title: si-negative control

description: Gene expression data from LNCaP cells transfected with negative control siRNA for 72hrs .

source_name: LNCap cells transfected with si-negative


title: siSE2

status: Public on Jul 24 2012

type: RNA

city: Charlottesville

first: Hui

last: Li

address: 345 Crispell Dr.

country: USA

institute: University of Virginia

description: Gene expression data from LNCaP cells transfected with siSE2 for 72hrs .

hyb_protocol: Hybridize: Incubate arrays in oven 45C, 60rpm, 17hrs. Stain/block: FS450_0007 on Fluidics Station 450

scan_protocol: After hybridization and clean up, the Genechips were scanned in an Affymetrix GeneArray Scanner 3000 7G, following the manufacturer's instruction. (See www.affymetrix.com)

data_processing: The image files produced by the scanning were handled by the software- Affymetrix® GeneChip® Command Console® Software (AGCC, See www.affymetrix.com), to first assembled into a .DAT file which then converted into a digitized .CEL file. The .CEL files were later analyzed by both Affymetrix Expression Console and R/BioConductor (www.bioconductor.org) to generate expression table in excel or text format.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: LNCap cells transfected with siSE2

label_protocol: Ambion WT Expression Kit (p/n 4411974), GeneChip WT Terminal Labeling and Controls Kit (p/n 901524)

growth_protocol: LNCap cells growing in RPMI1640+10%FBS

extract_protocol: trizol

treatment_protocol: siRNAs were trasnfected into LNCaP cells using RNAiMAX

tag: cell line

value: LNCaP

tag: transfection

value: LNCaP cells transfected with siSE1 for 72hrs


title: Placenta (E9.5) Prdm1-/-_10

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

description: Prdm1BEH/BEH biological replicate 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Rank invariant normalisation with background subtraction using the Gene Expression Module V1.6.0 of Illumina GenomeStudio V2009.2

organism: Mus musculus

source_name: Placenta (E9.5)

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: tissue

value: placenta

tag: developmental stage

tag: strain

value: Mixed 129SvEv and C57Bl/6

tag: prdm1 genotype


title: UZHRCC022_RCC_clear_cell_S4_BI_mRNA_rep3

city: Zurich

first: Michael

last: Baudis

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

hyb_protocol: standard Affymetrix protocol; Broad institute

data_processing: Affymetrix GeneChip data was normalized using MAS5 from Bioconductor

label: Biotin

source_name: renal cell carcinoma ,clear cell RCC

growth_protocol: untreated tissue and cell line samples

extract_protocol: All tumor tissues were selected according to the histologically verified presence of at least 80% tumor cells.  RNA was extracted using the RNeasy minikit (Qiagen).

treatment_protocol: untreated tissue and cell line samples

tag: grade

tag: stage

tag: sample type

value: neoplasia

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

value: clear cell renal cell carcinoma

tag: organ site

value: kidney

tag: gender

tag: tissue type

value: renal cell carcinoma [clear cell RCC]

tag: cluster id

value: C


title: Placenta (E9.5) Prdm1-/-_11

description: Prdm1BEH/BEH biological replicate 11


title: Placenta (E9.5) Prdm1-/-_9

description: Prdm1BEH/BEH biological replicate 9


title: EtOH_24h_ctrl, biological rep1

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description: Gene expression in chronic ethanol-fed liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

organism: Rattus norvegicus

source_name: Chronic ethanol-fed liver

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was purified using RNeasy mini kit (Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100

treatment_protocol: Liver tissue was freeze-clamped in liquid nitrogen at the time of partial hepatectomy (PHx) and 1 h, 6 h, 12 h, and 24 h after PHx.  Tissue was then stored at -80 degrees C.

value: liver

tag: hepatectomy

value: no

tag: animal id

tag: diet

value: Ethanol

tag: timepoint

value: 0 (control)

tag: array scan date

tag: outlier


title: EtOH_6h_phx, biological rep3

description: Gene expression in chronic ethanol-fed liver 6h after PHx

source_name: Chronic ethanol-fed liver 6h after PHx

tag: tissue

value: yes

value: 6 hours


title: EtOH_6h_ctrl, biological rep4


title: clonal adipose cell line from inguinal depot [B13]

city: Boston

first: jun

last: wu

address: 450 brookline ave. CLSB11117A

institute: dana-farber cancer institute

description: Gene expression data from clonal adipose cell line of inguinal depot

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: The label, hyb and scan were performed by the Dana-Farber Cancer institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods.

data_processing: The data were normalized using the DNA-chip Analyzer(dChip) software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: clonal adipose cell line fully differentiated

extract_protocol: Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

treatment_protocol: treated with  forskolin (10mM) for 4 hrs.

tag: background strain

value: 129SVE from Taconic

tag: cell line


title: Placenta (E9.5) Prdm1-/-_8

description: Prdm1BEH/BEH biological replicate 8

tag: developmental stage

tag: strain

tag: prdm1 genotype


title: EtOH_6h_phx, biological rep4


title: EtOH_24h_phx, biological rep1

description: Gene expression in chronic ethanol-fed liver 24h after PHx

source_name: Chronic ethanol-fed liver 24h after PHx

value: 24 hours


title: clonal adipose cell line from inguinal depot [D12]


title: UZHRCC020_RCC_clear_cell_S4_BI_mRNA_rep1

scan_protocol: standard Affymetrix protocol; Broad institute

tag: grade

tag: stage

tag: sample type

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

value: male


title: UZHRCC018_RCC_clear_cell_S3_BI_mRNA_rep5

label_protocol: standard Affymetrix protocol; Broad institute

tag: organ site

tag: gender

tag: tissue type

tag: cluster id

value: A


title: UZHRCC021_RCC_clear_cell_S4_BI_mRNA_rep2


title: clonal adipose cell line from inguinal depot [B5]


title: osteosarcoma 35 miRNA

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing: The software used for normalization of the mRNA dataset was Genome Studio, Gene Expression Module v1.0, Illumina. For the miRNA data, the normalization and analysis was done in BRB ArrayTools stable release 4.1.0. Sample intensities are scaled by a factor equal to the ratio of median intensity of a virtual reference sample to the median intensity of a given sample. Background is subtracted prior to the scaling.

source_name: osteosarcoma

label_protocol: Arrays are washed and stained with strepatavidin-Cy3 then scanned in array reader

extract_protocol: RNA extracted from FFPE blocks using Qiagen Rneasy kit according to company protocol

value: osteosarcoma


title: clonal adipose cell line from inguinal depot [A5]


title: Placenta (E9.5) Prdm1-/-_7

description: Prdm1BEH/BEH biological replicate 7

value: placenta

value: Mixed 129SvEv and C57Bl/6


title: Placenta (E9.5) Prdm1-/-_6

description: Prdm1BEH/BEH biological replicate 6


title: UZHRCC019_RCC_clear_cell_S3_BI_mRNA_rep6

value: neoplasia

value: clear cell renal cell carcinoma


title: UZHRCC017_RCC_clear_cell_S3_BI_mRNA_rep4

value: kidney

value: renal cell carcinoma [clear cell RCC]


title: Placenta (E9.5) Prdm1-/-_5

description: Prdm1BEH/BEH biological replicate 5


title: EtOH_6h_phx, biological rep2

value: liver

tag: hepatectomy

tag: animal id

tag: diet

tag: timepoint

tag: array scan date


title: Placenta (E9.5) Prdm1-/-_4

description: Prdm1BEH/BEH biological replicate 4

tag: tissue

tag: developmental stage


title: EtOH_6h_ctrl, biological rep3

value: no

tag: outlier


title: Twist1 + Ras- transgenic mouse derived mammary tumor C

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

country: France

institute: Inserm U590

hyb_protocol: According to manufacturer's instructions (Affymetrix).

