title: 13281474 - ca1-2 vs wt2

hyb_protocol: wt2 Cy5 / ca1-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia

tag: genotype/variation


title: 6C-secondary-day15-adherent

status: Public on Mar 25 2012

type: RNA

city: Toronto

first: David

last: Fluri

address: 160 College Street

country: Canada

institute: University of Toronto

hyb_protocol: Samples were hybridized and washed using FS450_0007 protocol

scan_protocol: Affimetrix GeneChip Scanner 3000

data_processing: Data was processed using Affimetrix Expression Console (RMA normalization)

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Ambion Wt Kit

growth_protocol: cells were reprogrammed in standard cell culture conditions

extract_protocol: total RNA was extracted using the QIAGEN RNAeasy extraction kit according to the manufacturer's protocol

treatment_protocol: cells were treated with doxycycline at day 0 to induce reprogramming

tag: strain background

value: mixed (mainly R1 and ICR)

tag: tissue

value: secondary mouse embryonic fibroblasts

tag: cell type

value: adherent cells


title: 6C-secondary-day25-adherent


title: 6C-secondary-day2-adherent


title: 6C-secondary-day0


title: 6C-secondary-day6-adherent


title: 6C-secondary-day2-suspension

value: suspension cells


title: ESRD-RCC case 29

status: Public on Mar 24 2012

type: genomic

city: Yufu-City, Oita

first: Toru

last: Inoue

address: Hasama-machi 1-1

department: Department of Molecular Pathology

country: Japan

institute: Faculty of medicineOita University

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

molecule: genomic DNA

organism: Homo sapiens

source_name: ESRD-RCC : FFPE sample

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

tag: gender

value: Male

value: tumor

tag: disease state

value: ESRD-RCC

tag: individual

source_name: control : FFPE sample

tag: sample type

value: 12 mixed normal control

tag: sample source

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 30


title: ESRD-RCC case 32 cle-pap

tag: disease subtype

value: cle-pap


title: ESRD-RCC case 31


title: ESRD-RCC case 28


title: 1936-MEL - repeat 1 - mAdbID:104979

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 104979

hyb_protocol: Sample Hybridization Protocol Other: Combine Cy3 and Cy5 labeled target (adjust the color to purple), add 1/10 volume of 10 X fragmentation buffer (Ambion # 8740) and incubate for 15 min at 70 C. Add 3 ul of stop solution (Ambion # 8730) and complete dry the sample by speed vacuum. Add 19 ul of the following mixture to the dried target: 15 ul Kreatech hybridization buffer (Kraetech Diagnostics), 2 ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 2 ul yeast tRNA (4mg/ml Sigma Cat# R8759). Incubate for 3 min at 99 C and subsequently add 44.5 ul of the following mixture: 12.5 ul 20X SSC, 2ul 10% SDS, 30 ul formamide. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 42C for 20 hrs.

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 10, and spot size less than 10um; 2. genes were filtered out if >80% of experiment with missing data values; 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were processed by averaging results in replicate experiments for the same genes.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-NonAT_95_Feb07 (Read Only)

label_protocol:
Cy5 Sample Labeling Protocol
Other: Sample aRNA were labelled using ULS aRNA Fluorescent Labeling kit (Kreatech) with Cy5.

extract_protocol:
RNA extraction with miRNeasy kit
Other: Total RNA (T-RNA) from melanoma cells was isolated using the miRNeasy Mini kit (Qiagen). RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: skin

tag: cell line

value: melanoma cells

value: melanoma

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Reference Labeling Protocol
Other: Reference aRNA were labelled using ULS aRNA Fluorescent Labeling kit (Kreatech) with Cy3.

value: blood

value: PBMC


title: U251 - mAdbID:104976

description: mAdb experiment ID: 104976

value: CNS

value: central nervous sistem (CNS) cells

value: brain cancer


title: ESRD-RCC case 32 ACD-RCC

value: ACD-RCC


title: SF-539 - repeat 1 - mAdbID:104977

description: mAdb experiment ID: 104977


title: SNB 75 - mAdbID:104973

description: mAdb experiment ID: 104973

source_name: SNB 75

value: SNB 75


title: ESRD-RCC case 27

value: Male


title: ESRD-RCC case 21

value: tumor


title: ESRD-RCC case 24

value: ESRD-RCC


title: T-47D - mAdbID:104975

description: mAdb experiment ID: 104975

value: hematopoietic cells

value: hematopoietic cancer


title: ESRD-RCC case 23

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: SNB 19 - repeat 2 - mAdbID:104972

