36) was assigned a ΔCt =22. Fold change sheet shows the RQ for each gene: RQ= 2^- ΔΔCt, where ΔΔCt for each gene is the difference between the average value of expression in the ependymal region of that gene by the average value of expression of that gene in the gray matter. For RQs < 1, the inverse value is shown.

label: FAM

source_name: Laser Capture Microdissection of human ventral horn region

label_protocol: Reverse transcription of amplified RNA was performed with ExpressArt® TR cDNA synthesis kit (#8994-A30, AmpTec, AMSBIO, UK). We then added 60 ng of our samples pre-mixed with TaqMan® Universal Master Mix II (Life Technologies, Madrid, Spain) into each loading port of the TLDA (1.25 ng cDNA/well). Cards were then centrifuged and run on an Applied Biosystems® 7900HT Fast Real-Time PCR System.

growth_protocol: Fresh frozen postmortem human tissue samples

extract_protocol: Microdissected pieces were collected on RNA Extraction Buffer, and RNA extracted according to the manufacturer's instructions (Arcturus PicoPure® RNA Isolation Kit, Applied Biosystems, CA, USA). Evaluation of RNA integrity, purity and concentration was assessed with chip-based automated electrophoresis performed with the Experion™ RNA HighSens Analysis Kit (BioRad, USA).

treatment_protocol: Cryostat sectioning, toluidin blue staining, Laser Capture Microdissection

tag: subject id

value: Individual 3

value: female

tag: age (yrs)

tag: Cause of death

value: Carcinoma and metastasis. With brain but not spinal cord metastasis.

tag: postmortem delay

value: ventral horn region


title: VentralHorn, Individual 5

description:
Reference Region
SAMPLE 8

value: Individual 5

value: male

value: Endocarditis. No neuropathological features


title: chrII Tamp pool: YBR294W

description: SUL1_pilot_507c2_redo; ACB552


title: +_+_pH 6.7_1

city: Zurich

first: Cheryl

last: de Valliere

address: Steinwartstrasse 14

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Array hybridization and washing were performed on a Gene Atlas Instrument according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

scan_protocol: Arrays were scanned with Affymetrix's Gene Atlas Instrument (Control Software Version 1.0)

data_processing: Data was summarized with RMA using R/bioconductor (R version 2.15.2 and Bioconductor version 2.11)

source_name: WT_low pH

growth_protocol: Primary mouse residential peritoneal macrophages were isolated and cultured RPMI 1640, 10% FCS

extract_protocol: Qiagen Rneasy mini kit, DNase treatment followed by high-capacity reverse cDNA transcription (Applied Biosystems)

treatment_protocol: 24hrs at acidic (6.8) or control (7.6) pH

value: wild type (+/+)

value: primary mouse residential peritoneal macrophages

value: pH 6.7 (low pH)


title: VentralHorn, Individual 2

description:
Reference Region
SAMPLE 6

value: Individual 2

value: Multiorganic failure. Severe broncopathy

value: 3 h 55 min


title: chrII Tamp pool: YBR281C

description: SUL1_pilot_488c11; ACB532


title: chrII Tamp pool: YBR278W

description: SUL1_pilot_487c1; ACB530


title: chrII deletion pool: YBR291C

description: SUL1_pilot_S6x445; ACB567


title: chrII Tamp pool: YBR277C

description: SUL1_pilot_486c2; ACB528


title: chrII Tamp pool: YBR276C

description: SUL1_pilot_502c2_redo; ACB546


title: chrII Tamp pool: YBR283C

description: SUL1_pilot_490c9; ACB589


title: chrII deletion pool: YBR300C

description: SUL1_pilot_S6x451; ACB573

source_name: ACB571 (I think this is wrong it should be ACB573, edited 140806)


title: chrII Tamp pool: YBR282W

description: SUL1_pilot_489c1; ACB534


title: WT Th1, biological rep1


title: chrII deletion pool: YBR289W

description: SUL1_pilot_S6x456; ACB578


title: +_+_pH 6.7_3


title: chrII deletion pool: YBR287W

description: SUL1_pilot_S6x454; ACB576


title: chrII deletion pool: YBR285W

description: SUL1_pilot_S6x442; ACB564


title: +_+_pH 7.7_4

source_name: WT_high pH

value: pH 7.7 (high pH)


title: chrII Tamp pool: YBR280C

description: SUL1_pilot_503c1_redo; ACB547


title: chrII deletion pool: YBR296C

description: SUL1_pilot_S6x448; ACB570


title: -_-_pH 6.7_2

source_name: KO_low pH


title: +_+_pH 7.7_3


title: +_+_pH 6.7_2


title: -_-_pH 6.7_3


title: -_-_pH 6.7_4


title: -_-_pH 6.7_1


title: Ependymal, individual 4

description:
Test Region
SAMPLE 4

source_name: Laser Capture Microdissection of human ependymal region

value: individual 4

value: Cardiac arrest. No neuropathological features

value: ependymal region


title: +_+_pH 7.7_2


title: Ependymal, individual 1

description:
Test Region
SAMPLE 1

value: individual 1

value: Refractary septic shock


title: chrII deletion pool: YBR277C

description: SUL1_pilot_S6x436; ACB558


title: VentralHorn, Individual 1

description:
Reference Region
SAMPLE 5

value: Individual 1


title: -_-_pH 7.7_3

source_name: KO_high pH


title: -_-_pH 7.7_4


title: -_-_pH 7.7_1


title: Ependymal, individual 2

description:
Test Region
SAMPLE 2

value: individual 2


title: +_+_pH 6.7_4


title: Tissue_engineered_Psoriatic_human_skin_control_rep1

status: Public on Apr 11 2015

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

description: TEPHS Control replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tissue-engineered Psoriatic human skin control, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl (Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON)  from Tissue-engineered Psoriatic human skin and cultivated with or without cytokines (IL-17a, IL-6, IL1a, TNF-a).

value: Tissue-engineered Psoriatic human skin

value: Female

tag: age

value: 47 years


title: Tissue_engineered_Psoriatic_human_skin_control_rep2

description: TEPHS Control replicate 2

source_name: Tissue-engineered Psoriatic human skin control, replicate 2

value: Male

value: 49 years


title: +_+_pH 7.7_1

source_name: WT_high Ph

value: wild type (+/+)

value: primary mouse residential peritoneal macrophages


title: -_-_pH 7.7_2


title: Suction blister sample from subject 18740 at t1

city: BETHESDA

first: Vincent

last: Hearing

state: MD

address: BG 37 RM 2132B 37 CONVENT DR

institute: National Cancer Institute

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing  protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: skin biospy

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA  InputLinear Amp Kit (Agilent Technologies) following the manufac-turer’s protocol.

extract_protocol: RNA was prepared from each biopsy using standard RNA extraction protocols (Trizol, Sigma, St Louis, MO), and were quality-checked using an Agilent 2100 Bioanalyzer platform (Agilent Technologies,Waldbronn, Germany).

treatment_protocol: 4mm human skin punch biopsies were taken from subjects

tag: time

tag: sample type

value: suction blister

tag: phase

tag: hybridization

value: whole human skin


title: Tissue_engineered_Psoriatic_human_skin_control_rep3

description: TEPHS Control replicate 3

source_name: Tissue-engineered Psoriatic human skin control, replicate 3

value: 64 years


title: Suction blister sample from subject 18740 at t4


title: Suction blister sample from subject 18740 at t3


title: Tissue_engineered_Psoriatic_human_skin_cytokines_rep1

description: TEPHS Cytokines replicate 1

source_name: Tissue-engineered Psoriatic human skin cultivated with cytokines replicate 1


title: Tissue_engineered_Psoriatic_human_skin_cytokines_rep3

description: TEPHS Cytokines replicate 3

source_name: Tissue-engineered Psoriatic human skin cultivated with cytokines replicate 3


title: Tissue_engineered_Psoriatic_human_skin_cytokines_rep2

description: TEPHS Cytokines replicate 2

source_name: Tissue-engineered Psoriatic human skin cultivated with cytokines replicate 2


title: control sample from subject 18740 at t5

value: control


title: control sample from subject 18740 at t3


title: Suction blister sample from subject 18740 at t2


title: control sample from subject 18740 at t4


title: control sample from subject 18740 at t1


title: Suction blister sample from subject 18740 at t5


title: Ependymal, individual 3

description:
Test Region
SAMPLE 3

value: individual 3

value: female

value: Carcinoma and metastasis. With brain but not spinal cord metastasis.