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0.

data_processing: CHP files were processed using RMA analysis algorithm with Affymetrix Expression Console software 1.1

source_name: Mouse Breast cancer tumor

extract_protocol: Total RNA were extract with with the Qiagen RNeasy minikit (Qiagen), then 100 ng of total RNA were amplified using Kit GeneChip 3’ IVT Express (Affymetrix).

tag: cell type

value: Twist1 + Ras- transgenic mouse-derived metaplastic breast tumor


title: UZHRCC015_RCC_clear_cell_S3_BI_mRNA_rep2

tag: grade

tag: stage


title: Mouse Breast cancer tumor cell line 2

data_processing: CHP files were processed using RMA analysis algorithm with Affymetrix Expression Console software 1.1.

source_name: Mouse Breast cancer tumor cell line

label_protocol: According to manufacturer's instructions (Affymetrix).

tag: cell line

value: luminal MMTV-ErbB2-breast tumor-derived cell line


title: Placenta (E9.5) Prdm1-/-_2

description: Prdm1BEH/BEH biological replicate 2

tag: strain

tag: prdm1 genotype


title: UZHRCC012_RCC_clear_cell_S1_BI_mRNA_rep4

tag: sample type

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

tag: organ site

tag: gender


title: osteosarcoma 28 miRNA


title: clonal adipose cell line from inguinal depot [A3]

tag: background strain


title: UZHRCC013_RCC_clear_cell_S1_BI_mRNA_rep5

value: female

tag: tissue type

tag: cluster id

value: B


title: Placenta (E9.5) Prdm1+/+_10

description: Prdm1+/+ biological replicate 10

tag: tissue


title: Twist1 + Ras- transgenic mouse derived mammary tumor A


title: Placenta (E9.5) Prdm1+/+_9

description: Prdm1+/+ biological replicate 9

tag: developmental stage


title: UZHRCC016_RCC_clear_cell_S3_BI_mRNA_rep3

value: C


title: UZHRCC014_RCC_clear_cell_S3_BI_mRNA_rep1


title: Placenta (E9.5) Prdm1+/+_8

description: Prdm1+/+ biological replicate 8


title: osteosarcoma 27 miRNA


title: Twist1 + Ras- transgenic mouse derived mammary tumor B


title: EtOH_6h_ctrl, biological rep2

tag: hepatectomy

tag: animal id

tag: diet

value: Ethanol

tag: timepoint

value: 0 (control)

tag: array scan date

tag: outlier


title: EtOH_6h_ctrl, biological rep1


title: EtOH_1h_ctrl, biological rep4


title: Mouse Breast cancer tumor cell line 1

tag: cell line


title: EtOH_6h_phx, biological rep1

value: yes

value: 6 hours


title: Placenta (E9.5) Prdm1-/-_3

description: Prdm1BEH/BEH biological replicate 3

value: placenta

tag: strain

tag: prdm1 genotype


title: Placenta (E9.5) Prdm1-/-_1

description: Prdm1BEH/BEH biological replicate 1

value: Mixed 129SvEv and C57Bl/6


title: Placenta (E9.5) Prdm1+/+_7

description: Prdm1+/+ biological replicate 7


title: EtOH_1h_phx, biological rep4

description: Gene expression in chronic ethanol-fed liver 1h after PHx

source_name: Chronic ethanol-fed liver 1h after PHx

value: 1 hour


title: MFH mod 25.2 mod miRNA

source_name: MFH mod

value: MFH mod


title: UZHRCC011_RCC_clear_cell_S1_BI_mRNA_rep3

tag: grade

tag: stage

tag: sample type

value: neoplasia

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

value: clear cell renal cell carcinoma

value: kidney


title: osteosarcoma 26 miRNA

value: osteosarcoma


title: MFH mod 25 mod miRNA


title: MFH 25.2 miRNA

source_name: MFH

value: MFH


title: MFH 25 miRNA


title: EtOH_1h_phx, biological rep3

value: liver

value: no


title: EtOH_1h_ctrl, biological rep3


title: UZHRCC008_RCC_clear_cell_BI_mRNA_rep3

tag: organ site

tag: gender

tag: tissue type

value: renal cell carcinoma [clear cell RCC]

tag: cluster id

value: A


title: EtOH_1h_ctrl, biological rep2

tag: tissue

tag: hepatectomy

tag: animal id

value: Ethanol


title: spindle cell tumor 24.2 miRNA

source_name: spindle cell tumor

value: spindle cell tumor


title: EtOH_1h_phx, biological rep2

value: yes

tag: diet

tag: timepoint

tag: array scan date


title: Placenta (E9.5) Prdm1+/+_6

description: Prdm1+/+ biological replicate 6

tag: developmental stage

tag: strain


title: UZHRCC010_RCC_clear_cell_S1_BI_mRNA_rep2

tag: grade

value: B


title: UZHRCC007_RCC_clear_cell_BI_mRNA_rep2

tag: stage


title: Placenta (E9.5) Prdm1+/+_4

description: Prdm1+/+ biological replicate 4

value: placenta

tag: prdm1 genotype


title: EtOH_1h_ctrl, biological rep1

value: 0 (control)

tag: outlier


title: UZHRCC009_RCC_clear_cell_S1_BI_mRNA_rep1

tag: sample type

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

value: male

value: C


title: spindle cell tumor 23 miRNA


title: Placenta (E9.5) Prdm1+/+_3

description: Prdm1+/+ biological replicate 3

value: Mixed 129SvEv and C57Bl/6


title: Placenta (E9.5) Prdm1+/+_1

description: Prdm1+/+ biological replicate 1


title: Placenta (E9.5) Prdm1+/+_2

description: Prdm1+/+ biological replicate 2


title: EtOH_1h_phx, biological rep1

value: 1 hour


title: spindle cell tumor 24 miRNA


title: spindle cell tumor 22 miRNA


title: Cell Death 1

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Apoptosis, Cell-cycle factors
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9371.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the mean

organism: Arabidopsis thaliana

source_name: Cells mock-treated with water

label_protocol: not provided

extract_protocol: not provided

tag: treatment

value: mock-treated with water

value: suspension cultures

source_name: Cells treated with hydrogen peroxide

value: treated with hydrogen peroxide


title: UZHRCC006_RCC_clear_cell_BI_mRNA_rep1

value: neoplasia

value: clear cell renal cell carcinoma

tag: organ site

value: kidney

tag: gender

tag: tissue type

tag: cluster id


title: spindle cell tumor 21 miRNA

tag: tissue


title: osteosarcoma 32 miRNA

value: osteosarcoma


title: Cell Death 2

description:
Simple annotation: Apoptosis, Cell-cycle factors
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7523.gif


title: p19 siTLE1 V

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 3

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

growth_protocol: MCF-7 human cell lines were grown as described previously (Neve et al. 2006, Cancer Cell 10:515–527).