description: mAdb experiment ID: 104972

source_name: SNB 19

value: SNB 19


title: SK-OV-3 - mAdbID:104971

description: mAdb experiment ID: 104971

value: colon

value: colon cells

value: colon cancer


title: ESRD-RCC case 25


title: ESRD-RCC case 26 ACD-RCC


title: ESRD-RCC case 20


title: ESRD-RCC case 22


title: SF-298 - mAdbID:104969

description: mAdb experiment ID: 104969

value: CNS

value: blood

value: PBMC


title: Siha - repeat 2 - mAdbID:104970

description: mAdb experiment ID: 104970

source_name: Siha

value: cervix

value: Siha

value: cervical cells

value: cervical cancer


title: ESRD-RCC case 17

value: Male

value: tumor

value: ESRD-RCC


title: SR - mAdbID:104974

description: mAdb experiment ID: 104974

source_name: SR

value: SR

value: hematopoietic cells

value: hematopoietic cancer


title: ESRD-RCC case 18

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 16


title: ESRD-RCC case 19


title: ESRD-RCC case 15


title: SF-295 - mAdbID:104968

description: mAdb experiment ID: 104968

value: central nervous sistem (CNS) cells

value: brain cancer


title: RPMI 8226 - mAdbID:104967

description: mAdb experiment ID: 104967

source_name: RPMI 8226

value: blood

value: RPMI 8226


title: ESRD-RCC case 13 cle-pap pre2

value: Female


title: ESRD-RCC case 13 PRCC

value: PRCC


title: Panc 1 - mAdbID:104964

description: mAdb experiment ID: 104964

source_name: Panc 1

value: pancreas

value: Panc 1

value: pancreatic cells

value: pancreatic cancer

value: PBMC


title: PC3 p35 - mAdbID:104965

description: mAdb experiment ID: 104965

source_name: PC 3 p7

value: prostate

value: PC 3

value: prostatic cells

value: prostatic cancer


title: OVCAR 3 p7 - mAdbID:104962

description: mAdb experiment ID: 104962

source_name: OVCAR 3 p42

value: colon

value: OVCAR 3

value: colon cells

value: colon cancer


title: OVCAR 3 p42 - mAdbID:104961

description: mAdb experiment ID: 104961

source_name: OVCAR 3 p7

value: blood


title: OVCAR 4 - mAdbID:104963

description: mAdb experiment ID: 104963

source_name: OVCAR 4

value: ovaries

value: OVCAR 4

value: ovarian cells

value: ovarian cancer


title: PC3 p7 - mAdbID:104966

description: mAdb experiment ID: 104966


title: NCI-ADR-RES - mAdbID:104960

description: mAdb experiment ID: 104960

source_name: NCI-ADR-RES

value: NCI-ADR-RES


title: ESRD-RCC case 13 ACD-RCC

value: Male

value: tumor

value: ESRD-RCC

value: ACD-RCC

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 12


title: ESRD-RCC case 11  cle-pap

value: cle-pap


title: MDA-MB-435 - mAdbID:104957

description: mAdb experiment ID: 104957

value: breast

value: breast cells

value: breast cancer

value: PBMC


title: ESRD-RCC case 11  CCRCC

value: CCRCC


title: MOLT-4 - mAdbID:104959

description: mAdb experiment ID: 104959

value: blood

value: hematopoietic cells

value: hematopoietic cancer


title: ESRD-RCC case 10


title: MIA PACA2 - mAdbID:104958

description: mAdb experiment ID: 104958

source_name: MIA PACA 2

value: pancreas

value: MIA PACA 2

value: pancreatic cells

value: pancreatic cancer


title: ESRD-RCC case 7 cle-pap

value: Male

value: tumor

value: ESRD-RCC


title: MDA-MB-231 p6 - mAdbID:104955

description: mAdb experiment ID: 104955

source_name: MDA-MB-231 p6


title: K-562 - mAdbID:104953

description: mAdb experiment ID: 104953


title: ESRD-RCC case 5 PRCC

value: Female

value: PRCC

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 8 tubulocystic

value: tubulocystic


title: ESRD-RCC case 7 ACD-RCC

value: ACD-RCC


title: MDA-MB-231 p41 - mAdbID:104956

description: mAdb experiment ID: 104956

value: breast

value: breast cells

value: breast cancer

value: blood

value: PBMC


title: ESRD-RCC case 8 cle-pap

value: cle-pap


title: ESRD-RCC case 8 PRCC


title: ESRD-RCC case 9


title: MCF 7 - mAdbID:104954

description: mAdb experiment ID: 104954

source_name: MCF 7

value: MCF 7


title: ESRD-RCC case 4

source_name: ESRD-RCC : FFPE sample


title: HCC 2998 - mAdbID:104948

description: mAdb experiment ID: 104948

value: colon

value: colon cells

value: colon cancer


title: HL-60 - mAdbID:104949

description: mAdb experiment ID: 104949

value: hematopoietic cells

value: hematopoietic cancer


title: HS-578T - mAdbID:104950

description: mAdb experiment ID: 104950


title: CCRF-CEM - mAdbID:104944

description: mAdb experiment ID: 104944

source_name: CCRF-CEM

value: CCRF-CEM


title: ESRD-RCC case 3

value: Female

value: tumor

value: ESRD-RCC

source_name: control : FFPE sample

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA


title: ESRD-RCC case 2

value: Male

value: non-neoplastic tissue


title: Huh 7.5.1 - mAdbID:104951

description: mAdb experiment ID: 104951

value: liver

value: liver cells

value: hepatic cancer

source_name: Pooled Normal Donor PBMC

value: blood


title: ESRD-RCC case 64 CCRCC

value: CCRCC


title: IGROV - mAdbID:104952

description: mAdb experiment ID: 104952

source_name: IGROV

value: ovaries

value: IGROV

value: ovarian cells

value: ovarian cancer

value: PBMC


title: ESRD-RCC case 63 PRCC

value: PRCC


title: ESRD-RCC case 63 ACD-RCC

value: Female

value: tumor

value: ACD-RCC


title: ESRD-RCC case 5 tubulocystic

value: ESRD-RCC

value: tubulocystic

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA


title: ESRD-RCC case 65

value: Male

value: non-neoplastic tissue


title: Colo 205 - mAdbID:104945

description: mAdb experiment ID: 104945

source_name: Colo 205

value: colon

value: Colo 205

value: colon cells

value: colon cancer

value: blood


title: ESRD-RCC case 62


title: GI-101A - mAdbID:104947

description: mAdb experiment ID: 104947

value: breast

value: breast cells

value: breast cancer


title: ESRD-RCC case 1


title: ESRD-RCC case 64 ACD-RCC


title: SNB 19 - repeat 1 - mAdbID:104942

description: mAdb experiment ID: 104942

source_name: SNB 19

value: CNS

value: SNB 19

value: central nervous sistem (CNS) cells

value: brain cancer

value: PBMC


title: Du-145 - mAdbID:104946

description: mAdb experiment ID: 104946

value: prostate

value: prostatic cells

value: prostatic cancer


title: ESRD-RCC case 61

value: Female

value: tumor

value: ESRD-RCC

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: BT-549 - mAdbID:104943

description: mAdb experiment ID: 104943

value: breast

value: blood


title: Siha - repeat 1 - mAdbID:104941

description: mAdb experiment ID: 104941

source_name: Siha

value: cervix

value: Siha

value: cervical cells

value: cervical cancer


title: OVCAR 5 - mAdbID:104939

description: mAdb experiment ID: 104939

value: ovaries

value: OVCAR 4

value: ovarian cells

value: ovarian cancer


title: UO-31 - mAdbID:104938

description: mAdb experiment ID: 104938

value: kidney

value: renal cells

value: renal cancer

value: PBMC


title: ESRD-RCC case 60

value: Male

value: tumor

value: ESRD-RCC

value: 12 mixed normal control


title: ESRD-RCC case 57

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: OVCAR 8 - mAdbID:104940

description: mAdb experiment ID: 104940

source_name: OVCAR 8

value: OVCAR 8

value: blood


title: ESRD-RCC case 59


title: RXF 393 - mAdbID:104929

description: mAdb experiment ID: 104929


title: ESRD-RCC case 58


title: NCI-H522 - mAdbID:104927

description: mAdb experiment ID: 104927

value: lung

value: lung cells

value: lung cancer


title: SN12C - mAdbID:104933

description: mAdb experiment ID: 104933


title: ESRD-RCC case 54


title: ESRD-RCC case 55 ACD-RCC

value: Female

value: ACD-RCC


title: NCI-H1299 - mAdbID:104928

description: mAdb experiment ID: 104928


title: ESRD-RCC case 53


title: ESRD-RCC case 52 CCRCC

value: CCRCC


title: ESRD-RCC case 56 c-pRCC

value: c-pRCC


title: TK-10 - mAdbID:104935

description: mAdb experiment ID: 104935

value: kidney

value: renal cells

value: renal cancer


title: NCI-H460 - mAdbID:104926

description: mAdb experiment ID: 104926

value: PBMC


title: NCI-H322M - mAdbID:104925

description: mAdb experiment ID: 104925


title: ESRD-RCC case 56 ACD-RCC

value: Male

value: tumor

value: ESRD-RCC


title: ESRD-RCC case 55 PRCC

value: PRCC

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 56 PRCC


title: NCI-H23 - mAdbID:104923

description: mAdb experiment ID: 104923

value: lung

value: lung cells

value: blood


title: SW-620 - mAdbID:104934

description: mAdb experiment ID: 104934

value: colon

value: colon cells

value: colon cancer


title: NCI-H266 - mAdbID:104924

description: mAdb experiment ID: 104924

value: lung cancer


title: ESRD-RCC case 52 ACD-RCC

value: Female

value: ACD-RCC


title: ESRD-RCC case 49


title: ESRD-RCC case 50


title: KM-12 - mAdbID:104920

description: mAdb experiment ID: 104920

value: PBMC


title: HOP-92 - mAdbID:104917

description: mAdb experiment ID: 104917


title: HOP-62 - mAdbID:104916

description: mAdb experiment ID: 104916


title: HT-29 p155 - mAdbID:104919

description: mAdb experiment ID: 104919


title: HT-29 p9 - mAdbID:104918

description: mAdb experiment ID: 104918


title: ESRD-RCC case 48 ACD-RCC


title: HCT-116 - mAdbID:104915

description: mAdb experiment ID: 104915


title: CAKI I - mAdbID:104912

description: mAdb experiment ID: 104912

source_name: CAKI-I

value: kidney

value: CAKI I

value: renal cells

value: renal cancer


title: ESRD-RCC case 51

value: Male

value: tumor

value: ESRD-RCC

value: 12 mixed normal control


title: ESRD-RCC case 48 CCRCC

value: CCRCC

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: AL of Adult silence control replicate 6