title: Suction blister sample from subject 17061 at t2


title: Suction blister sample from subject 17061 at t3


title: control sample from subject 17061 at t4


title: control sample from subject 17061 at t1


title: Suction blister sample from subject 17061 at t4


title: control sample from subject 17061 at t2


title: Suction blister sample from subject 17061 at t5


title: control sample from subject 18740 at t2


title: Suction blister sample from subject 17061 at t1


title: Suction blister sample from subject 16967 at t5


title: Suction blister sample from subject 16967 at t2


title: Suction blister sample from subject 16967 at t3


title: control sample from subject 16967 at t5


title: control sample from subject 16967 at t2


title: Suction blister sample from subject 16967 at t1


title: Suction blister sample from subject 16967 at t4


title: control sample from subject 16967 at t3


title: control sample from subject 16967 at t1


title: control sample from subject 17061 at t5


title: Suction blister sample from subject 14958 at t2


title: control sample from subject 14958 at t4


title: Suction blister sample from subject 14958 at t4


title: control sample from subject 14958 at t5


title: control sample from subject 14958 at t3


title: control sample from subject 16967 at t4


title: Suction blister sample from subject 14958 at t3


title: Suction blister sample from subject 14958 at t1


title: Suction blister sample from subject 14958 at t5


title: control sample from subject 14958 at t2


title: Suction blister sample from subject 14295 at t4


title: control sample from subject 14958 at t1


title: Suction blister sample from subject 14295 at t3


title: control sample from subject 14295 at t5


title: control sample from subject 14295 at t2


title: Suction blister sample from subject 14295 at t1


title: control sample from subject 14295 at t3


title: Suction blister sample from subject 13466 at t5


title: Suction blister sample from subject 13466 at t4


title: control sample from subject 13466 at t4


title: Suction blister sample from subject 13466 at t2


title: CshF_2

hyb_protocol: Labeled RNA was hybridized overnight to high-density human genome (HG) U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: Microarray scan was carried out under strictly controlled conditions with the Affymetrix Fluidics Station and Scanner. The intensity values of different probe sets (genes) were imported into R 2.13.1 for data analysis.

data_processing: gcRMA, SVA batch correction. The feature number was reduced due to the filtering step. In order to reduce the false discovery rate, filtering step was incorporated into the analysis program. Probes with low intensities (less than log2(8)) in more than 80% samples and probes with small variations (IQR<0.2) across samples were excluded from the statistical analysis. 23416 probes were selected for further differential analysis.

label_protocol: About 100 ng of total RNA samples were reverse transcribed, 1 cycle target labeled with 3’ IVT Express labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The human melanoma cell line A375M2 were obtained from ATCC and cultured using DMEM supplemented with 10% Fetal Bovine Serum (FBS, Atlanta Biologicals). Cells were cultured at 5% CO2 unless indicated.

extract_protocol: Total RNA was extracted with RNAeasy kit (Qiagen,Valencia, CA) as requested per application and RNA quantity. DNA was obtained using the SuperScript III First-Strand Synthesis System for RT (Invitrogen). PCR was performed using Taq DNA Polymerase (Invitrogen) according to manufacturer’s instructions

treatment_protocol: CMV-IRES lentiviral mediated gene vectors containing the full length His6X-Tag PMEL (lvPMEL) or an empty vector expressing GFP (lvGFP) were used for transduction. Lentiviral vectors were constructed using a pDEST-688 vector containing a CMV promoter into an IRESeGFP element after the gene of interest that permits expression of eGFP in the infected cells (Protein Expression Laboratory, NCI, Frederick, MD). Viral content was measured using flow cytometry (Lentiviral Vector Laboratory, Frederick, MD). Transduced cells were then selected for at least 5 days with increased doses of blasticidine (Invitrogen). For shRNA knockdown stable transduction, lentiviral vectors with a pool of 3 target-specific constructs that encode 19-25 nt (plus hairpin) shRNA proprietary sequences against the human FHL-2 (sc-37891-V) at the concentration of 1x106 infection units of virus were purchased from Santa Cruz Biotechnology (Santa Cruz). CopGFP control lentiviral particles to express GFP (sc-108084) were used as control. Cells were then selected with puromycin (Invitrogen). After selection, cells expressing the highest GFP levels were FACS sorted and placed in culture under continuous selection.

tag: cell line

tag: transduction

value: lentiviral vectors containing specific target sequences of shRNAs against human FHL2


title: Suction blister sample from subject 13466 at t1


title: control sample from subject 13466 at t3


title: Suction blister sample from subject 14295 at t2


title: Suction blister sample from subject 14295 at t5


title: control sample from subject 14295 at t1


title: Suction blister sample from subject 12565 at t5


title: control sample from subject 13466 at t1


title: Suction blister sample from subject 13466 at t3


title: CshF_3


title: Suction blister sample from subject 12565 at t3


title: control sample from subject 12565 at t5


title: CGFP_3

value: lentiviral vectors containing GFP


title: Suction blister sample from subject 12565 at t2


title: control sample from subject 12565 at t4


title: Suction blister sample from subject 12565 at t4


title: control sample from subject 14295 at t4


title: control sample from subject 13466 at t5


title: control sample from subject 13466 at t2


title: CshF_1


title: Suction blister sample from subject 12565 at t1


title: control sample from subject 12565 at t2


title: control sample from subject 17061 at t3


title: control sample from subject 12565 at t3


title: CGFP_2


title: CGFP_1


title: AshN_1

value: lentiviral vectors containing specific target sequences of shRNAs against human NFYA


title: AshN_2


title: control sample from subject 12565 at t1


title: Suction blister sample from subject 7614 at t3


title: AshN_3


title: AshF_3


title: Suction blister sample from subject 7614 at t4


title: Suction blister sample from subject 7614 at t1


title: Suction blister sample from subject 7614 at t2


title: Suction blister sample from subject 7614 at t5


title: AshF_2


title: control sample from subject 7614 at t4


title: control sample from subject 7614 at t1


title: control sample from subject 7614 at t3


title: Suction blister sample from subject 6665 at t3


title: Suction blister sample from subject 6665 at t5


title: AGFP_3


title: Suction blister sample from subject 6665 at t2


title: control sample from subject 7614 at t2


title: AP17_3

value: lentiviral vectors containing the human full length PMEL/Silv gene


title: AGFP_1


title: control sample from subject 7614 at t5


title: AP17_1


title: AshF_1


title: Suction blister sample from subject 6665 at t4


title: control sample from subject 6665 at t2


title: control sample from subject 6665 at t5


title: control sample from subject 6665 at t4


title: Suction blister sample from subject 6382 at t1


title: AGFP_2


title: AP17_2


title: Suction blister sample from subject 6382 at t4


title: Suction blister sample from subject 6382 at t2


title: control sample from subject 6665 at t1


title: Suction blister sample from subject 6665 at t1


title: control sample from subject 6382 at t5


title: LY030

type: SRA

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

library_source: transcriptomic

data_processing:
Align with Bowtie 2
Analyze with cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: Expression FPKM

extract_protocol:
Total RNA was extracted.  No selection for polyA was performed.
Standard adaptors were used for Illumina sequencing