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. A DNase I digestion was included. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Estrogen was added at a final concentration of 100 nM for 6 hours.

tag: cell line


title: macrophage control, biological rep1

city: hangzhou

first: weilin

last: chen

state: zhejiang

address: yuhangtang road 866

country: China

institute: zhejiang university

description: Gene expression data from untreated mouse peritoneal macrophages.

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 controlled by Affymetrix GeneChip Command Console(AGCC).

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

source_name: Mouse macrophage untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (The Ambion® WT Expression Kit protocol, 2009, Applied Biosystems).

growth_protocol: Peritoneal macrophages were harvested from mice 4 days after thioglycollate injection, and cultured in RPMI1640 supplemented with 10%FBS.

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

treatment_protocol: Mouse peritoneal macrophages cells were plated into 6-cm dishes  and infected with VSV (MOI=1) for 8 hours or uninfected.

tag: age

value: 6 weeks

value: female

tag: infection

value: control

tag: cell type

value: peritoneal macrophage


title: HeLaOA1myc_-MC_rep1

city: Milan

first: Ilaria

last: Palmisano

address: Via Olgettina, 58

department: Center for Translational Genomics and BioInformatics

country: Italy

institute: San Raffaele Scientific Institute

hyb_protocol: 1500ng of cRNA were hybridized to the BeadChip Array and stained with streptavidin-Cy3 according to the manufacturer’s protocol.

scan_protocol: BeadChips were imaged using the Illumina® BeadArray Reader, a two-channel 0.8 μm-resolution confocal laser scanner, and the Illumina BeadScan software.

data_processing: The software Illumina BeadStudio v.3 was used to elaborate the fluorescence signal to a value, whose intensity corresponds to the quantity of the respective transcript in the original sample. The gene expression data were normalized using the quantile algorithm. Detection P-value<0.01 corresponds to transcripts whose intensity value is significantly different from that of background.

source_name: HeLaOA1myc, methionine/cysteine starved

label_protocol: 500ng of total RNA were reverse transcribed into cRNA (complementary RNA) and biotin-UTP labelled using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) according to the manufacturer’s protocol.

growth_protocol: HeLa and HeLaOA1myc epithelial cells were maintained in Dulbecco’s Modified Eagle’s Medium containing glutaMAX (Invitrogen), supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin G (Invitrogen), 100 μg/ml streptomycin (Invitrogen) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted with the RNeasy minikit (Qiagen), quantified with the Nanodrop-2000 spectrophotometer (Celbio) and qualitatively analysed by agarose gel electrophoresis.

treatment_protocol: Cells were collected by trypsinization and centrifugation.

value: HeLa

tag: transgene

value: human OA1+myc tag

value: stable transfected cell clone

tag: passage

tag: medium

value: DMEM-MC

tag: time

value: 5 days

tag: antibiotic selection

value: G418 800 microg/ml


title: HeLaOA1myc_+MC_rep1

source_name: HeLaOA1myc, control

value: DMEM


title: HeLaOA1myc_+MC_rep2


title: p18 siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 2


title: HeLaOA1myc_-MC_rep2


title: osteosarcoma 19 miRNA


title: macrophage VSV, biological rep1

description: Gene expression data from mouse peritoneal macrophages with VSV infection for 8 hours.

source_name: Mouse macrophage VSV infected with 8 hours

tag: strain

value: VSV


title: osteosarcoma 18.2 miRNA


title: osteosarcoma 18 miRNA


title: p19 siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 3


title: HeLa_-MC_rep2

source_name: HeLa, methionine/cysteine starved

value: cell population

value: no G418


title: p17 siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 1


title: p20 siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 5


title: HeLa_+MC_rep1

source_name: HeLa, control


title: osteosarcoma 15 miRNA


title: HeLaOA1myc_-Y

source_name: HeLaOA1myc, tyrosine starved

value: RPMI-Y


title: p21 siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 6


title: Placenta (E9.5) Prdm1+/+_5

description: Prdm1+/+ biological replicate 5

source_name: Placenta (E9.5)

value: placenta

tag: developmental stage

value: Mixed 129SvEv and C57Bl/6

tag: prdm1 genotype


title: HeLa_-MC_rep1


title: osteosarcoma 30 miRNA

source_name: osteosarcoma

value: osteosarcoma


title: p17 siTLE1 V

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 1


title: HeLaOA1myc_+Y

value: RPMI


title: HeLa_+MC_rep2


title: HeLa_-Y

source_name: HeLa, tyrosine starved


title: HMEC-hTert-Twist1

hyb_protocol: According to  manufacturer's instructions (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

source_name: HMEC, hTert, Twist1

growth_protocol: cells were grown in DMEM/HAMF12 medium supplemented with penicillin/strptomycin, L-glutamin, 10% fetal bovine serum, 10ng/ml hEGF, 0.5µg/ml hydrocortisone and 10µg/ml insulin

extract_protocol: Total RNAs were extract with with the Qiagen RNeasy minikit (Qiagen), then 100 ng of total RNAs were amplified using Kit GeneChip 3’ IVT Express (Affymetrix)

value: HMEC-derivatives

value: expressed hTert, Twist1


title: p21 siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 6


title: p19B siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 4


title: MPNST 12 miRNA

source_name: MPNST

value: MPNST


title: MPNST 11.2 miRNA


title: MPNST 11 miRNA


title: HMEC-hTert-Zeb1

source_name: HMEC, hTert, Zeb1

label_protocol: According to  manufacturer's instructions  (Affymetrix)

value: expressed hTert, zeb1


title: eAFSC77_VPA_rep2

city: Berlin

first: Katharina

last: Drews

address: Ihnestr. 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing: The data were normalised using rank invariant normalisation after background subtraction with GenomeStudio V2010.3 (Illumina)

source_name: eAFSC77, VPA treated

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand   reverse transcription step, followed by a single in vitro transcription   (IVT) amplification that incorporates biotin-labeled nucleotides.   Subsequent steps include array hybridization, washing, blocking, and   streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively   detected for downstream analysis.