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

country: USA

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: no data processing (providing only raw data)

organism: Taeniopygia guttata

source_name: Silence

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using RNAqueous Mini kit (Ambion) and DNase treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng total RNA was amplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Post-hatch day 20 male zebra finches that had been raised in acoustic isolation with a foster female were placed in a song playback chamber. The next day, birds heard either silence (control) or 30 minutes of novel song. Birds were then sacrificed and the AL (auditory lobule) was dissected and flash frozen.

tag: song exposure

value: Silence

tag: brain region

value: AL (auditory lobule)

tag: age

value: Adult

source_name: universal SoNG reference

value: Telencephalon

value: Male and female


title: ESRD-RCC case 47

value: Female


title: AL of Adult novel song replicate 6

source_name: Novel song

value: 30 min of Novel song


title: ESRD-RCC case 45


title: HCT-15 - mAdbID:104914

description: mAdb experiment ID: 104914

value: colon

value: colon cells

value: colon cancer

value: blood

value: PBMC


title: AL of Adult silence control replicate 5

value: Male


title: ESRD-RCC case 40 ACD-RCC

value: tumor

value: ESRD-RCC

value: ACD-RCC

value: 12 mixed normal control


title: ESRD-RCC case 39

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: ESRD-RCC case 46


title: ACHN - mAdbID:104911

description: mAdb experiment ID: 104911

source_name: ACHN

value: kidney

value: ACHN

value: renal cells

value: renal cancer


title: ESRD-RCC case 44


title: AL of Adult silence control replicate 4

value: Silence

value: AL (auditory lobule)

value: Adult

value: Telencephalon

value: Male and female


title: AL of Adult novel song replicate 5

value: 30 min of Novel song


title: ESRD-RCC case 40 c-pRCC

value: Male

value: c-pRCC


title: ESRD-RCC case 41

value: Female

value: tumor

value: ESRD-RCC


title: AL of Adult novel song replicate 3


title: AL of Adult silence control replicate 3


title: A549 p7 - mAdbID:104909

description: mAdb experiment ID: 104909

value: lung

value: lung cells

value: lung cancer

value: blood

value: PBMC


title: A549 p107 - mAdbID:104910

description: mAdb experiment ID: 104910


title: AL of Adult novel song replicate 4


title: 1858-MEL - mAdbID:104883

description: mAdb experiment ID: 104883

value: skin

value: melanoma cells

value: melanoma


title: EKVX - mAdbID:104913

description: mAdb experiment ID: 104913

source_name: EKVX

value: EKVX


title: ESRD-RCC case 42

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: 888-MEL - mAdbID:104882

description: mAdb experiment ID: 104882


title: 786-O - mAdbID:104881

description: mAdb experiment ID: 104881

value: kidney

value: renal cells

value: renal cancer


title: ESRD-RCC case 38

value: Male

value: tumor


title: ESRD-RCC case 36

value: ESRD-RCC


title: AL of Adult silence control replicate 2

value: Silence

value: AL (auditory lobule)

value: Adult

value: Telencephalon

value: Male and female


title: A498 - mAdbID:104908

description: mAdb experiment ID: 104908

value: blood

value: PBMC


title: AL of Adult novel song replicate 2

value: 30 min of Novel song


title: AL of Adult novel song replicate 1


title: AL of p20 Silence replicate 4

value: male

value: day 20 post-hatch


title: AL of p20 Novel song replicate 6

value: telencephalon

value: male and female

value: adult

value: 30 minutes of Novel song


title: AL of p20 Silence replicate 6

value: Male


title: AL of p20 Silence replicate 5


title: AL of p20 Novel song replicate 4


title: ESRD-RCC case 43

value: tumor

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: AL of p20 Silence replicate 3

value: Silence

value: AL (auditory lobule)


title: AL of Adult silence control replicate 1

value: Telencephalon

value: Male and female

value: Adult


title: AL of p20 Novel song replicate 2


title: AL of p20 Novel song replicate 3


title: ESRD-RCC case 35

value: ESRD-RCC


title: AL of p20 Silence replicate 2

value: male


title: AL of p20 Novel song replicate 1

value: day 20 post-hatch


title: AL of p20 Novel song replicate 5


title: ESRD-RCC case 37


title: ESRD-RCC case 33


title: AL of p20 Silence replicate 1


title: UACC 257 cell line - mAdbID:104937

description: mAdb experiment ID: 104937

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 10, and spot size less than 10um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-NonAT_95_Feb07 (Read Only)

source_name: UACC 257

label_protocol:
Cy5 Sample Labeling Protocol
Other: Reference and sample aRNA were labelled using ULS aRNA Fluorescent Labeling kit (Kreatech) with Cy3 and Cy5 respectively and co-hybridized to whole-genome human 36K oligo arrays, representing 25,100 unique human genes of the Operon Human Genome Array–Ready Oligo Set version 4.0, printed in house.

value: skin

value: UACC 257

value: melanoma cells

value: Melanoma

label_protocol:
Cy3 Reference Labeling Protocol
Other: Reference and sample aRNA were labelled using ULS aRNA Fluorescent Labeling kit (Kreatech) with Cy3 and Cy5 respectively and co-hybridized to whole-genome human 36K oligo arrays, representing 25,100 unique human genes of the Operon Human Genome Array–Ready Oligo Set version 4.0, printed in house.

value: Blood

value: PBMC


title: furanone-free control C2

city: Syracuse

first: Jiachuan

last: Pan

state: NY

address: 121 Link Hall

institute: Syracuse Unievrsity

description: Control

hyb_protocol: Fragmented cDNA was hybridized on the Affymetrix P aeroginosa Genome Array for 16 h at 50oC. Arrays were washed and stained in an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 fluidics protocol as specified in the Prokaryotic Target Preparation Protocol

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 7G Plus

data_processing: GeneChip Operating Software (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, genes with a p-value of less than 0.0025 or greater than 0.9975 were considered statistically significant based on Wilcoxon signed rank test and Tukey Byweight, labeled as I and D in the attached txt file. To ensure the significance of microarray data, an additional criterion was applied to only select the genes with an expression ratio of 2 or high from this group as induced and repressed genes.

organism: Pseudomonas aeruginosa PAO1

source_name: furanone-free control

label_protocol: Biotinylated cDNA was prepared from 10 ug total RNA using the Prokaryotic Target Preparation protocol in the Affymetrix Expression Analysis Technical Manual

growth_protocol: PAO1 was inoculated in 100 mL LB and grown for 18 h (200 rpm, 37oC). Persister cells were isolated by lysing the normal cells with 200 ug/mL Ciprofloxacin (3.5h, 200 rpm, 37oC), followed by centrifugation and washing with 0.85% NaCl buffer.

extract_protocol: RNeasy Mini Kit (Qiagen, Austin, TX, USA) with on-column DNase treatment (RNase-Free DNase Set, Qiagen).

treatment_protocol: The isolated persisters were incubated in 0.85% NaCl buffer for 1 h (200 rpm, 37oC) with or without 1 ug/mL BF8.