tag: histology

value: BL

tag: storage

value: FFPE

tag: ebv

value: EBV+


title: LY031

value: DLBCL


title: LY029

value: PBL


title: Suction blister sample from subject 6382 at t5

tag: tissue


title: control sample from subject 6665 at t3


title: LY024

value: EBV-


title: LY023

value: Frozen


title: LY022


title: LY021


title: control sample from subject 6382 at t2

value: whole human skin


title: control sample from subject 6382 at t4


title: control sample from subject 6382 at t1


title: LY020


title: Suction blister sample from subject 5848 at t5

value: suction blister


title: control sample from subject 5848 at t5

value: control


title: Suction blister sample from subject 5848 at t3


title: LY019


title: LY018


title: control sample from subject 5848 at t1


title: control sample from subject 5848 at t2


title: Suction blister sample from subject 5848 at t4


title: LY017


title: Suction blister sample from subject 4510 at t5


title: Suction blister sample from subject 5848 at t1


title: control sample from subject 5848 at t3


title: control sample from subject 5848 at t4


title: Suction blister sample from subject 5848 at t2


title: LY016


title: Suction blister sample from subject 4510 at t4


title: Suction blister sample from subject 4436 at t5


title: LY015


title: Suction blister sample from subject 4510 at t2


title: Suction blister sample from subject 4510 at t1


title: LY014


title: Suction blister sample from subject 4436 at t4


title: Suction blister sample from subject 4510 at t3


title: control sample from subject 4510 at t4


title: control sample from subject 4510 at t3


title: control sample from subject 4510 at t5


title: control sample from subject 4510 at t2


title: LY011


title: LY009


title: LY013


title: control sample from subject 4510 at t1


title: Suction blister sample from subject 4436 at t3


title: control sample from subject 4436 at t3


title: control sample from subject 4436 at t5


title: Suction blister sample from subject 4436 at t1


title: control sample from subject 4436 at t4


title: Suction blister sample from subject 4436 at t2


title: control sample from subject 4436 at t1


title: Human hepatocellular carcinoma tissue 2

city: Guangzhou

first: Bin

last: Wu

state: Guangdong

address: No. 600, Tianhe Road, Tianhe District

department: Gastroenterology of The 3rd affiliated Hospital

country: China

institute: Sun Yat-sen University

description: HCC tissue with hepatitis B virus-infection

hyb_protocol: Array hybridization was performed in a Agilent Hybridization oven overnight at a rotation speed of 20 rpm at 42 °C and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42 °C for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: Human hepatocellular carcinoma tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been improved using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) for producing higher yields of labeled cDNA.

extract_protocol: total RNA from each tissue sample was isolated according to the manufacturer’s instructions of TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and was further purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacturer’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000).

value: HCC

value: male


title: LY007


title: Human hepatocellular paracancer tissue 3

description: paracancerous tissues of HCC with hepatitis B virus-infection

source_name: Human hepatocellular paracancer tissue

value: paracancer tissue


title: Suction blister sample from subject 3291 at t3


title: control sample from subject 4436 at t2


title: Suction blister sample from subject 3291 at t4


title: Human hepatocellular carcinoma tissue 3


title: LY005

value: Follicular lymphoma


title: Suction blister sample from subject 3291 at t5


title: LY004


title: LY008


title: LY006


title: LY002


title: Human hepatocellular paracancer tissue 1


title: LY003


title: Human hepatocellular paracancer tissue 2


title: Human normal liver tissue 3

description: parahemangioma sites of hepatic hemangioma patients without hepatitis

source_name: Human normal liver tissue

value: normal


title: Human normal liver tissue 2


title: Suction blister sample from subject 3291 at t1


title: Suction blister sample from subject 3291 at t2


title: control sample from subject 3291 at t5


title: control sample from subject 3291 at t2


title: control sample from subject 3291 at t4


title: control sample from subject 3291 at t3


title: Human hepatocellular carcinoma tissue 1


title: Human normal liver tissue 1

value: female


title: LY010


title: control sample from subject 3291 at t1


title: Biological replicates, time 9-16 hours

status: Public on Apr 10 2015

city: Pretoria

first: Ingrid

last: Rossouw

state: Gauteng

address: Lynnwoodroad

department: Genetics

country: South Africa

institute: University of Pretoria

description:
Sample name: C16-C9
Biological replicates, B. divergens parasites harvested between 9-16 hours

hyb_protocol: To ensure successful hybridization, 20 pmol of each Cy3 (reference pool) and Cy5 (target) –cDNA samples were combined in 0.2 µl tubes, with several buffers, including a 10x blocking buffer, 25x fragmentation buffer, 2x GE hybridization buffer and Wash Buffers 1 and 2 supplied by Agilent Technologies (Proprietary, Agilent Technologies). To each labelled cDNA sample mixture, 5 µl 10x blocking buffer, 1 µl 25x fragmentation buffer, RNAse-free water was added (to adjust the final reaction volume to 25 µl) and incubated for 30 minutes at 60°C (in a PE2400 thermal cycler, Applied Biosystems). Following incubation, 25 µl 2x GE hybridization buffer was carefully added to each sample and placed on ice (±4°C). The 8-array gasket slide (Agilent Technologies) was placed in the hybridization assembly chamber (Agilent Technologies) and 40 µl of each individually labelled cDNA sample slowly pipetted onto the separate gasket slide chambers, taking care so as to not introduce bubbles. The printed Agilent microarray slide was carefully placed onto the loaded gasket slide which was firmly closed, sealed and placed in the pre-heated Agilent Hybridization Oven (G2545A, Agilent Technologies) for overnight hybridization at 65°C (rotation speed of 10).

scan_protocol: Scanned on a 4000B microarray laser scanner (Molecular devices Inc., USA)

data_processing: Axon GenePix Pro 6.0 software (Molecular Devices) measured, recorded and analyzed images based on the software’s default settings as well as visual inspection of spots (adjusting the grid and flagging of low quality spots). Flagged features were ignored in subsequent analyses and given a zero weight value. Initial data analysis was performed using CLUSTER and TREEVIEW software. Data was log transformed, normalized and mean centered prior to hierarchical clustering and subsequently ordered according to expression values (M-values) identified over time. Pearson correlation coefficients (r) were calculated within the R-statistical environment to identify expression similarities between each of the time points. The linear model for microarray data analysis (LIMMA) within the R-statistical environment (http://cran.r-project.org/) was used to simultaneously assess differential expression between several transcripts, collected at different time points. Adaptive background correction (offset = 50) was followed by within-array normalization (global LOWESS) and between-array normalization (Gquantile).

organism: Babesia divergens

source_name: Asynchronous B. divergens cultures; 5% hematocrit, 12% parasitemia, 10 ml

label_protocol: For gene expression profiling, a reference pool design strategy was followed which consisted of equal RNA quantities (4 µg), prepared from all biological replicates collected over the 16 hour time period. First-strand cDNA synthesis was performed by incubating 4 µg RNA with 250 pmol oligo(dT25) and 775 pmol random primer 9 for 10 minutes at 70°C, followed by cooling for 10 minutes on ice. Reverse transcription and aminoallyl-dUTP (5-(3-aminoallyl)-2’-deoxyuridine-5’ triphosphate) incorporation were performed simultaneously, with minor modifications in reaction time using 340 units Superscript III (Invitrogen). Contaminating RNA template was removed by RNA hydrolysis of the cDNA template with 0.5 M EDTA and 1 M NaOH for 15 minutes at 65°C before samples were purified with a NucleoSpin Extract II PCR Clean-up kit (Macherey-Nagel). Purified cDNA samples (1.5 µg) were dried in vacuo and resuspended in 2.5 µl RNAse-free water. Both Cy3 (reference pool) and Cy5 (samples) fluorescent dyes (GE Healthcare Life Sciences) were dissolved in DMSO and coupled to the cDNA samples at pH 9. Excess (unincorporated) dye was removed using the QIAquick PCR Purification Kit (Qiagen).