extract_protocol: The RNA was isolated using the RNeasy Mini Kit (Qiagen), including RNase-free Dnase (Qiagen) digestion   (RNase-free DNase Set, Quiagen) has been applied on the columns during   isolation.

value: early gestation human amniotic fluid cells

value: male, mixture of cells

value: first trimester, passage 8

tag: tissue/source

value: amniotic fluid


title: HeLa_+Y

value: HeLa

value: 5 days


title: p18 siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 2


title: AFSC55_VPA_rep2

source_name: AFSC 55, VPA treated

value: mid gestation human amniotic fluid cells

value: second trimester, passage 8


title: p20 siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 5


title: leiomyosarcoma 10.2 miRNA

source_name: leiomyosarcoma

value: leiomyosarcoma


title: p19B siTLE1 V

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 4


title: eAFSC77_VPA_rep1


title: HMEC-hTert-Zeb2

source_name: HMEC, hTert, Zeb2

value: expressed hTert, Zeb2


title: HMEC-hTert-Zeb2+Ras+TGF

description: transformed + treated TGF

source_name: HMEC, hTert, Zeb2+Ras+TGF

value: expressed hTert, Zeb2 and HRasG12V


title: HMEC-hTert-Twist1+Ras+TGF

description: transformed + treated TGF

source_name: HMEC, hTert, Twist1+Ras+TGF

value: expressed hTert, Twist1 and HRasG12V


title: HMEC-hTert-Ras

source_name: HMEC, hTert, Ras

value: expressed HRasG12V


title: p17 siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 1


title: AFSC55_VPA_rep1


title: leiomyosarcoma 9 miRNA


title: MDAMB157

description: transformed

label_protocol: According to manufacturer's instructions  (Affymetrix).

growth_protocol: Cells were grown in DMEM/HAMF12 medium supplemented with penicillin/strptomycin, L-glutamin, 10% fetal bovine serum, 10ng/ml hEGF, 0.5µg/ml hydrocortisone and 10µg/ml insulin.

extract_protocol: Total RNAs were extract with with the Qiagen RNeasy minikit (Qiagen), then 100 ng of total RNAs were amplified using Kit GeneChip 3’ IVT Express (Affymetrix).

value: basal B cell


title: MCF7

description: transformed

value: luminal cell


title: leiomyosarcoma 8 miRNA


title: p19 siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 3


title: p21 siTLE1 V

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 6


title: p20 siTLE1 V

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 5


title: leiomyosarcoma 10 miRNA


title: hESCH9_undiff_rep2

source_name: hESC H9, undifferentiated

value: human embryonic stem cells

value: Passage 55

value: blastocyst-derived embryonic stem cells


title: synovial sarcoma 7 miRNA

source_name: synovial sarcoma

value: synovial sarcoma


title: hESCH9_undiff_rep1


title: hESCH9_undiff_rep3

value: Passage 56


title: p19B siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 4


title: HMEC-hTert-Zeb1+Ras

description: transformed

source_name: HMEC, hTert, Zeb1+Ras

value: HMEC-derivatives

value: expressed hTert, zeb1 and HRasG12V


title: hESCH1_undiff_rep3

source_name: hESC H1, undifferentiated


title: HMEC-hTert-Twist1+Ras

description: transformed

source_name: HMEC, hTert, Twist1+Ras


title: p18 siTLE1 V

description: MCF-7 cell line treated with TLE1 siRNA and vehicle (EtOH) rep 2


title: HMEC-hTert-Zeb2+Ras

description: transformed

source_name: HMEC, hTert, Zeb2+Ras


title: synovial sarcoma 6 miRNA


title: synovial sarcoma 6.2 miRNA


title: osteosarcoma 19.2 miRNA

source_name: osteosarcoma

value: osteosarcoma


title: p20 siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 5


title: liposarcoma 4 miRNA

source_name: liposarcoma

value: liposarcoma


title: hESCH1_undiff_rep2


title: hESCH1_undiff_rep1


title: liposarcoma 5 miRNA


title: p19B siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 4


title: liposarcoma 5.2 miRNA


title: eAFSC77_untr_rep1

source_name: eAFSC 77, untreated

value: early gestation human amniotic fluid cells

value: male, mixture of cells

value: first trimester, passage 5

value: amniotic fluid


title: p21 siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 6


title: HMEC-hTert

description: immortalized

source_name: HMEC, hTert

value: HMEC immortalized

value: expressed hTert


title: eAFSC78_untr_rep1

source_name: eAFSC 78, untreated


title: primary neurons_shRNA FUS1_rep2

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

description: RMA expression value derived from Expression Console software; all-exon analysis

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps

source_name: primary cortical neurons, shRNA FUS1

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: Mouse fetal brain was taken from C57Bl/6 E15 mouse embryos. After removing meninges cortical tissue was dissociated into a single-cell suspension by using Sumilon dissociation solution. Cells were plated at a density of 1.5x10^6 cells/60mm-well culture plates with the medium containing 50% of Sumilon nerve-culture medium and 50% of neurobasal mix which includes Neurobasal plus 2% FBS, 1x B27 supplements, 1x Glutamax, 10ug/ml of BDNF, 10ug/ml of CNTF and 1% PS. A day after plating (Day2), 10ng/ul of AraC was added to media and incubated for overnight.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) followed by DnaseI (Qiagen) treatment.

treatment_protocol: At Day5 neurons were infected with 1.5x10^7copies/ul (2x1010 copies/well) of lentivirus expressing shRNA against mouse Fus (FUS1 or FUS2). After 4-hr of infection, the media was changed, and then incubated for 6 days. Neurons were collected at Day11 and total RNA was extracted followed by cDNA synthesis.

value: embryo

value: primary cortical neurons

tag: genotype/variation

value: FUS1 knockdown


title: PC-3/Mc cell line biological replicate 3

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: PC-3/Mc cell line

hyb_protocol: Standard Affymetrix protocol

scan_protocol: The labelled arrays were scanned with a Gene chip scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) 'affy' in R.2.9.1

source_name: PC-3/Mc cell line

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were grown to 70-80% confluence, lysed and RNA isolated with the RNeasy Kit (Qiagen, Hilden, Germany)


title: primary neurons_shRNA FUS2_rep3

source_name: primary cortical neurons, shRNA FUS2

value: FUS2 knockdown


title: PC-3/S cell line biological replicate 2

description: PC-3/S cell line

source_name: PC-3/S cell line


title: p19 siGFP E

description: MCF-7 cell line treated with control siRNA and 100nM Estrogen rep 3


title: AFSC60_untr_rep1

source_name: AFSC 60, untreated

value: mid gestation human amniotic fluid cells

value: female, mixture of cells

value: second trimester, passage 7


title: AFSC55_untr_rep1

source_name: AFSC 55, untreated

value: second trimester, passage 6


title: eAFSC79_untr_rep1

source_name: eAFSC 79, untreated

value: first trimester, passage 4


title: liposarcoma 1 miRNA


title: p18 siGFP V

description: MCF-7 cell line treated with control siRNA and vehicle (EtOH) rep 2


title: PC-3/S cell line biological replicate 3

description: PC-3/S cell line


title: PC-3/Mc cell line biological replicate 1

description: PC-3/Mc cell line


title: PC-3/Mc cell line biological replicate 2

description: PC-3/Mc cell line


title: liposarcoma 2 miRNA


title: MmES_new3

status: Public on Jul 23 2012

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: newly synthetised RNA was enriched by biotinylation of thioU and straptevidin RNA-IP on biotin