value: Persister cells

tag: treatment

value: furanone-free control


title: ESRD-RCC case 34

source_name: ESRD-RCC : FFPE sample

value: Male

value: tumor

value: 12 mixed normal control

value: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

value: non-neoplastic tissue


title: SK-MEL-5 cell line - mAdbID:104931

description: mAdb experiment ID: 104931

tag: strain


title: M14 cell line - mAdbID:104922

description: mAdb experiment ID: 104922


title: furanone-free control C3

description: Control


title: UACC 62 cell line - mAdbID:104936

description: mAdb experiment ID: 104936

source_name: UACC 62

value: UACC 62


title: SK-MEL-2 cell line - mAdbID:104930

description: mAdb experiment ID: 104930


title: furanone-free control C1

description: Control


title: SK-MEL-28 cell line - mAdbID:104932

description: mAdb experiment ID: 104932


title: LOX IMVI cell line - mAdbID:104921

description: mAdb experiment ID: 104921

source_name: LOX IMVI

value: LOX IMVI


title: 397 cell line - mAdbID:104880

description: mAdb experiment ID: 104880

source_name: Pooled Normal Donor PBMC


title: A375 cell line - mAdbID:104907

description: mAdb experiment ID: 104907


title: HS_205

status: Public on Mar 23 2012

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: pheochromocytoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: Tumor DNA was extracted from frozen tissue samples using a QIAamp DNA mini kit or an AllPrep kit (Qiagen).

tag: sample

tag: M

value: pheochromocytoma

tag: germline mutation - gene

value: VHL

tag: germline mutation - nucleotide


title: HS_101

description: pheochromocytoma

tag: F


title: HS_130

description: pheochromocytoma


title: HS_066

description: paraganglioma

value: paraganglioma


title: HS_098

description: pheochromocytoma


title: DeltaHepKlf6#2, 8 weeks HFD

city: New York

first: Weijia

last: Zhang

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: KO 2

hyb_protocol: Exon chips were hybed according to Affymetrix hybridization protocol

scan_protocol: Exon chips were  scanned using Affymetrix GeneChip Scanner 7g

data_processing: The data were analyzed with  Affymetrix Expression Console using Affymetrix default analysis settings and RMA normalization method and differentially expressed genes were identified by LIMMA program.

source_name: Liver tissue, Knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Three mice with a hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6) on high fat diet and 3 littermate controls on the same diet were sacrificed after 8 weeks of diet (Teklad TD06415, Harlan, South Easton, MA).

extract_protocol: Trizol (Invitrogen, Carlsbad, CA) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Liver tissue was preserved in RNAlater® (Ambion, Austin, TX).

tag: tissue

value: liver

tag: genotype/variation

tag: glucose metabolism

value: improved glucose tolerance

tag: liver histology

value: less steatosis


title: DeltaHepKlf6#3, 8 weeks HFD

description: KO 3

value: hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6)


title: HS_048

description: paraganglioma

tag: disease state

value: SDHD


title: HS_072

description: pheochromocytoma


title: HS_001

description: pheochromocytoma


title: HS_068

description: pheochromocytoma


title: HS_127

description: pheochromocytoma


title: HS_055

description: pheochromocytoma


title: HS_200

description: pheochromocytoma

value: SDHB


title: HS_011

description: pheochromocytoma


title: Control#1, 8 weeks HFD

description: Control 1

source_name: Liver tissue, Control

value: wild type

value: glucose intolerance

value: marked steatosis


title: Control#3, 8 weeks HFD

description: Control 3


title: HS_158

description: paraganglioma


title: HS_100

description: pheochromocytoma


title: HS_053

description: pheochromocytoma


title: HS_131

description: pheochromocytoma


title: HS_123

description: pheochromocytoma


title: DeltaHepKlf6#1, 8 weeks HFD

description: KO 1


title: HS_062

description: pheochromocytoma


title: HS_086

description: pheochromocytoma

value: NF1 (Clinical diagnosis)

value: ND (not determined)


title: HS_017

description: pheochromocytoma


title: HS_160

description: pheochromocytoma


title: HS_093

description: pheochromocytoma


title: HS_115

description: pheochromocytoma


title: HS_092

description: pheochromocytoma


title: HS_041

description: pheochromocytoma


title: HS_107

description: pheochromocytoma


title: HS_080

description: pheochromocytoma


title: HS_036

description: pheochromocytoma


title: DU, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 1

city: Northbrook

first: Michael

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Human Whole Genome Microarrays in hybridization buffer. Arrays were hybridized at 37° C for 18 hrs. in a shaking incubator, washed at 46° C for 1 hr, and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Arrays were rinsed and dried: 60 samples were scanned on an Axon GenePix 4000B Scanner. 18 samples were scanned on an Agilent G2565 Microarray Scanner.

data_processing: CodeLink software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: DU145 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 2hrs after last dose

label_protocol: Biotin-labelled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample.  Briefly, 2 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.  Hybridization was performed at 37°C overnight in a temperature-controlled shaking incubator.

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% FBS, glutamine, and antibiotics.

extract_protocol: Total RNA was extracted and collected at multiple time points 2, 6, and 24 hours after the final radiation doses using (QIAshredder Spin Columns (Catalog no. 79654, Qiagen).    . All extracted RNA was purified with an RNeasy Mini Kit (Qiagen). The total RNA concentration was measured by spectrophotometry at A260/280.  Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies) was used to assess the quality of RNA samples.

treatment_protocol: Cells were plated into 175-cm2 culture flasks (1.6x106 for single dose and 0.8x106 for fractionated radiation). After 24h cells were exposed to a total of 5Gy or 10Gy radiation administered either as a single dose or multi-fractionated radiation in an irradiator using an Eldorado 8 60C0 teletherapy unit that delivered dose rates between 150 and 180 cGy per minute.

tag: radiation protocol

tag: cell collection time

value: 2hrs after last dose


title: DU, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 2

source_name: DU145 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 6hrs after last dose

tag: cell line

value: 6hrs after last dose


title: DU, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 1

value: multiple fraction of 2Gy once daily for 5 days


title: DU, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 2

source_name: DU145 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 24hrs after last dose

value: 24hrs after last dose


title: DU, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 3

source_name: DU145 cells, multiple fraction of 1Gy twice daily at 6hr intervals for 5 days, cells collected 24hrs after last dose


title: DU, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 1

value: multiple fraction of 1Gy twice daily at 6hr intervals for 5 days


title: DU, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 3


title: DU, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 2


title: DU, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 1

source_name: DU145 cells, multiple fraction of 1Gy twice daily at 6hr intervals for 5 days, cells collected 6hrs after last dose


title: DU, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 3


title: DU, Multiple Fraction, 0 Gy Control, Rep 2

source_name: DU145 cells, multiple fraction radiation control

value: multiple fraction radiation control

value: control


title: DU, Multiple Fraction, 0 Gy Control, Rep 1


title: DU, Single Dose, 10 Gy, 24hr, Rep 3

source_name: DU145 Cells, single dose of 10Gy, cells collected 24 hrs after last dose

value: single dose of 10Gy


title: DU, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 1


title: HS_124

description: pheochromocytoma

value: pheochromocytoma


title: Control#2, 8 weeks HFD

description: Control 2

value: liver


title: DU, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 3


title: DU, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 2


title: DU, Multiple Fraction, 0 Gy Control, Rep 3


title: DU, Single Dose, 10 Gy, 6hr, Rep 3

source_name: DU145 Cells, single dose of 10Gy, cells collected 6 hrs after last dose


title: DU, Single Dose, 10 Gy, 24hr, Rep 2


title: DU, Single Dose, 10 Gy, 6hr, Rep 2


title: LNCap, 0 Gy Ctrl, Single Dose, Rep 1

source_name: LNCap cells, single dose radiation control

value: LNCAP

value: single dose radiation control


title: DU, Single Dose, 10 Gy, 6hr, Rep 1


title: WT1

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s): Hybridization volume increased to 250.0µL. Fluidics Script: EukGE ws2v5

scan_protocol: GeneChip® Scanner 3000, GCOS version 1.2

data_processing: All data analyzed using Genespring 7.0 or R/Bioconductor using GCRMA and limma

source_name: jejunum crypt samples of wild type control mice

label_protocol: Affymetrix One Cycle Target and Labeling Protocol, exactly as described in Affymetrix Expression Analysis Technical Manual

extract_protocol: Total RNA was extracted from crypt samples of Sox9 mutant mice and their littermate controls using the TRIzol reagent (Invitrogen) and treated with Rnase-free DNase (Roche).