growth_protocol: The Rouen 1987 strain of B. divergens was kindly provided by Dr. Stephane Delbecq (Laboratoire de Biologie Cellulaire et Moleculaire UFR Pharmacie, Montpellier, France). Asynchronous B. divergens parasite cultures were maintained in human erythrocytes (type O+) suspended in complete culture medium [RPMI-1640 medium supplemented with 25.2 mM HEPES, 22.2 mM D-glucose, 50 mg/l hypoxanthine, 21.4 mM sodium bicarbonate, 48 mg/l gentamycin (Sigma)] further supplemented with 10% human serum. Cultures were maintained at 37°C in a gaseous environment of 90% N2, 5% O2 and 5% CO2 on a rotary platform (60 rpm) at ~5% hematocrit and 10-15% parasitemia, with daily media replacement.

extract_protocol: Total RNA was isolated from the biological replicate samples (5% hematocrit, 12% parasitemia, 10 ml) collected at four time-points (0, 4, 9 and 16 hours) from newly initiated cultures and washed three times with 15 ml 1xPBS solution under RNAse-free conditions. TRI-Reagent fractionation was followed by clean-up using the Qiagen RNeasy Protect Mini kit (Qiagen). Contaminating genomic DNA was removed with a DNase I treatment (Qiagen). RNA integrity and quality was subsequently analyzed using the Experion automated electrophoresis system (Bio-Rad) at the ACGT Microarray Facility (University of Pretoria).

tag: strain

value: Rouen 1987 strain

value: erythrocytes

value: 9-16 hours

source_name: Reference pool sample; all B. divergens replicates

value: reference pool


title: Biological replicates, time 4-16 hours

description:
Sample name: C16-C4
Biological replicates, B. divergens parasites harvested between 4-16 hours

value: 4-16 hours


title: Biological replicates, time 0-16 hours

description:
Sample name: C16-C0
Biological replicates, B. divergens parasites harvested bewteen 0-16 hours

value: 0-16 hours


title: Biological replicates, time 0-4 hours

description:
Sample name: C4-C0
Biological replicates, B. divergens parasites harvested bewteen 0-4 hours

value: 0-4 hours


title: Biological replicates, time 4-9 hours

description:
Sample name: C9-C4
Biological replicates, B. divergens parasites harvested between 4-9 hours

value: 4-9 hours


title: Biological replicates, time 0-9 hours

description:
Sample name: C9-C0
Biological replicates, B. divergens parasites harvested between 0-9 hours

value: 0-9 hours


title: Pax5_het042

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description:
Pax5 het042
MMLV

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

source_name: non-leukemic bone marrow

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: DNA was extracted from tumor cells and normal B cells of Pax5 heterozygous mice.

extract_protocol: Phenol-chloroform

value: stage-matched bone marrow

source_name: leukemic bone marrow

value: Pax5+/- primary tumor sample


title: Pax5_het040

description:
Pax5 het040
MMLV


title: Pax5_het041

description:
Pax5 het041
MMLV


title: Pax5_het049

description:
Pax5 het049
MMLV


title: Pax5_het051

description:
Pax5 het051
MMLV


title: Pax5_het047

description:
Pax5 het047
MMLV


title: Pax5_het053

description:
Pax5 het053
MMLV


title: Pax5_het050

description:
Pax5 het050
MMLV


title: Pax5_het036

description:
Pax5 het036
MMLV


title: Pax5_het031

description:
Pax5 het031
MMLV


title: Pax5_het054

description:
Pax5 het054
MMLV


title: Pax5_het022

description:
Pax5 het022
ENU


title: Pax5_het037

description:
Pax5 het037
MMLV


title: Pax5_het043

description:
Pax5 het043
MMLV


title: Pax5_het025

description:
Pax5 het025
ENU


title: Pax5_het021

description:
Pax5 het021
ENU


title: Pax5_het035

description:
Pax5 het035
MMLV


title: Pax5_het016

description:
Pax5 het016
ENU


title: Pax5_het045

description:
Pax5 het045
MMLV


title: Pax5_het032

description:
Pax5 het032
MMLV


title: Pax5_het034

description:
Pax5 het034
MMLV


title: Pax5_het038

description:
Pax5 het038
MMLV


title: Pax5_het015

description:
Pax5 het015
ENU


title: Pax5_het017

description:
Pax5 het017
ENU


title: Pax5_het018

description:
Pax5 het018
ENU


title: Pax5_het019

description:
Pax5 het019
ENU


title: WP3ΔcrpD2-20℃-rep4

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
9793 D2cy3-WP3cy5.LSR
WP3ΔcrpD2 cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing: S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C

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

tag: treatment

value: WP3 cells were cultured at 20°C in 2216E medium

value: WP3 cells were cultured at 20℃ in 2216E medium


title: WP3ΔcrpD2-20℃-rep6


title: Pax5_het012

description:
Pax5 het012
ENU


title: WP3ΔcrpD2-20℃-rep5


title: WP3ΔcrpD1-20℃-rep5

description:
9796 D1cy3+WP3cy5.LSR
WP3ΔcrpD1 cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5


title: WP3ΔcrpD2-20℃-rep1

description:
9794 D2cy5-WP3cy3.LSR
WP3ΔcrpD2 cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: Pax5_het008

description:
Pax5 het008
ENU


title: Pax5_het010

description:
Pax5 het010
ENU


title: WP3ΔcrpD1-20℃-rep4


title: Pax5_het007

description:
Pax5 het007
ENU


title: Pax5_het011

description:
Pax5 het011
ENU


title: WP3ΔcrpD1-20℃-rep3

description:
9795 D1cy5+WP3cy3.LSR
WP3ΔcrpD1 cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: WP3ΔcrpD1-20℃-rep6


title: WP3ΔcrpD1-20℃-rep2


title: Pax5_het009

description:
Pax5 het009
ENU


title: WP3ΔcrpD1-20℃-rep1


title: Pax5_het001

description:
Pax5 het001
ENU


title: Pax5_het006

description:
Pax5 het006
ENU


title: Pax5_het003

description:
Pax5 het003
ENU


title: WP3ΔcrpD2-20℃-rep3


title: Pax5_het002

description:
Pax5 het002
ENU


title: WP3ΔcrpD2-20℃-rep2


title: Pax5_het005

description:
Pax5 het005
ENU


title: ArrayR3

city: Wilrijk

first: Lucia

last: Vergauwen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

hyb_protocol: 825 ng Cy3 and 825 ng Cy5 labeled and purified cRNA were hybridized onto 4x44K full genome zebrafish (version 3, Agilent, Diegem) microarrays for 17 h at 65 °C in a rotating (10 rpm) hybridization oven (Agilent, Diegem). An A-optimal design was used as the hybridization design for each body region separately (Knapen et al., 2009) and 4 biological replicates of each condition were used, resulting in n=12 RNA samples per design. A total of 72 labelled cRNA samples was analyzed on 42 arrays.

scan_protocol: Microarray slides were scanned using a Genepix 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm in an ozone-free environment (NoZone scanner enclosure, SciGene, Sunnyvale, CA, USA). Images were analyzed for spot identification and for quantification of the fluorescent signal intensities using the Genepix Pro software 6.1 (Axon Instruments).

data_processing:
Statistical analyses of raw microarray data were performed using the R package Limma as described by Vergauwen et al. (2010). Both knockdown conditions were contrasted against SCMO. Spots for which the criterion FG < BG + 2SD (FG: foreground, BG: background, SD: standard deviation of the local background of the entire array) was true for all arrays in the dataset, were excluded from analysis. Background correction was carried out using a normal-exponential convolution model . Within-array adjustment was done by Loess normalization, which performs an intensity-dependent normalization of the ratio of red and green. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential transcription using an empirical Bayes method.  The contrasts summarized across all replicates are available on the series record in the file: genes.all.contrasts_tail.txt.
Contrasts were fitted to the linear models and cut off at FDR < 0.05 (false discovery rate, multiple testing correction using the Benjamini-Hochberg procedure) and |log2FC| > 0.585 (log2 fold change, corresponding to a fold induction of at least 1.5 or -1.5).

organism: Danio rerio

source_name: Larval tail, 20 pool, D1D2MO

label_protocol: Total RNA was amplified and labeled using the Low Input Quick Amplification Labelling Kit (LIQA, Agilent, Diegem) according to the manufacturer’s instructions. In brief, 100 ng RNA was reverse transcribed into cDNA using oligo dT primers. Subsequently, cDNA was amplified and converted into cRNA and the resulting cRNA of each sample was labeled once with Cy3-CTP and once with Cy5-CTP. The RNeasy mini spin column kit (Qiagen, Venlo) was then used to purify each amplified and labeled cRNA sample. cRNA yield, quality and dye incorporation efficiency were verified using the nanodrop spectrophotometer.

growth_protocol: zebrafish embryos were microinjected with SCMO, D1D2MO and D3MO and kept in Danieu's solution at 28,5C until 72 hpf. 72 hpf-old zebrafish larvae were manually dissected in ice-cold RNAse free water to separate the head, abdomen and tail region.