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanningwas performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were processed by RMA, with in between array normalization. We used Bioconductor for all data anaylsis. Values in the expression table are in log2 space.

source_name: Embryonic Stem (ES) Cells

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: RNA was extracted using Trizol

treatment_protocol: Cells were treated with 200µM thioU for 1hr, total RNA was isolated with Trizol. Biotinylation, RNA-IP and clean-up was perfomred as described previously in Dölken et al. 2008

value: Embryonic Stem (ES) cells

tag: sample type

value: newly synthetized RNA fraction


title: MmES_pre2

description: pre-existing RNA was collected as the remainder of the RNA-IP on biotin

value: pre-existing RNA fraction


title: MmES_pre1


title: MmES_new2


title: MmES_pre3


title: MmES_total3

description: totalRNA from ES cells after 60mins of thioU lableling

value: total RNA


title: MmES_new1


title: MmES_total2


title: PC-3/S cell line biological replicate 1

description: PC-3/S cell line


title: 10 actinomycin D Y 8hr

description: 8 hours after treatment

data_processing:
Arrays were normalized with R/Bioconductor's 'oligo' package and RMA without 'normalization'
geneCore <- rma(affyGeneFS, target=core, normalize=FALSE)
## no in between array normalization was done to keep the relative total abundance shift between them
featureData(geneCore) <- getNetAffx(geneCore, transcript)
## annotation is by transcript and the relevant ids can be matched to refSeq by the pheno Data of featureData(geneCore)

treatment_protocol: Cells were treated with actinomycinD in concentrations previously decribed (Sharova L., DNA Research, 2009 vol. 16(1))

value: 8 hours after treatment

tag: treatment

value: actinomycin D

tag: genetic background


title: 07 actinomycin D Y 1hr

description: 1 hours after treatment

value: 1 hours after treatment


title: p17 siTLE1 E

description: MCF-7 cell line treated with TLE1 siRNA and 100nM Estrogen rep 1

tag: cell line


title: primary neurons_conrtol shRNA_rep2

source_name: primary cortical neurons, conrtol shRNA

tag: age

value: control


title: MmES_total1


title: primary neurons_shRNA FUS1_rep3

value: embryo


title: 03 actinomycin D B 2hr

description: 2 hours after treatment

value: 2 hours after treatment


title: 01 actinomycin D B 0hr

description: 0 hours after treatment

value: 0 hours after treatment


title: 04 actinomycin D B 4hr

description: 4 hours after treatment

value: 4 hours after treatment


title: primary neurons_conrtol shRNA_rep3

value: primary cortical neurons


title: 06 actinomycin D Y 0hr

description: 0 hours after treatment


title: primary neurons_shRNA FUS2_rep2

value: FUS2 knockdown


title: 08 actinomycin D Y 2hr

description: 2 hours after treatment


title: primary neurons_conrtol shRNA_rep1


title: primary neurons_shRNA FUS1_rep1

value: FUS1 knockdown


title: primary neurons_shRNA FUS2_rep1


title: AM206_rep3

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

scan_protocol: Standard Illumina scan protocol

data_processing: Data was transformed using “lumiT” function and normalized using “lumiN” function from “lumi” package in Bioconductor

source_name: C2C12 cells transftected with antimiR-206 and cultured for 48h

label_protocol: Standard Illumina labeling protocol

growth_protocol: Cells were cultured in growth medium (DMEM 4.5g Glucose/L; 10%FBS; 1% penicillin-streptomycin ) or differentiation medium (DMEM 4.5% g Glucose/L; 2% horse serum; 1% penicillin/streptomycin)

extract_protocol: RNA was isolated using Trizol according to manufacturer's protocol

treatment_protocol: Cells were transfected using Lipofectamine 2000 according to manufacturer's instructions

tag: differentiation state

value: beginning of differentiation


title: Day2_rep3

source_name: C2C12 cells cultured in differentiation medium for 48h


title: Day2_rep1


title: Day1_rep1

source_name: C2C12 cells cultured in differentiation medium for 24h

value: undifferentiated


title: 05 actinomycin D B 8hr

description: 8 hours after treatment

tag: cell type

value: Embryonic Stem (ES) cells


title: Day2_rep2


title: rheumatoid arthritis343

type: genomic

city: Jinan

first: Xiaotian

last: Chang

address: Jingshi road 18877

institute: Shandong Acedemy of medicinal sciences

hyb_protocol: Genomic DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from peripheral blood was genotyped using  using Illumina VeraCode microarray. Genotype clustering and calling were performed using BeadStudio software (Genomestudio V2010.2 Genotyping module V1.6, Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: rheumatoid arthritis

label_protocol: 500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from whole blood samples with the Omega E-Z 96 Blood DNA kit (Omega, USA) according to the manufacturer’s protocol.

tag: gender

value: female

tag: tissue

value: peripheral blood


title: rheumatoid arthritis340


title: rheumatoid arthritis342


title: rheumatoid arthritis345

value: male


title: rheumatoid arthritis341


title: rheumatoid arthritis344


title: rheumatoid arthritis338


title: rheumatoid arthritis339


title: AM206_rep1


title: Day1_rep2


title: 02 actinomycin D B 1hr

description: 1 hours after treatment


title: 09 actinomycin D Y 4hr

description: 4 hours after treatment


title: AM206_rep2


title: Day1_rep3


title: siRNA_rep3

source_name: C2C12 cells transftected with siRNA mimicking miR-206 cultured for 24h