value: jejunum crypt

value: wild type


title: DU, Single Dose, 10 Gy, 24hr, Rep 1


title: WT3


title: DU, 0 Gy Ctrl, Single Dose, Rep 3

source_name: DU145 Cells, single dose radiation control


title: KO1

source_name: jejunum crypt samples of Sox9 deficient mice

value: Sox9 deficient mice


title: DU, Single Dose, 10 Gy, 2hr, Rep 3

source_name: DU145 Cells, single dose of 10Gy, cells collected 2 hrs after last dose


title: DU, Single Dose, 10 Gy, 2hr, Rep 2


title: DU, 0 Gy Ctrl, Single Dose, Rep 1


title: PC3, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 3

source_name: PC3 cells, multiple fraction of 1Gy twice daily at 6hr intervals for 5 days, cells collected 6hrs after last dose


title: DU, Single Dose, 10 Gy, 2hr, Rep 1


title: PC3, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 1


title: DU, 0 Gy Ctrl, Single Dose, Rep 2


title: PC3, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 2

source_name: PC3 cells, multiple fraction of 1Gy twice daily at 6hr intervals for 5 days, cells collected 24hrs after last dose


title: KO2


title: KO3


title: PC3, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 2


title: PC3, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 3


title: PC3, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 3

source_name: PC3 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 24hrs after last dose


title: PC3, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 3

source_name: PC3 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 6hrs after last dose


title: PC3, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 1

source_name: PC3 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 2hrs after last dose


title: PC3, Multiple Fraction, 0 Gy Control, Rep 1

source_name: PC3 cells, multiple fraction radiation control


title: PC3, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 2


title: PC3, Multiple Fraction, 0 Gy Control, Rep 3


title: PC3, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 2


title: PC3, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 3


title: PC3, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 1


title: PC3, Multiple Fraction, 2Gy, 5 times, 6hr, Rep 1


title: PC3, Multiple Fraction, 0 Gy Control, Rep 2


title: PC3, Multiple Fraction, 2Gy, 5 times, 2hr, Rep 2


title: PC3, Single Dose, 10 Gy, 24hr, Rep 2

source_name: PC3 Cells, single dose of 10Gy, cells collected 24 hrs after last dose


title: PC3, Multiple Fraction, 1Gy, 10 times, 24hr, Rep 1


title: PC3, Single Dose, 10 Gy, 24hr, Rep 1


title: PC3, Single Dose, 10 Gy, 24hr, Rep 3


title: DU, Multiple Fraction, 2Gy, 5 times, 24hr, Rep 3

source_name: DU145 cells, multiple fraction of 2Gy once daily for 5 days, cells collected 24hrs after last dose


title: PC3, Single Dose, 10 Gy, 2hr, Rep 2

source_name: PC3 Cells, single dose of 10Gy, cells collected 2 hrs after last dose


title: PC3, Single Dose, 10 Gy, 6hr, Rep 2

source_name: PC3 Cells, single dose of 10Gy, cells collected 6 hrs after last dose


title: PC3, Single Dose, 10 Gy, 2hr, Rep 1


title: PC3, Single Dose, 10 Gy, 2hr, Rep 3


title: PC3, Single Dose, 10 Gy, 6hr, Rep 1


title: PC3, 0 Gy Ctrl, Single Dose, Rep 3

source_name: PC3 Cells, single dose radiation control


title: PC3, 0 Gy Ctrl, Single Dose, Rep 1


title: LNCap, 1Gy, 10 times, Multiple Fraction, Rep 4

source_name: LNCAP cells, multiple fraction of 1Gy twice daily for 5 days, cells collected 24hrs after last dose


title: PC3, 0 Gy Ctrl, Single Dose, Rep 2


title: PC3, Single Dose, 10 Gy, 6hr, Rep 3


title: DU, Multiple Fraction, 1Gy, 10 times, 6hr, Rep 2

source_name: DU145 cells, multiple fraction of 1Gy twice daily at 6hr intervals for 5 days, cells collected 6hrs after last dose


title: LNCap, 1Gy, 10 times, Multiple Fraction, Rep 1

value: multiple fraction of 1Gy twice daily for 5 days


title: LNCap, 1Gy, 10 times, Multiple Fraction, Rep 2


title: WT.unstim.1

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

hyb_protocol: The labeled cRNA was hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 array using standard protocols and reagents from Affymetrix

scan_protocol: Probe intensities were measured using the Affymetrix GeneChip Scanner 3000

data_processing:
Scanned images were processed into CEL files using the Affymetrix GeneChip Operating Software
Probe-level intensities were background-adjusted, quantile-normalzed, and probeset-summarized using the justRMA procedure in the affy package v1.26.1 in Bioconductor v2.6, using probeset definitions from the CustomCDF project ENSG v13, loaded through the R package mouse4302mmensgcdf).

source_name: Bone marrow-derived macrophages

label_protocol: mRNA was labeled using the Affymetrix One-Cycle Target Labeling protocol and reagents for eukaryotic target preparation

growth_protocol: Bone marrow cells collected from femurs were plated on non-tissue culture-treated plastic in complete RPMI medium [RPMI 1640 (Cellgro) containing L-glutamine, supplemented with 10% (v/v) FBS (Hyclone), 100 IU/mL penicillin (Cellgro) and 100 μg/mL streptomycin (Cellgro)] plus 50 ng/mL recombinant human macrophage colony-stimulating factor (rhM-CSF, Chiron) (hereafter, BMDM medium). On day four, the medium was replaced, and on day six, adherent cells were lifted in PBS + 1 mM EDTA, counted, pelleted, resuspended in BMDM medium, and plated into six-well tissue culture plates.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent 2100 Bioanalyzer.

treatment_protocol: On day seven, for samples intended for LPS stimulation, LPS (List Biological Labs) was introduced into the culture medium, at 10 ng/mL. Cells were then incubated for 4 hours. Stimulation of the cells was verified by the presence of TNF in the culture supernatants detected by ELISA (Duoset ELISA System, R&D Systems)

tag: cell type

value: BMDM

tag: agent

tag: gender

value: female

value: 8-12 weeks


title: LNCap, 0.5Gy, 10 times, Multiple Fraction, Rep 1

source_name: LNCAP cells, multiple fraction of 05Gy twice daily for 5 days, cells collected 24hrs after last dose

value: multiple fraction of 0.5Gy twice daily for 5 days


title: WT.unstim.2

tag: strain

tag: age


title: LNCap, 0.5Gy, 10 times, Multiple Fraction, Rep 4

value: 24hrs after last dose


title: 01MKP_EO

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects.