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

treatment_protocol: Zebrafish tail from 20 larvae per replicate were pooled, snap frozen in dry ice and stored at -80C. Samples were homogenized in Qiazol using mortar and plastic pestle

value: Wild type WIK

value: 72 hours post fertilization

source_name: Larval tail, 20 pool, SCMO


title: ArrayQ3


title: ArrayP3

source_name: Larval tail, 20 pool, D3MO


title: Pax5_het044

description:
Pax5 het044
MMLV


title: ArrayO3


title: ArrayN3


title: Uncut, 0h-cultured, A1/4, biological rep3

city: Basel

first: Tomonori

last: Katsuyama

address: Mattenstrasse 26

department: D-BSSE

institute: ETH Zurich

description: The correspondng region to A1/4 samples were isolated from prothorasic leg discs of 100h-old male Drosophila larvae.

hyb_protocol: cRNA (10 µg) was hybridized for 16 hr at 45˚C on GeneChip® Drosophila Genome 2.0 Array. Following hybridization, the arrays were processed using a GeneChip Fluidics  Station 400 (Affymetrix).

scan_protocol: Fluorescent images of arrays were captured using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Microarray data were preprocessed and analyzed using R and BioConductor. First, diagnostic plots were produced and used to exclude spatial artifacts. Then, probeset level intensities were background subtracted and quantile-quantile normalized using RMA. Hierarchical clustering analysis of expression values indicated the presence of batch effects. Data were therefore adjusted for this systematic error by performing a gene-wise one-way analysis of variance using PAMR (Prediction Analysis of Microarrays, for R) (Tibshirani R. et al., PNAS 99:6567-6572 (2002)). Differential expression analysis was carried out by computing moderated F-statistics using limma. Test p-values were adjusted for multiple comparisons using the Benjamini-Hochberg correction and genes with adjusted p < 0.001 were deemed significantly differentially expressed in at least a core comparison (C12A-UC12A, C24A-UC24A, C12P-UC12P, or C24P-UC24P). Series supplementary files 'anova_p10-3_4core-comparisons_YableS1.txt' and 'anova_p10-3_4culturing.txt' list expression values, defined as gene-wise one-way ANOVA residuals (after batch effect removal with PAMR).

organism: Drosophila melanogaster

source_name: Prothorasic leg discs of 100h-old male Drosophila larvae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols of GeneChip® Two-Cycle CDNA Synthesis kit and GeneChip® IVT labeling kit (Affymetrix).

growth_protocol: To obtain a stage-synchronized cohorts of larvae, embryos were collected in one hour and incubated for exactly 100 hours at 25˚C. Cut or uncut discs were cultured in female adult fly abdomens for exactly 12 or 24 hours at 25˚C.

extract_protocol: RNA of regenerating cells or control cells were extracted using PicoPureTM RNA Isolation Kit (ARCTRUS/Life Technologies).

treatment_protocol: To minimize the time variance among each sample preparation, disc fragmentation and transplantation were performed within one hour.

tag: genotype

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

tag: gender

value: male

tag: developmental stage

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 0h-cultured

tag: region

value: anterior 1/4


title: Uncut, 0h-cultured, P3/4, biological rep2

description: The correspondng region to P3/4 samples were isolated from prothorasic leg discs of 100h-old male Drosophila larvae.

value: posterior 3/4


title: 74_3_niCD

city: Copenhagen

first: Aashiq

middle: H.

last: Mirza

state: Herlev

address: Herlev Ringvej 75

department: University of Copenhagen, Herlev Hospital

country: Denmark

institute: Center for non-coding RNA in Technology and Health

description: Agilent Design ID (AMADID): 047718

hyb_protocol: The labeled cRNA was hybridized to the Agilent Custom 8x60K format lncRNA expression microarray (AMADID 047718, based on Gencodev15 catalog of human long noncoding RNAs, probe length = 60 nt) according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 μm resolution. Intensity data was extracted using the Feature Extraction software (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software  (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Intestinal biospies

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit v6.5 (Agilent 5190-2305) following manufacturer instructions

growth_protocol: In total 96 colonic biopsy samples were collected from 45 subjects and stored in RNAlater solution (QIAGEN) until RNA extraction.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions. RNA quility was assessed by analysis of rRNA band integrity on an Agilent 2100 Bioanalyzer RNA 6000 LabChip kit (Agilent Technologies).

tag: patient number

value: Patient 74

tag: biopsy location

value: Colon transversum

tag: diagnosis

value: niCD

tag: Sex

value: F

tag: age


title: B11_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient B11

value: Rectum

value: iUC

value: M


title: 74_6_iCD

description: Agilent Design ID (AMADID): 047718

value: iCD


title: B57_Control

description: Agilent Design ID (AMADID): 047718

value: Control B57

value: Control


title: 74_5_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon sigmoideum


title: G3_G1_Control

description: Agilent Design ID (AMADID): 047718

value: Control G3

value: Bulbus duodenum


title: Uncut, 0h-cultured, P3/4, biological rep1

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 0h-cultured


title: Uncut, 0h-cultured, P3/4, biological rep3

value: posterior 3/4


title: 74_4_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 74

value: Colon desendens

value: F


title: ArrayM3

value: Wild type WIK

value: 72 hours post fertilization


title: Uncut, 0h-cultured, A1/4, biological rep2

value: anterior 1/4


title: 73_3_Control

description: Agilent Design ID (AMADID): 047718

value: Control 73

value: M


title: Pax5_het014

description:
Pax5 het014
ENU

tag: sample type

value: stage-matched bone marrow

value: Pax5+/- primary tumor sample


title: 74_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum

value: niCD


title: genomic DNA from 4b treated HD fibroblasts 1

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing: GenomeStudio software v2011.1. For 450K data, β values for each probe were range-scaled with data collected from DNA controls that were fully methylated [DNA methyltransferase-treated (New England Biolabs), bisulfite-converted DNA], unmethylated (untreated gDNA), and half-methylated (50:50 mix of methylated and unmethylated controls). For HD vs. normal comparisons, we used a multiple hypothesis corrected P value of 0.001 and a difference in methylation cutoff of beta change of >|0.2|. Due to the lower number of methylation changes induced by HDACi 4b treatment, a statistical cutoff of P < 0.1 and a beta change of |0.2| were used. The unmethylated and methylated signal intensities are available on the series level and in the .idat files.

label: Cy5 and Cy3

source_name: HD fibroblasts treated

label_protocol: Standard Illumina Protocol

growth_protocol: HD patient and control fibroblast cells were purchased from the Coriell Institute. HD and control fibroblast cells were cultured to 80% confluence in DMEM with 10% (wt/vol) FBS and 1% antibiotic penicillin-streptomycin according to the instructions of the supplier. Cells were plated in 12-well plates, treated with HDACi 4b at 500 nM for 48 h, and then harvested to extract genomic DNA (gDNA) using a QIAamp DNA Mini Kit (Qiagen) for methyl-array analysis.