title: siRNA_rep2


title: rheumatoid arthritis337


title: rheumatoid arthritis336


title: siRNA_rep1


title: rheumatoid arthritis334


title: rheumatoid arthritis335


title: rheumatoid arthritis329


title: rheumatoid arthritis332


title: rheumatoid arthritis330


title: rheumatoid arthritis331


title: rheumatoid arthritis333


title: rheumatoid arthritis326


title: rheumatoid arthritis328


title: rheumatoid arthritis312


title: rheumatoid arthritis314


title: rheumatoid arthritis317


title: rheumatoid arthritis316


title: rheumatoid arthritis320


title: rheumatoid arthritis323


title: rheumatoid arthritis318


title: rheumatoid arthritis313


title: rheumatoid arthritis325


title: rheumatoid arthritis319


title: rheumatoid arthritis315


title: rheumatoid arthritis322


title: rheumatoid arthritis308


title: rheumatoid arthritis324


title: rheumatoid arthritis306


title: rheumatoid arthritis307


title: rheumatoid arthritis305


title: rheumatoid arthritis304


title: rheumatoid arthritis309


title: rheumatoid arthritis300


title: rheumatoid arthritis299


title: rheumatoid arthritis303


title: rheumatoid arthritis298


title: rheumatoid arthritis297


title: rheumatoid arthritis301


title: rheumatoid arthritis302


title: rheumatoid arthritis296


title: rheumatoid arthritis295


title: rheumatoid arthritis294


title: rheumatoid arthritis286


title: rheumatoid arthritis292


title: rheumatoid arthritis293


title: rheumatoid arthritis291


title: rheumatoid arthritis288


title: rheumatoid arthritis289


title: rheumatoid arthritis290


title: rheumatoid arthritis281


title: rheumatoid arthritis283


title: rheumatoid arthritis285


title: rheumatoid arthritis282


title: rheumatoid arthritis280


title: rheumatoid arthritis287


title: rheumatoid arthritis284


title: rheumatoid arthritis279


title: rheumatoid arthritis278


title: rheumatoid arthritis267


title: rheumatoid arthritis266


title: rheumatoid arthritis268


title: rheumatoid arthritis272


title: rheumatoid arthritis269


title: rheumatoid arthritis275


title: rheumatoid arthritis271


title: rheumatoid arthritis276


title: rheumatoid arthritis273


title: rheumatoid arthritis277


title: rheumatoid arthritis264


title: rheumatoid arthritis265


title: rheumatoid arthritis263


title: rheumatoid arthritis262


title: rheumatoid arthritis260


title: rheumatoid arthritis261


title: rheumatoid arthritis259


title: rheumatoid arthritis258


title: rheumatoid arthritis270


title: rheumatoid arthritis257


title: rheumatoid arthritis255


title: rheumatoid arthritis253


title: rheumatoid arthritis251


title: rheumatoid arthritis250


title: rheumatoid arthritis254


title: rheumatoid arthritis247


title: rheumatoid arthritis249


title: rheumatoid arthritis248


title: rheumatoid arthritis240


title: rheumatoid arthritis246


title: rheumatoid arthritis245


title: rheumatoid arthritis241


title: rheumatoid arthritis235


title: rheumatoid arthritis233


title: rheumatoid arthritis234


title: rheumatoid arthritis237


title: rheumatoid arthritis239


title: rheumatoid arthritis236


title: rheumatoid arthritis231


title: rheumatoid arthritis228


title: rheumatoid arthritis227


title: rheumatoid arthritis222


title: rheumatoid arthritis224


title: rheumatoid arthritis221


title: rheumatoid arthritis223


title: rheumatoid arthritis220


title: rheumatoid arthritis215A


title: rheumatoid arthritis216


title: rheumatoid arthritis217


title: rheumatoid arthritis274


title: rheumatoid arthritis214


title: rheumatoid arthritis215


title: rheumatoid arthritis213


title: rheumatoid arthritis211


title: rheumatoid arthritis207


title: rheumatoid arthritis209


title: rheumatoid arthritis206


title: rheumatoid arthritis204


title: rheumatoid arthritis212


title: rheumatoid arthritis197


title: rheumatoid arthritis201


title: rheumatoid arthritis200


title: rheumatoid arthritis196


title: rheumatoid arthritis187


title: rheumatoid arthritis191


title: rheumatoid arthritis186


title: rheumatoid arthritis185


title: rheumatoid arthritis183


title: rheumatoid arthritis177


title: rheumatoid arthritis210


title: rheumatoid arthritis178


title: rheumatoid arthritis181


title: rheumatoid arthritis203


title: rheumatoid arthritis176


title: rheumatoid arthritis174


title: rheumatoid arthritis173


title: rheumatoid arthritis172


title: rheumatoid arthritis170


title: rheumatoid arthritis171


title: rheumatoid arthritis168


title: rheumatoid arthritis167


title: rheumatoid arthritis163


title: rheumatoid arthritis166


title: rheumatoid arthritis164


title: rheumatoid arthritis161


title: rheumatoid arthritis162


title: rheumatoid arthritis157


title: rheumatoid arthritis158


title: rheumatoid arthritis159


title: rheumatoid arthritis310


title: rheumatoid arthritis156


title: rheumatoid arthritis155


title: rheumatoid arthritis153


title: rheumatoid arthritis154


title: rheumatoid arthritis150


title: rheumatoid arthritis151


title: rheumatoid arthritis149


title: rheumatoid arthritis147


title: rheumatoid arthritis148


title: rheumatoid arthritis146


title: rheumatoid arthritis160


title: rheumatoid arthritis145


title: rheumatoid arthritis144


title: rheumatoid arthritis138


title: rheumatoid arthritis140


title: rheumatoid arthritis137


title: rheumatoid arthritis142


title: rheumatoid arthritis135


title: rheumatoid arthritis152


title: rheumatoid arthritis133


title: rheumatoid arthritis132


title: rheumatoid arthritis131


title: rheumatoid arthritis134


title: rheumatoid arthritis128


title: rheumatoid arthritis127


title: rheumatoid arthritis126


title: rheumatoid arthritis125


title: rheumatoid arthritis143


title: rheumatoid arthritis123


title: rheumatoid arthritis124


title: rheumatoid arthritis129


title: rheumatoid arthritis141


title: rheumatoid arthritis120


title: rheumatoid arthritis122


title: rheumatoid arthritis136


title: rheumatoid arthritis118


title: rheumatoid arthritis121


title: rheumatoid arthritis117


title: rheumatoid arthritis130


title: rheumatoid arthritis116


title: rheumatoid arthritis114


title: rheumatoid arthritis113


title: rheumatoid arthritis110


title: rheumatoid arthritis112


title: rheumatoid arthritis109


title: rheumatoid arthritis106


title: rheumatoid arthritis105


title: rheumatoid arthritis102


title: rheumatoid arthritis101


title: rheumatoid arthritis101A


title: rheumatoid arthritis103


title: rheumatoid arthritis100


title: rheumatoid arthritis98


title: rheumatoid arthritis99


title: rheumatoid arthritis97


title: rheumatoid arthritis90


title: rheumatoid arthritis89


title: rheumatoid arthritis94


title: rheumatoid arthritis95


title: rheumatoid arthritis96


title: rheumatoid arthritis86


title: rheumatoid arthritis85


title: rheumatoid arthritis104


title: rheumatoid arthritis71


title: rheumatoid arthritis81


title: rheumatoid arthritis84


title: rheumatoid arthritis82


title: rheumatoid arthritis74


title: rheumatoid arthritis70


title: rheumatoid arthritis67


title: rheumatoid arthritis68


title: rheumatoid arthritis66


title: rheumatoid arthritis64


title: rheumatoid arthritis53


title: rheumatoid arthritis54


title: rheumatoid arthritis52


title: rheumatoid arthritis56


title: rheumatoid arthritis55