label: Biotin

source_name: Peripheral blood mononuclear cells

label_protocol: NuGEN Ovation labeling

extract_protocol: Peripheral blood was drawn and PBMC were isollated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

value: Juvenile idiopathic arthritis

tag: ttf

tag: race

value: Caucasian/White

tag: Sex

value: Female


title: LNCap, 0.5Gy, 10 times, Multiple Fraction, Rep 2


title: WT.unstim.3


title: WT.LPS.1

value: LPS

tag: concentration

value: 10 ng/mL

tag: time (duration)

value: 4 h


title: 01N3K_EO


title: Atf3KO.unstim.1

tag: genotype/variation


title: WT2

source_name: jejunum crypt samples of wild type control mice

tag: tissue


title: Atf3KO.unstim.3


title: 01JMF_EO


title: LNCap, 0 Gy Ctrl, Multiple Fraction, Rep 4

source_name: LNCap cells, multiple fraction radiation control

value: LNCAP

value: multiple fraction radiation control

value: control


title: Atf3KO.unstim.2


title: WT.LPS.2

value: wild type


title: LNCap, 0 Gy Ctrl, Multiple Fraction, Rep 2


title: LNCap, 0 Gy Ctrl, Multiple Fraction, Rep 1


title: LNCap, 10Gy, Single Dose, Rep 2

source_name: LNCAP cells, single dose of 10Gy cells collected 24hrs after last dose

value: single dose of 10Gy


title: LNCap, 5Gy, Single Dose, Rep 4

source_name: LNCAP cells, single dose of 5Gy, cells collected 24hrs after last dose

value: single dose of 5Gy


title: LNCap, 10Gy, Single Dose, Rep 1


title: LNCap, 5Gy, Single Dose, Rep 1


title: LNCap, 5Gy, Single Dose, Rep 2


title: LNCap, 10Gy, Single Dose, Rep 4


title: Atf3KO.LPS.1

value: BMDM


title: LNCap, 0 Gy Ctrl, Single Dose, Rep 2

source_name: LNCap cells, single dose radiation control

value: single dose radiation control


title: Day 26 cells, replicate 2

city: La Jolla

first: Kai

last: Tan

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

hyb_protocol: according to the instruction manual, as described in the Affymetrix website.

data_processing: Microarray data were normalized using the RMA algorithm.

source_name: Day 26 cells

label_protocol: Total RNA underwent first-strand and second strand cDNA synthesis. Complementary RNA was generated and used to produce sense-strand cDNA, which was fragmented and end-labeled with biotin. Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix.

growth_protocol: To differentiate ES cells into HSCs, a 2-stage culture strategy was adopted. Initially, ES cells were subjected to embryoid body (EB) formation over 6 days. At this stage, ES cells were plated to an ultra-low attachment Petri dish at a concentration of 2000 cells/mL in a methycellulose-based differentiation medium containing Iscove modified Dulbecco medium (Invitrogen), 15% FCS, 300 μg/mL transferrin, 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, 5% protein-free hybridoma medium (Invitrogen), 4x10-4 M monothioglycerol, and 50 μg/mL ascorbic acid. At second stage, EBs were dissociated into single-cell suspension using trypsin (2.75%), and 3.5x106 cells/mL cells were re-plated on another ultra-low attachment Petri dish in a serum-free hematopoietic differentiation medium that contained StemPro34 plus nutrient supplement (Invitrogen) and a cocktail of hematopoietic cytokines including murine stem cell factor (mSCF; 100 ng/mL; R&D Systems, Minneapolis, MN), mIL-3 (2 ng/mL), mIL-6 (5 ng/mL), Flt3-L (10 ng/mL), insulin-like growth factor-1 (IGF-1; 40 ng/mL; Promega, Madison, WI), and dexamethasone (1 μM; Sigma-Aldrich, St Louis, MO). Culture medium was changed every other day and cell density maintained below 4x106 cells/mL.

extract_protocol: Total RNA was isolated from cultured cells using Trizol reagent according to the manufacturer's protocol (Invitrogen). RNA samples were treated with Dnase I to remove genomic DNA contamination. RNA quality was assessed by its absorbance at 260nm and 280nm using a NanoDrop spectrophotometer and its integrity was assessed bioanalyzer.

value: EB cells cultured with a hematopietic cytokine cocktail for 20 days


title: LNCap, 0 Gy Ctrl, Single Dose, Rep 4


title: Atf3KO.LPS.2

value: female

value: 8-12 weeks


title: RVSMC treated with Ang II (24h), biological rep3

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description:
Gene expression data from RVSMC stimulated Ang II for 24h
D949_(12_24hr.3)_(RaGene-1_0-st-v1).CEL

hyb_protocol: Affymetrix GeneChip Whole Transcript (WT) Gene 1.0 Array hybridization protocol using 5.5 ug fragmented and biotinylated cDNA (sense strand), hybridized at 45 C for ~16 hrs, and the Rat Gene 1.0 Arrays were stained and washed using Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip Rat Gene 1.0 ST Arrays were scanned using the GeneChip Scanner 3000 7G controlled by Affymetrix GeneChip Command Console Software (AGCC).

data_processing: raw CEL files were imported to Partek Genomic Suite and pre-processed using Robust Multichip Average (RMA) method

organism: Rattus norvegicus

source_name: vascular smooth muscle cells,  Ang II stimulation for 24h

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target labeling Protocol V4 using 100 ng total RNA to start the labeling reaction.

growth_protocol: rat vascular smooth muscle cells were cultured in M199 medium supplemented with 10% FBS.

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

treatment_protocol: serum depleted for 48h and treated with or without Ang II (100nM) for 1h, 3h or 24h.

tag: stain

value: Sprague-Dawley

value: aorta

tag: development

value: differentiated

value: vascular smooth muscle cells

value: Angiotensin II

tag: time


title: Day 26 cells, replicate 3

scan_protocol: according to the instruction manual, as described in the Affymetrix website.


title: 14227536 - sphk2_12_1 vs wt_12_1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Role of PI4 kinase and Long-chain bases kinases in response to cold stress

hyb_protocol: wt_12_1 Cy5 / sphk2_12_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - media: Murashige and Skoog (MS) medium  hygrometry: 80%  temperature: 22°C  light: 80 micro Enstein

extract_protocol: wt_12_1:16ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:cold stress 12 degrees - abiotic stress - temperature,temperature:quantity 12 time 4hour . Plantlets of wild type and mutant were grown vitro for 14 days in a growth chamber (80% humidity, 80 micro Enstein without photoperiod). The 15th day, a part of wild type plantlets, pi4kinaseb1b2 and sphingosine kinase2 mutants were transferred at 4°C during 4 hours (80 micro Enstein) for a cold stress. Another part of wild type and sphk2 mutant were transferred at 12°C during 4 hours (80 micro Enstein) for a cold stress.

tag: ecotype

value: columbia

tag: treatment

value: cold stress 12 degrees - abiotic stress - quantity 12 time 4hour

extract_protocol: sphk2_12_1:10ug. (Qiagen_RNeasy.pdf)

value: mutant sphk2


title: RVSMC treated with Ang II (24h), biological rep2

description:
Gene expression data from RVSMC stimulated Ang II for 24h
D948_(11_24hr.2)_(RaGene-1_0-st-v1).CEL

tag: cell type


title: RVSMC treated with Ang II (24h), biological rep1

description:
Gene expression data from RVSMC stimulated Ang II for 24h
D947_(10_24hr.1)_(RaGene-1_0-st-v1).CEL

tag: agent


title: Day 26 cells, replicate 1


title: RVSMC treated with Ang II (12h), biological rep3

description:
Gene expression data from RVSMC stimulated Ang II for 12h
D946_(9_12hr.3)_(RaGene-1_0-st-v1).CEL

source_name: vascular smooth muscle cells,  Ang II stimulation for 12h


title: Day 16 cells, replicate 3

source_name: Day 16 cells

value: EB cells cultured with a hematopietic cytokine cocktail for 10 days


title: EB cells, replicate 2

source_name: EB cells

value: Embryoid body cells


title: EB cells, replicate 3


title: Day 16 cells, replicate 2


title: Day 16 cells, replicate 1


title: RVSMC treated with Ang II (12h), biological rep2

description:
Gene expression data from RVSMC stimulated Ang II for 12h
D945_(8_12hr.2)_(RaGene-1_0-st-v1).CEL