extract_protocol: Extracted genomic DNA (gDNA) using a QIAamp DNA Mini Kit (Qiagen) for methyl.

treatment_protocol: Cells were plated in 12-well plates, treated with HDACi 4b at 500 nM for 48 h, and then harvested.

value: female

tag: cell type

value: fibroblasts

tag: disease state

value: Huntington's disease

tag: cell line


title: genomic DNA from 4b treated HD fibroblasts 2


title: genomic DNA from 4b treated HD fibroblasts 3


title: 60_G1_Control

description: Agilent Design ID (AMADID): 047718

value: Control 60

value: Bulbus duodenum

value: Control


title: ArrayG3


title: 73_4_Control

description: Agilent Design ID (AMADID): 047718

value: Rectum


title: 59_4_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 59

value: Colon transversum

value: iCD


title: 59_6_niCD

description: Agilent Design ID (AMADID): 047718

value: Colon sigmoideum


title: genomic DNA from 4b treated normal fibroblasts 3

source_name: normal fibroblasts 4b treated

value: normal


title: Uncut, 24h-cultured, P3/4, biological rep2

description: Prothorasic leg discs of 100h-old male Drosophila larvae were 24h-cultured, and the correspondng region to P3/4 samples were isolated.

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 24h-cultured

value: posterior 3/4


title: 58_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 58

value: iUC

value: F


title: genomic DNA from untreated HD fibroblasts 2

source_name: HD fibroblasts

value: female

value: fibroblasts

value: Huntington's disease


title: 59_7_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 59

value: Rectum

value: niCD

value: M


title: Uncut, 24h-cultured, P3/4, biological rep3


title: ArrayI3

value: Wild type WIK

value: 72 hours post fertilization


title: 59_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum


title: genomic DNA from untreated HD fibroblasts 3


title: genomic DNA from 4b treated normal fibroblasts 1

value: normal


title: ArrayB3


title: genomic DNA from untreated normal fibroblasts 1

source_name: normal fibroblasts


title: ArrayC3


title: ArrayA3


title: 57_4_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 57

value: niUC


title: 54_2_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 54

value: Colon sigmoideum


title: ArrayM4

data_processing:
Statistical analyses of raw microarray data were performed using the R package Limma as described by Vergauwen et al. (2010). Both knockdown conditions were contrasted against SCMO. Spots for which the criterion FG < BG + 2SD (FG: foreground, BG: background, SD: standard deviation of the local background of the entire array) was true for all arrays in the dataset, were excluded from analysis. Background correction was carried out using a normal-exponential convolution model. Within-array adjustment was done by Loess normalization, which performs an intensity-dependent normalization of the ratio of red and green. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential transcription using an empirical Bayes method. The contrasts summarized across all replicates are available on the series record in the file: genes.all.contrasts_abdomen.txt.
Contrasts were fitted to the linear models and cut off at FDR < 0.05 (false discovery rate, multiple testing correction using the Benjamini-Hochberg procedure) and |log2FC| > 0.585 (log2 fold change, corresponding to a fold induction of at least 1.5 or -1.5).

source_name: Larval abdomen, 20 pool, SCMO

treatment_protocol: Zebrafish abdomen from 20 larvae per replicate were pooled, snap frozen in dry ice and stored at -80C. Samples were homogenized in Qiazol using mortar and plastic pestle

source_name: Larval abdomen, 20 pool, D3MO


title: Uncut, 24h-cultured, P3/4, biological rep1

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 24h-cultured

value: posterior 3/4


title: 52_5_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 52

value: iCD


title: Uncut, 12h-cultured, P3/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were 12h-cultured, and the correspondng region to P3/4 samples were isolated.

value: Uncut, 12h-cultured


title: Uncut, 12h-cultured, P3/4, biological rep1


title: Uncut, 24h-cultured, A1/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were 24h-cultured, and the correspondng region to A1/4 samples were isolated.

value: anterior 1/4


title: ArrayN4

value: Wild type WIK

value: 72 hours post fertilization

source_name: Larval abdomen, 20 pool, D1D2MO


title: Uncut, 12h-cultured, P3/4, biological rep2


title: 53_3_Control

description: Agilent Design ID (AMADID): 047718

value: Control 53

value: Colon transversum

value: Control

value: F


title: genomic DNA from untreated normal fibroblasts 2

value: female

value: fibroblasts

value: normal


title: 53_1_Control

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum


title: 50_3_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 50

value: Rectum

value: niCD

value: M


title: genomic DNA from 4b treated normal fibroblasts 2


title: genomic DNA from untreated HD fibroblasts 1

value: Huntington's disease


title: genomic DNA from untreated normal fibroblasts 3


title: ArrayL4


title: ArrayK4


title: ArrayJ4


title: 50_2_niCD

description: Agilent Design ID (AMADID): 047718


title: ArrayI4


title: ArrayH4


title: 49_1_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 49

value: Colon sigmoideum

value: niUC


title: Uncut, 24h-cultured, A1/4, biological rep1

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 24h-cultured

value: anterior 1/4


title: 47_3_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 47 (technical replicate 1, Sample 47_3_iUC)

value: iUC


title: 48_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 48

value: F


title: 45_6_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 45

value: Rectum


title: 47_3_iUC 2

description: Agilent Design ID (AMADID): 047718

value: Patient 47 (technical replicate 2, Sample 47_3_iUC)

value: M


title: Uncut, 12h-cultured, A1/4, biological rep1

description: Prothorasic leg discs of 100h-old male Drosophila larvae were 12h-cultured, and the correspondng region to A1/4 samples were isolated.

value: Uncut, 12h-cultured


title: ArrayG4

value: Wild type WIK

value: 72 hours post fertilization


title: 44_1_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 44

value: Colon sigmoideum

value: niUC


title: ArrayJ3


title: Uncut, 24h-cultured, A1/4, biological rep2

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc


title: 44_2_iUC

description: Agilent Design ID (AMADID): 047718

value: iUC


title: 42_1_Control

description: Agilent Design ID (AMADID): 047718

value: Control 42

value: Terminal Ileum

value: Control


title: Uncut, 12h-cultured, A1/4, biological rep2

value: anterior 1/4


title: 40_3_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 40

value: Colon transversum

value: niCD


title: 50_1_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 50

value: iCD

value: M


title: Cut, 24h-cultured, P3/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were cut to P3/4 fragments and 24h-cultured, and the GFP-positive region (regenerating cells) were isolated.

value: Cut, 24h-cultured

value: posterior 3/4


title: 40_1_niCD

description: Agilent Design ID (AMADID): 047718


title: 40_6_niCD

description: Agilent Design ID (AMADID): 047718

value: Rectum


title: ArrayH3

value: Wild type WIK

value: 72 hours post fertilization


title: Uncut, 12h-cultured, A1/4, biological rep3

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Uncut, 12h-cultured


title: ArrayF4


title: Uncut, 0h-cultured, A1/4, biological rep1

value: Uncut, 0h-cultured

value: anterior 1/4


title: 59_5_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 59

value: Colon desendens


title: 36_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 36

value: iUC

value: F


title: ArrayE4


title: 39_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 39

value: Colon sigmoideum


title: Cut, 24h-cultured, P3/4, biological rep2

value: Cut, 24h-cultured

value: posterior 3/4


title: 42_3_Control

description: Agilent Design ID (AMADID): 047718

value: Control 42

value: Colon transversum

value: Control


title: ArrayD4

value: Wild type WIK

value: 72 hours post fertilization


title: ArrayC4


title: Cut, 24h-cultured, P3/4, biological rep1

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc


title: ArrayB4


title: ArrayA4


title: 36_1_niUC

description: Agilent Design ID (AMADID): 047718

value: Rectum

value: niUC


title: Cut, 12h-cultured, P3/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were cut to P3/4 fragments and 12h-cultured, and the GFP-positive region (regenerating cells) were isolated.