title: rheumatoid arthritis57


title: rheumatoid arthritis40


title: rheumatoid arthritis51


title: rheumatoid arthritis49


title: rheumatoid arthritis50


title: rheumatoid arthritis37


title: rheumatoid arthritis91


title: rheumatoid arthritis39


title: rheumatoid arthritis69


title: rheumatoid arthritis38


title: rheumatoid arthritis65


title: rheumatoid arthritis36


title: rheumatoid arthritis35


title: rheumatoid arthritis33


title: rheumatoid arthritis34


title: rheumatoid arthritis87


title: rheumatoid arthritis16


title: rheumatoid arthritis15


title: rheumatoid arthritis19


title: rheumatoid arthritis13


title: rheumatoid arthritis46


title: rheumatoid arthritis12


title: rheumatoid arthritis10


title: rheumatoid arthritis11


title: rheumatoid arthritis9


title: rheumatoid arthritis6


title: rheumatoid arthritis7


title: rheumatoid arthritis17


title: rheumatoid arthritis2


title: rheumatoid arthritis3


title: rheumatoid arthritis4


title: rheumatoid arthritis1


title: health control313

source_name: health control


title: health control315


title: health control311


title: health control309


title: health control306


title: health control305


title: health control307


title: health control303


title: rheumatoid arthritis14


title: health control304


title: health control300


title: health control302


title: health control299


title: health control280


title: health control290


title: health control283


title: health control284


title: health control282


title: health control267


title: health control272


title: health control264


title: health control258


title: health control263


title: health control277


title: health control274


title: health control254


title: health control271


title: health control250


title: health control285


title: health control245


title: health control243A


title: health control246


title: health control249


title: health control243


title: health control242


title: health control248


title: health control241A


title: health control308


title: health control286


title: health control268


title: health control259


title: health control241


title: health control239


title: health control233


title: health control238


title: health control235


title: health control228


title: health control236


title: health control224


title: health control220


title: health control223


title: health control217


title: health control222


title: health control218


title: health control221


title: health control215


title: health control216


title: health control214


title: health control211


title: health control212


title: health control237


title: health control210


title: health control231


title: health control209


title: health control226


title: health control213


title: health control229


title: health control219


title: health control207


title: health control232


title: health control200


title: health control204


title: health control202


title: health control208


title: health control194


title: health control197


title: health control201


title: health control203


title: rheumatoid arthritis88


title: health control199


title: health control193


title: health control192


title: health control191


title: health control190


title: CHO 24h LLM

first: Rachael

last: Dippold

address: 1020 Locust St., JAH 222

department: Pathology, Anatomy, and Cell Biology

description: miRNA expression in pair-fed carbohydrate control liver

hyb_protocol: Hybrdization was performed according to the manufacturer's instructions as given in Agilent's miRNA Complete Labeling and Hybridization Kit

scan_protocol: Slides were scanned on an Agilent DNA Microarray Scanner (G2539A, Agilent) using the recommended settings for miRNA microarrays

data_processing: miRNA microarray data were extracted with Agilent Feature Extraction Software 10.7.3.1 (Agilent) and quantile normalized with GeneSpring GX version 11.0.2 (Agilent).  An EtOH LLM sample found to be a technical outlier was not used in further analysis and was replaced in analysis with the mean of the three remaining EtOH LLM samples.

source_name: pair-fed liver, t=0, paired to 24h PHx

label_protocol: RNA was labeled with Agilent's miRNA Complete Labeling and Hybridization Kit, according to the manufacturer's instructions

value: liver

tag: diet

value: carbohydrate

tag: partial hepatectomy time point

tag: animal identifiers within pooled samples

tag: time post surgery

value: before hepatectomy


title: health control206


title: health control188


title: health control189


title: EtOH 24h PHx

description: miRNA expression in chronic ethanol-fed liver 24h after PHx

source_name: ethanol-fed liver, 24h after PHx

value: ethanol

value: after hepatectomy


title: health control187


title: CHO 12h PHx

description: miRNA expression in pair-fed carbohydrate control liver 12h after PHx

source_name: pair-fed liver, 12h after PHx


title: EtOH 12h PHx

description: miRNA expression in chronic ethanol-fed liver 12h after PHx

source_name: ethanol-fed liver, 12h after PHx


title: CHO 12h LLM

source_name: pair-fed liver, t=0, paired to 12h PHx


title: health control185


title: health control186


title: health control184


title: EtOH 12h LLM

description: miRNA expression in chronic ethanol-fed liver

source_name: ethanol-fed liver, t=0, paired to 12h PHx


title: health control181


title: CHO 24h PHx

description: miRNA expression in pair-fed carbohydrate control liver 24h after PHx

source_name: pair-fed liver, 24h after PHx


title: health control180


title: CHO 6h PHx

description: miRNA expression in pair-fed carbohydrate control liver 6h after PHx

source_name: pair-fed liver, 6h after PHx


title: CHO 6h LLM

source_name: pair-fed liver, t=0, paired to 6h PHx


title: health control176


title: health control175


title: EtOH 6h LLM

source_name: ethanol-fed liver, t=0, paired to 6h PHx


title: health control178


title: health control174


title: CHO 1h LLM

source_name: pair-fed liver, t=0, paired to 1h PHx


title: CHO 1h PHx

description: miRNA expression in pair-fed carbohydrate control liver 1h after PHx

source_name: pair-fed liver, 1h after PHx


title: health control171


title: health control173


title: EtOH 1h LLM

source_name: ethanol-fed liver, t=0, paired to 1h PHx


title: EtOH 1h PHx

description: miRNA expression in chronic ethanol-fed liver 1h after PHx

source_name: ethanol-fed liver, 1h after PHx


title: EtOH 6h PHx

description: miRNA expression in chronic ethanol-fed liver 6h after PHx

source_name: ethanol-fed liver, 6h after PHx


title: health control156


title: health control154


title: health control153


title: health control152


title: health control157


title: health control158


title: health control161


title: health control163


title: health control169


title: health control159


title: health contro 164


title: health control165


title: health control167


title: health control166


title: CTIF siRNA treated Replication 2

city: Seoul

first: Kyoung Mi

last: Kim

address: Anam-Dong

department: School of Life sciences and biotechnology

country: South Korea

institute: Korea University

description: CTIF siRNA treated Replication 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3(Gene Expression Module v3.3.8).