title: 14227535 - wt_12_1 vs sphk2_12_1

hyb_protocol: sphk2_12_1 Cy5 / wt_12_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wild type


title: 14227534 - sphk2_22_1 vs wt_22_1

hyb_protocol: wt_22_1 Cy5 / sphk2_22_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: wt_22_1:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

extract_protocol: sphk2_22_1:12ug. (Qiagen_RNeasy.pdf)


title: RVSMC treated with Ang II (12h), biological rep1

description:
Gene expression data from RVSMC stimulated Ang II for 12h
D944_(7_12hr.1)_(RaGene-1_0-st-v1).CEL


title: RVSMC treated with Ang II (6h), biological rep3

description:
Gene expression data from RVSMC stimulated Ang II for 6h
D943_(6_6hr.3)_(RaGene-1_0-st-v1).CEL

source_name: vascular smooth muscle cells,  Ang II stimulation for 6h


title: RVSMC treated with Ang II (6h), biological rep1

description:
Gene expression data from RVSMC stimulated Ang II for 6h
D941_(4_6hr.1)_(RaGene-1_0-st-v1).CEL


title: RVSMC treated without Ang II (0h), biological rep3

description:
Gene expression data from RVSMC without Ang II stimulation
D940_(3_Ctrl.3)_(RaGene-1_0-st-v1).CEL

source_name: vascular smooth muscle cells,  no Ang II stimulation

value: untreated

value: control


title: ES cells, replicate 3

source_name: CCE ES cells

value: undifferentiated ES cells


title: RVSMC treated with Ang II (6h), biological rep2

description:
Gene expression data from RVSMC stimulated Ang II for 6h
D942_(5_6hr.2)_(RaGene-1_0-st-v1).CEL


title: 14227294 - b1/b2_22_1 vs wt_22_1

hyb_protocol: wt_22_1 Cy5 / b1/b2_22_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: b1/b2_22_1:19ug. (Qiagen_RNeasy.pdf)

value: mutant b1/b2


title: EB cells, replicate 1


title: ES cells, replicate 1


title: 14227293 - wt_22_1 vs b1/b2_22_1

hyb_protocol: b1/b2_22_1 Cy5 / wt_22_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GFP-Rep2

city: Boulder

first: Min

last: Han

state: CO

address: Campus Box 347

department: Molecular Cellular and Developmental Biology

institute: Univeristy of Colardo, Boulder/HHMI

description:
Sample name: GFP IP Replicate 2
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

hyb_protocol: Hybridization Application 1.0 PURPOSE: To provide a standard operating procedure for hybridization of fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass slides. 2.0 SPECIAL NOTES: 3.0 AUTHORS: Mike Heinz 4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0 5.0 REQUIRED MATERIALS AND EQUIPMENT: Labeled probe Hybridization chamber apparatus Hybridization oven Heat block 4xSSC Air gun/ canister Timers Microcentrifuge Hybridization buffer (check vendor) Forceps Microarray(s) Pipettes Coverslips (Erie Scientific) 6.0 DEFINITIONS: 7.0 PROCEDURE: 7.1 Set up 7.1.1 Using an air gun canister, blow off all hybridization chamber parts to ensure they are clean, especially the microarray and the coverslip. 7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip apparatus. Make sure that the coverslip is appropriately placed over the entire arrayed area. 7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization chamber. 7.1.4 If frozen, remove probes from the -20C freezer and thaw at room temperature in the dark if frozen. Ensure that each probe has enough volume for the hybridization (ie. For a 25x25mm coverslip, 20ul is needed to cover the array surface). Each probe should have at least +2ul of probe in the tube compared to that of the volume to be applied to the array. If a probe does not contain the appropriate volume, add hybridization buffer (use appropriate vendor) to reach desired volume. Make sure to mix the solution if adding hyb buffer. 7.1.5 By checking the paperwork/ jobticket, make sure that the appropriate probes have been thawed and that the appropriate arrays have been placed in the chambers. 7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for appropriate denaturing temperatures and times). 7.1.7 Centrifuge the probes for 1 min. at max speed. 7.2 Application 7.2.1 Carefully pipette 20ul (or other amount) under the coverslip covering the arrayed surface. Ensure that the array is completely covered. If not completely covered, pipette additional probe under the coverslip in increments of 2ul. Note any bubbles or abnormalities. 7.2.2 Apply the coverglass and clamps. Using the torque wrench, tighten the clamps. Make sure that the metal arms of the clamps are not resting on the edge of the coverglass. Also, make certain that the wrench is set at 46 lb/in. 7.2.3 Place the hybridization chambers in the hybrization box, then place the hyb. box in the oven at 42C and hybridize overnight (minimum of 12 hours). Make certain to place the chambers in the hyb. box so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0.

data_processing: Microarray data (median spot value – median local background) was first filtered to remove low-signal spots (spots with values < 25 in either the channel representing the Total RNA or the channel representing IP RNA).   For each remaining probe, the enrichment value was defined as IP/Total.  We next calculated the percent rank of the enrichment value for all spots within a given biological replicate.  Finally, for any given probe (representing a specific mRNA) the mean value of all non-missing percent ranks was calculated.  A given probe was defined as “testable” if at least two biological replicates yielded non-missing values (i.e. at least two replicates yielded sufficiently robust signal in both the IP and Total RNA channels).  For all testable mRNAs, a p-value for enrichment was calculated by using a one-tailed t-test for each percent rank value compared to all percent rank values within the dataset.  Therefore, for a given mRNA, the enrichment value is represented as the mean percent rank over all biological replicates as well as a p-value indicating statistical significance of the percent ranks compared to the whole data set.  This methodology was based on previous work (Roy et al., 2002).  p value cut-offs for enrichment were p < 0.01 for all tissue-specific IPs, with the exception of the L4-syncrhonized worms in which we chose a cut-off of p < 0.001.  An mRNA was considered to be IP-enriched if it showed above average enrichment (i.e. mean percent rank was greater than 0.500) and the p-value for its enrichment was below the indicated cut-off.

organism: Caenorhabditis elegans

source_name: IP RNA from Pain-2::gfp

label_protocol: The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

growth_protocol: For experiments on asynchronous worms, worms were grown to high density on HB101 and harvested when well-fed.  For synchroinization at L4, worms were grown to gravid adults on 20x10cm NGM plates with a thick lawn of HB101 E. coli.  Just prior to starvation, worms were washed from the plates, and embryos were isolated by the hypochlorite method followed by sucrose floatation to remove carcasses.  The purified embryos were rinsed several times with M9, and allowed to hatch for 20 h at 20oC in M9.  The synchronized L1s were then mixed with HB101 and allowed to grow for 48 h at 20oC before they were harvested, sucrose floated to remove remaining HB101, split in two, and distributed between 30x10cm peptone-enhanced (0.35% final) plates seeded with OP50 or PA14.  The worms were exposed to each bacterium at 25oC for 8 h before harvesting, cross-linking and subsequent IP.