value: Cut, 12h-cultured


title: 29_2_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 29

value: Colon desendens

value: iCD

value: F


title: 30_3_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 30

value: iUC

value: M


title: ArrayO2.1

data_processing:
Statistical analyses of raw microarray data were performed using the R package Limma as described by Vergauwen et al. (2010). Both knockdown conditions were contrasted against SCMO. Spots for which the criterion FG < BG + 2SD (FG: foreground, BG: background, SD: standard deviation of the local background of the entire array) was true for all arrays in the dataset, were excluded from analysis. Background correction was carried out using a normal-exponential convolution model . Within-array adjustment was done by Loess normalization, which performs an intensity-dependent normalization of the ratio of red and green. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential transcription using an empirical Bayes method. The contrasts summarized across all replicates are available on the series record in the file: genes.all.contrasts_head.txt.
Contrasts were fitted to the linear models and cut off at FDR < 0.05 (false discovery rate, multiple testing correction using the Benjamini-Hochberg procedure) and |log2FC| > 0.585 (log2 fold change, corresponding to a fold induction of at least 1.5 or -1.5).

source_name: Larval head, 20 pool, D3MO

treatment_protocol: Zebrafish head from 20 larvae per replicate were pooled, snap frozen in dry ice and stored at -80C. Samples were homogenized in Qiazol using mortar and plastic pestle

source_name: Larval head, 20 pool, SCMO


title: 28_3_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 28 (technical replicate 1, Sample 28_3_iUC)


title: 31_1_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 31

value: Colon sigmoideum


title: ArrayP2.1

value: Wild type WIK

value: 72 hours post fertilization

source_name: Larval head, 20 pool, D1D2MO


title: 27_2_iUC 2

description: Agilent Design ID (AMADID): 047718

value: Patient 27 (technical replicate 2, Sample 27_2_iUC)


title: 35_6_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 35


title: Cut, 12h-cultured, P3/4, biological rep2

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: posterior 3/4


title: 29_3_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 29

value: iCD


title: 28_3_iUC 3

description: Agilent Design ID (AMADID): 047718

value: Patient 28 (technical replicate 2, Sample 28_3_iUC)

value: Rectum

value: F


title: 29_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Colon transversum

value: niCD


title: 38_2_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 38

value: Terminal Ileum


title: Cut, 24h-cultured, A1/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were cut to A1/4 fragments and 24h-cultured, and the GFP-positive region (regenerating cells) were isolated.

value: Cut, 24h-cultured

value: anterior 1/4


title: Cut, 24h-cultured, A1/4, biological rep2


title: ArrayN2.1

value: Wild type WIK

value: 72 hours post fertilization


title: 27_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 27 (technical replicate 1, Sample 27_2_iUC)

value: Colon sigmoideum

value: iUC


title: 31_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 31


title: Cut, 12h-cultured, A1/4, biological rep3

description: Prothorasic leg discs of 100h-old male Drosophila larvae were cut to A1/4 fragments and 12h-cultured, and the GFP-positive region (regenerating cells) were isolated.

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Cut, 12h-cultured


title: 25_3_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 25

value: Colon transversum

value: F


title: Cut, 24h-cultured, A1/4, biological rep1


title: 25_1_iCD

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum

value: iCD


title: 27_1_niUC

description: Agilent Design ID (AMADID): 047718

value: Patient 27

value: niUC


title: Cut, 12h-cultured, A1/4, biological rep2

value: anterior 1/4


title: ArrayM2.1

value: Wild type WIK

value: 72 hours post fertilization


title: Cut, 12h-cultured, P3/4, biological rep1

value: posterior 3/4


title: ArrayK2.1


title: ArrayL2.1


title: 22_4_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 22

value: M


title: 25_2_niCD

description: Agilent Design ID (AMADID): 047718

value: niCD


title: 22_6_niCD

description: Agilent Design ID (AMADID): 047718

value: Colon sigmoideum


title: 22_5_niCD

description: Agilent Design ID (AMADID): 047718

value: Colon desendens


title: Cut, 12h-cultured, A1/4, biological rep1

value: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp

value: male

value: 100h after embryo laying

value: Prothoracic leg imaginal disc

value: Cut, 12h-cultured


title: ArrayI2.1


title: 22_7_niCD

description: Agilent Design ID (AMADID): 047718

value: Rectum


title: ArrayH2.1


title: ArrayG2.1


title: 21_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 21 (technical replicate 1, Sample 21_2_iUC)

value: iUC


title: ArrayJ2.1


title: 18_3_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 18 (technical replicate 1, Sample 18_3_iUC)

value: F


title: 21_2_iUC 2

description: Agilent Design ID (AMADID): 047718

value: Patient 21 (technical replicate 2,  Sample 21_2_iUC)


title: ArrayF2.1

value: Wild type WIK

value: 72 hours post fertilization


title: insulin resistane high risk sample 23

city: Los Angeles

first: yong

last: zhang

address: 650 Charles E. Young Drive South

department: school of dentistry

institute: UCLA

description: Pre-diabetes, IR high risk

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

source_name: saliva supernatant

label_protocol: standard Affymetrix protocol

growth_protocol: Participants enrolled in this study were recruited in the overnight fasted state, then the collection and processing of glucose (fasting, 30, 60 and 120 minutes) and insulin from blood samples, hemoglobin A1c (HbA1c) , assessment of medical history, socio-demographic characteristics, lifestyle factors, blood pressure and anthropometric and body composition measurements were conducted. During baseline visit, participants were asked to refrain from eating, drinking and oral hygiene procedures for at least 1-hour prior to saliva collection.

extract_protocol: Total RNA was extracted from salia supernatant by using Qiagen RNeasy Mini kit

treatment_protocol: Based on the homeostasis model assessment of insulin resistance (HOMA-IR), using the formula [HOMA-IR= (fasting glucose*fasting insulin)/405], participants were divided into 2 groups: IR high risk group (HOMA-IR value ≥2.5) and IR low risk group (HOMA-IR value <2.5)

tag: risk

value: insulin risistance high risk

value: Pre-diabetes, IR high risk

value: saliva supernatant


title: 22_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 22

value: Terminal Ileum

value: niCD

value: M


title: 19_2_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 19

value: iCD


title: 18_3_iUC 2

description: Agilent Design ID (AMADID): 047718

value: Patient 18 (technical replicate 2, Sample 18_3_iUC)

value: Colon sigmoideum


title: insulin resistane low risk sample 15

description: Health, IR low risk

value: insulin resistance low risk

value: Health, IR low risk


title: 19_4_niCD

description: Agilent Design ID (AMADID): 047718

value: Colon desendens


title: 15_7_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 15

value: Rectum

value: F


title: insulin resistane high risk sample 20

description: Health, IR high risk

value: insulin risistance high risk

value: Health, IR high risk


title: insulin resistane high risk sample 21

description: Pre-diabetes, IR high risk

value: Pre-diabetes, IR high risk

value: saliva supernatant


title: insulin resistane high risk sample 22

description: Pre-diabetes, IR high risk


title: 16_2_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 16 (technical replicate 1, Sample 16_2_iUC)

value: iUC


title: 17_3_iUC

description: Agilent Design ID (AMADID): 047718

value: Patient 17


title: ArrayE2.1

value: Wild type WIK

value: 72 hours post fertilization


title: 16_2_iUC 2

description: Agilent Design ID (AMADID): 047718

value: Patient 16 (technical replicate 2, Sample 16_2_iUC)


title: insulin resistane low risk sample 14

description: Health, IR low risk


title: ArrayD2.1


title: 15_6_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon sigmoideum

value: iCD


title: 15_4_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon transversum


title: ArrayC2.1


title: insulin resistane high risk sample 19

description: Pre-diabetes, IR high risk


title: 11_5_Control

description: Agilent Design ID (AMADID): 047718

value: Control 11

value: Control


title: 15_5_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 15

value: Colon desendens


title: 15_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum

value: niCD

value: F


title: insulin resistane high risk sample18

description: Health, IR high risk

value: insulin risistance high risk

value: Health, IR high risk

value: saliva supernatant


title: insulin resistane low risk sample 13

description: Pre-diabetes, IR low risk

value: insulin resistance low risk

value: Pre-diabetes, IR low risk


title: ArrayA2.1

value: Wild type WIK

value: 72 hours post fertilization


title: 11_4_Control

description: Agilent Design ID (AMADID): 047718


title: ArrayB2.1


title: A549_miR-128 Rep_2

first: junchao

last: Cai

address: zhongshan er road

institute: Sun-yat sen university

description: A549 with miR-128 precursor stably transduced replicate 2.