extract_protocol: This was performed essentially as previously described (Zhang et al., 2007; Zhang et al., 2009). Worm cultures were expanded on 10 cm nematode growth medium (NGM) plates seeded with thick lawns of HB101 (KanR) E. coli.  For each experiment, approximately 20 plates of worms were grown to high density, without allowing starvation.  Worms were harvested and immediately cross-linked with 0.5% formaldehyde in M9 at 4oC for 1 h as performed by Roy et al. (Roy et al., 2002).  Cross-linked samples were washed twice with M9, snap-frozen in liquid nitrogen and stored at -80oC for subsequent lysis and IP.  Frozen samples were then homogenized with a mortar and pestle under liquid nitrogen.  The homogenate was extracted with three volumes lysis buffer [25 mM HEPES-NaOH (pH 7.4), 150 mM NaCl, 1 mM DTT, 10% glycerol, 1% Triton X-100, Complete Protease Inhibitors (Roche), 100 U/ml recombinant ribonuclease inhibitor (RNaseOUT by Invitrogen)].  The lysate was then clarified by centrifugation at 20,000xg for 20 min at 4oC.  The supernatant was then pre-cleared by incubation with 25 μl/ml protein A sepharose (Sigma) for 1 h at 4oC.  The cleared supernatant was then subjected to immunoprecipation with the 10 μg/ml 3E6 anti-GFP monoclonal antibody for 2 h, as previously described (Zhang et al., 2007; Zhang et al., 2009).  Immediately before addition of protein A sepharose beads, several 50 μl aliquots of lysate were removed and de-crosslinked as previously described (Roy et al., 2002).  The de-crosslinked aliquots were mixed with 1 ml of Trizol (Invitrogen) and used as Total RNA for subsequent microarray analysis.  After incubation with protein A sepharose and washing, as previously described, complexes precipitating with the protein A sepharose beads were decrosslinked twice, according to the method of Roy et al.  The de-crosslinked RNA was then mixed with Trizol, and split into two aliquots – one for microarray analysis and one for miRNA cloning.

treatment_protocol: In all instances, worms harvested, well-fed, from 10cm NGM plates.

tag: Stage

value: asynchronous

value: whole worm

tag: rip antibody

value: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120; various  lots)

source_name: Total RNA from Pain-2::gfp


title: 14227292 - wt_12_1 vs wt_4_1

hyb_protocol: wt_4_1 Cy5 / wt_12_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: wt_4_1:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:cold stress 4 degrees - abiotic stress - temperature,temperature:quantity 4 time 4hour . Plantlets of wild type and mutant were grown vitro for 14 days in a growth chamber (80% humidity, 80 micro Enstein without photoperiod). The 15th day, a part of wild type plantlets, pi4kinaseb1b2 and sphingosine kinase2 mutants were transferred at 4°C during 4 hours (80 micro Enstein) for a cold stress. Another part of wild type and sphk2 mutant were transferred at 12°C during 4 hours (80 micro Enstein) for a cold stress.

tag: age

value: cold stress 4 degrees - abiotic stress -  quantity 4 time 4hour


title: ES cells, replicate 2


title: L4-Intestine-Rep5

description:
Sample name: L4 Intestine IP Replicate 5
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

source_name: IP RNA from Pges-1::ain-2::gfp synchronized at L4

tag: strain

value: synchronized at L4

value: Intestine

source_name: Total RNA from Pges-1::ain-2::gfp synchronized at L4


title: 14227297 - wt_22_1 vs sphk2_22_1

hyb_protocol: sphk2_22_1 Cy5 / wt_22_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RVSMC treated without Ang II (0h), biological rep1

description:
Gene expression data from RVSMC without Ang II stimulation
D938_(1_Ctrl.1)_(RaGene-1_0-st-v1).CEL

value: Sprague-Dawley

value: aorta

value: differentiated

value: vascular smooth muscle cells


title: L4-Intestine-Rep4

description:
Sample name: L4 Intestine IP Replicate 4
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: 14227290 - wt_22_1 vs wt_4_1

hyb_protocol: wt_4_1 Cy5 / wt_22_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia


title: L4-Intestine-Rep3

description:
Sample name: L4 Intestine IP Replicate 3
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: HS_14

description: childhood adrenocortical tumor

hyb_protocol: standard Illumina protocol

extract_protocol: Proteinase K method. The detailed protocol can be found in PMID:18786438.

tag: geographical origin

value: Brazil

tag: genger

value: Female

tag: histological type

value: Carcinoma

tag: tnm

tag: tp53 mutation

tag: virilization

value: Yes

tag: cushing  syndrome

value: Surgery

tag: follow-up (months)

value: Alive (45)


title: L4-Intestine-Rep2

description:
Sample name: L4 Intestine IP Replicate 2
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

tag: tissue


title: 14227289 - wt_4_1 vs wt_22_1

hyb_protocol: wt_22_1 Cy5 / wt_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: genotype/variation

value: wild type


title: HS_13

description: childhood adrenocortical tumor

tag: treatment

value: Alive (29)


title: 14227288 - sphk2_4_1 vs wt_4_1

hyb_protocol: wt_4_1 Cy5 / sphk2_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: sphk2_4_1:14ug. (Qiagen_RNeasy.pdf)

value: mutant sphk2


title: L4-Intestine-Rep1

description:
Sample name: L4 Intestine IP Replicate 1
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

value: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120; various  lots)


title: GFP-Rep1

description:
Sample name: GFP IP Replicate 1
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

value: asynchronous

value: whole worm


title: 14227287 - wt_4_1 vs sphk2_4_1

description: Role of PI4 kinase and Long-chain bases kinases in response to cold stress

hyb_protocol: sphk2_4_1 Cy5 / wt_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cold stress 4 degrees - abiotic stress -  quantity 4 time 4hour


title: HS_09

description: childhood adrenocortical tumor

value: Adenoma

value: No

value: Alive (64)


title: HS_06

description: childhood adrenocortical tumor

value: Male

value: Surgery+Chemotherapy


title: Asynch-Muscle-Rep4

description:
Sample name: Asynch Muscle IP Replicate 4
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

source_name: IP RNA from Pmyo-3::ain-2::gfp

value: Muscle

source_name: Total RNA from pMyo-3::ain-2::gfp


title: HS_10

description: childhood adrenocortical tumor

value: Brazil

value: Female

value: Carcinoma

value: Alive (102)


title: HS_11

description: childhood adrenocortical tumor

value: Surgery

value: Alive (49)


title: Asynch-Muscle-Rep2

description:
Sample name: Asynch Muscle IP Replicate 2
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: 14227285 - wt_4_2 vs sphk2_4_2

hyb_protocol: sphk2_4_2 Cy5 / wt_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: sphk_4_2:19ug. (Qiagen_RNeasy.pdf)

value: columbia

value: mutant sphk2

extract_protocol: wt_4_2:15ug. (Qiagen_RNeasy.pdf)

value: wild type


title: 14227282 - wt_12_2 vs sphk2_12_2

hyb_protocol: sphk2_12_2 Cy5 / wt_12_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: sphk_12_2:14ug. (Qiagen_RNeasy.pdf)

value: cold stress 12 degrees - abiotic stress - quantity 12 time 4hour

extract_protocol: wt_12_2:16ug. (Qiagen_RNeasy.pdf)


title: Asynch-Muscle-Rep3

description:
Sample name: Asynch Muscle IP Replicate 3
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

source_name: Total RNA from Pmyo-3::ain-2::gfp

value: asynchronous

source_name: IP RNA from pMyo-3::ain-2::gfp

value: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120; various  lots)


title: 14227286 - sphk2_4_2 vs wt_4_2

hyb_protocol: wt_4_2 Cy5 / sphk2_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cold stress 4 degrees - abiotic stress -  quantity 4 time 4hour


title: 14227283 - sphk2_12_2 vs wt_12_2

hyb_protocol: wt_12_2 Cy5 / sphk2_12_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14227281 - sphk2_22_2 vs wt_22_2

hyb_protocol: wt_22_2 Cy5 / sphk2_22_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: wt_22_2:13ug. (Qiagen_RNeasy.pdf)

extract_protocol: sphk_22_2:18ug. (Qiagen_RNeasy.pdf)