hyb_protocol: Hybridization was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

scan_protocol: Scanning was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation were performed in GeneSpring GX 11 (Agilent) in Shanghai Biochip Corporation.

label_protocol: Labeling was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

growth_protocol: The A549 non-small cell lung cancer (NSCLC) cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: pMSCV-miR-128 or empty vector was co-transfected with the pIK packaging plasmid in 293FT cells by using standard calcium phosphate transfection method. Thirty-six hours after the co-transfection, supernatants were collected and incubated with cells to be infected for 24 hours in the presence of polybrene (2.5 μg/mL). Following infection, puromycin (1.5μg/mL) was used to select stably transduced cells for 10 days.

tag: stable transduction

value: miR-128 precursor

value: highly aggressive NSCLC cell line


title: A549_miR-128 Rep_1

description: A549 with miR-128 precursor stably transduced replicate 1.


title: A549_Vector Rep_1

description: A549 with retroviral vector stably transduced replicate 1.

value: retroviral vector

value: non-small cell lung cancer (NSCLC) cell line


title: 9_7_Control

description: Agilent Design ID (AMADID): 047718

value: Control 9

value: Rectum

value: Control


title: 10_5_Control

description: Agilent Design ID (AMADID): 047718

value: Control 10

value: Colon sigmoideum


title: Shoot, EDTA, pH 8.0, rep1

city: Mishima, Osaka

first: Jun

last: Murata

address: 1-1-1 Wakayamadai, Shimamoto

department: Bioorganic Research Institute

country: Japan

institute: Suntory Foundation for Life Sciences

description: Gene expression in EDTA-treated plant shoot at pH 8.0.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was used to hybridize Agilent-015241 Rice Gene Expression 4x44K Microarray slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacturer's instructions.

data_processing: Feature Extraction Software 9.1 (Agilent) was used to analyze scanned images using default parameters.

organism: Oryza sativa

source_name: rice shoot, 30 µM of EDTA, pH 8.0

label_protocol: Cy3-labeled cRNA was prepared from 0.5 ug RNA using One-Color Low RNA Input Linear Amplification PLUS kit (Agilent, CA), and purified using RNeasy column purification (QIAGEN). NanoDrop ND-1000 Spectrophotometer was used to monitor dye incorporation and cRNA yield.

extract_protocol: RNeasy Plant Mini Kit (Qiagen) was used for RNA extraction. The RNA samples were subjected to on-column DNase I digestion according to the manufacturer's instruction. RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific, DE). The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

treatment_protocol: Rice seedlings were treated with DMA or EDTA at pH 5.8 or 8.0. The control experiment was no chelator.

tag: tissue

value: shoot

value: EDTA

tag: ph


title: 10_6_Control

description: Agilent Design ID (AMADID): 047718

value: F


title: insulin resistane high risk sample16

description: Pre-diabetes, IR high risk

value: insulin risistance high risk

value: Pre-diabetes, IR high risk

value: saliva supernatant


title: 7_4_iCD

description: Agilent Design ID (AMADID): 047718

value: Patient 7

value: iCD


title: Shoot, DMA, pH 8.0, rep1

description: Gene expression in DMA-treated plant shoot at pH 8.0.

source_name: rice shoot, 30 µM of DMA, pH 8.0

tag: treatment

value: DMA


title: insulin resistane high risk sample17

description: Pre-diabetes, IR high risk


title: insulin resistane high risk sample14

description: Pre-diabetes, IR high risk


title: 7_3_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon transversum


title: insulin resistane low risk sample 12

description: Health, IR low risk

value: insulin resistance low risk

value: Health, IR low risk


title: insulin resistane high risk sample15

description: Health, IR high risk

value: Health, IR high risk


title: A549_Vector Rep_2

description: A549 with retroviral vector stably transduced replicate 2.

value: retroviral vector

value: non-small cell lung cancer (NSCLC) cell line


title: 7_1_niCD

description: Agilent Design ID (AMADID): 047718

value: Terminal Ileum

value: niCD


title: GF WT

city: Tsukuba

first: Chigusa

last: Nakahashi-Oda

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

hyb_protocol: Cy3 labeled cDNA was hybridized to SurePrint G3 Mouse GE 8X60K microarray (Agilent) by Gene Expression Hybridization Kit (Agilent). After hybridization, microarrays were washed with Gene Expression Wash Buffers Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8X66k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software  (Agilent) using Cookie Cutter Method to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Colonic lamina propria dendritic cells of BL6/J mice raised under GF conditions.

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared using the SureTag Complete DNA labeling kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the Isogen (Wako). RNA was quantified using a NanoDrop (Thermo Scientific) spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). Single strand cDNA was amplified by Ovation Pico WTA System V2 (NuGEN) and Ribo-SPIA amplification (Genomic DNA Enzymatic Labeling Kit).

treatment_protocol: Freshly isolated colonic DCs by flow cytometry from colonic laminapropria cells of WT and CD300a deficient mice.

tag: strain

tag: gender

value: male

tag: genotype/variation

value: WT

tag: growth condition

value: GF

value: colon

value: lamina propria DC


title: GF KO

source_name: Colonic lamina propria dendritic cells of CD300a deficient BL6/J mice raised under GF conditions.

value: CD300a deficient


title: Shoot, DMA, pH 5.8, rep1

description: Gene expression in DMA-treated plant shoot at pH 5.8.

source_name: rice shoot, 30 µM of DMA, pH 5.8

value: shoot


title: Shoot, EDTA, pH 5.8, rep1

description: Gene expression in EDTA-treated plant shoot at pH 5.8.

source_name: rice shoot, 30 µM of EDTA, pH 5.8

value: EDTA


title: insulin resistane low risk sample 11

description: Health, IR low risk

value: saliva supernatant


title: naïve KO

source_name: Colonic lamina propria dendritic cells of CD300a deficient BL6/J mice raised under SPF conditions.

value: female

value: SPF


title: naïve WT

source_name: Colonic lamina propria dendritic cells of BL6/J mice raised under SPF conditions.


title: Descending aorta from fibulin-4 knockout pup, biological replicate 2

city: Saint Louis

first: Jessica

last: Wagenseil

state: MO

address: 1 Brookings Dr.  Box 1185

department: Mechanical Engineering and Materials Sciences

institute: Washington University

description:
Gene expression data from descending aortic tissue from p0 pups
KODA2

hyb_protocol: 5ng of cDNA were fragmented and hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 2.0 ST Array.  Affymetrix Gene 2.0 microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip 7G 3000 scanner.

data_processing: The gene array data was analyzed with the Affymetrix GeneChip Command Console and raw .CEL files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.

source_name: Mouse lacking fibulin-4 gene p0, section of aorta from vena cava to diaphragm

label_protocol: Targets were labeled using Nugen Encore Biotin kit according to the standard NuGenOvationPico WTA System Amplification from 5ng of total RNA

extract_protocol: Total RNA was extracted according to manufacturer kit (Qiagen)

treatment_protocol: p0 pups were sacrificed and the tissues dissected and snap frozen. Mice were genotyped and like-gentoypes and like-tissue sections were pooled in groups of eight.

value: descending aorta

tag: genotype

value: fibulin-4 knockout


title: Shoot, control, pH 8.0, rep1

description: Gene expression in control plant shoot for pH 8.0.

source_name: rice shoot, control, pH 8.0

value: control