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3  (Gene Expression Module v3.3.8). Array data were filtered by detection p-value < 0.05 in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe(13276 probes) signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between Control and Test samples was carried out using fold-change.

source_name: CTIF siRNA treated Replication 2

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (Lonza) containing 10% fetal bovine serum (Lonza).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cells were transiently transfected with the indicated in vitro-synthesized siRNA (Invitrogen)

value: HeLa


title: health control155

source_name: health control


title: CTIF siRNA treated Replication 1

description: CTIF siRNA treated Replication 1

source_name: CTIF siRNA treated Replication 1


title: hemocyte-ecoli-cy5-rep3

city: Madison

first: Bruce

middle: M

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
Sample name: Cy5.EH4
raw data file: 251642810047_BLOCK2.gpr

hyb_protocol: Microarrays were hybridized using the Agilent Gene Expression Hybridization Kit according to manufacturers’ instructions. Two color hybridizations were performed using 125 pmol (700-1200 ng) of each labelled aRNA. Once assembled, arrays were secured in Agilent hybridization chambers and hybridized for 17 hours at 65 ºC in an Agilent hybridization oven rotating at 10 rpm. Microarrays were washed according to the manufacturers’ instructions and scanned immediately.

scan_protocol: Fluorescence images were obtained from hybridized microarrays at 5 µm resolution using a GenePix 4000B array scanner (Molecular Devices, Foster City, CA) with the PMT gain settings automatically adjusted to a saturation tolerance level of 0.001%.

data_processing: Array features were quantified in GenePix Pro 6.1 (Axon Instruments) and low quality fluorescence spots were flagged and excluded from subsequent analyses. GAL file was modified such that each unique probe sequence is represented by single ProbeID starting with AEG. Extracted results were imported into R environment for transcript abundance analysis using the Bioconductor limma package (Smyth, 2004). “Normexp” method (Ritchie et al., 2007) was used for background correction with an offset of 50 for both channels to damp down the variability of the log ratios for low intensity spots while avoiding negative corrected intensities. The A (average intensities) and M (log-ratios) values were averaged among within-array replicate spots, followed by between-array normalization using the “Aquantile” method (Smyth and Speed, 2003) such that the A-values have the same empirical distribution across arrays but the M-values remain unchanged. Following the approach developed in limma for separate channel analysis of two-color microarrays, a linear model was fit to log-intensity data rather than log-ratio data.

organism: Aedes aegypti

source_name: E. coli-challenged, hemocyte, Cy5, replicate 3

label_protocol: To generate amino allyl-modified cDNA (aRNA) coupled with CyDye (GE Healthcare, Piscataway, NJ), Amino Allyl MessageAmp™ II aRNA Kit (Ambion AM1753, Austin, TX) was used according to the manufacturers’ instructions. The in vitro transcription was performed for 14 hours for all samples starting with 500 ng of total RNA. The quantity and purity of all resulting modified aRNA were measured on a NanoDrop spectrophotometer. The measured aRNA concentrations and aRNA size distributions were evaluated by denaturing gel electrophoresis using GelRed™ staining. In order to utilize dye-swap pairs for hybridization, each sample was coupled to both Cy3 and Cy5. The same amount of input aRNA (5-7 µg) was used for all samples within a biological replicate. The dye labeled aRNA concentration, pmol/µl dye and frequency of incorporation (FOI) were measured on a NanoDrop spectrophotometer. If the FOI of the labeled aRNA was outside of the desirable range the dye coupling reaction was repeated.

growth_protocol: The A. aegypti Liverpool strain was originally obtained from a colony from the University of London in 1977 and was reared as previously described (Christensen and Sutherland, 1984). Adult female mosquitoes were used for experimentation within 3 days of eclosion.

extract_protocol: Hemocyte total RNA was isolated from hemolymph immediately following collection. The isolation utilized a modification of a method originally developed for isolation of RNA from tissue culture cells (Peppel and Baglioni, 1990). Hemolymph was directly perfused into a 1.5 ml microfuge tube containing 150 µl 5X cell lysis buffer (10% SDS, 1 M Tris pH 7.5, 5 mM EDTA), mixed, and stored on ice. Once all the perfusate was collected, the solution was adjusted to 1X with HBSS and vortexed at medium speed for 5 seconds. Next, 0.3 volumes of ice-cold Solution 2 (42.9 g potassium acetate, 11.2 ml acetic acid, water to 100 ml) was added and the solution was vortexed at medium speed both upright and inverted for 10 seconds, centrifuged (14 k, 4 ºC) for 15 min. and the supernatant transferred to a new tube. The solution was then centrifuged (14 k, 4 ºC) for 15 min. and the supernatant transferred to a new tube. One half volume of buffered phenol and one half volume of chloroform/isoamyl 24:1 were added, mixed, and centrifuged (14 k, 4 ºC) for 10 min. and the supernatant transferred to a new tube. One volume of chloroform/isoamyl 24:1 was added, mixed, centrifuged (14 k, 4 ºC) for10 min. and the supernatant transferred to a new tube.  One volume of ice-cold isopropanol was added, mixed, and the RNA was precipitated overnight at -20 ºC. RNA was pelleted (14 k, 4 ºC) for 30 min. and the supernatant discarded. RNA was washed with 750 µl ice-cold 80% ethanol, centrifuged (14 k, 4 ºC) for 10 min. and the supernatant discarded. The RNA was then air dried and resuspended in 10 µl nuclease-free water. Carcass total RNA was isolated using the single-step acid guanidinium thiocyanate-phenol-chloroform extraction method (Chomczynski and Sacchi, 1987) and resuspended in nuclease-free water. The quantity and purity of all RNA samples were measured on a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA). The measured RNA concentrations and RNA integrity were verified by denaturing gel electrophoresis using GelRed™ (Phenix Research Products, Candler, NC) staining.

treatment_protocol: Bacteria used for intrathoracic injections were E. coli DH5α and M. luteus (University of Wisconsin-Madison). Cultures were grown to stationary phase in LB (Luria-Bertani) broth at 37°C, with shaking at 300 rpm. A pulled glass capillary needle containing inoculum (0.5 μl undiluted bacterial culture) was inserted through the cervical membrane between the head and the thorax and the fluid injected as previously described (Hillyer et al., 2004). For each biological replicate, 50 individuals were injected per condition or remained naïve, and survivorship at 24 hours following injection was greater than 90%. At 24 hours post bacterial challenge, hemolymph was collected from 40 individuals by volume displacement (perfusion) as previously described (Beerntsen and Christensen, 1990). A tear was made above the penultimate abdominal segment of the mosquito, which was then placed on a vacuum saddle. A pulled glass capillary needle, attached to a syringe containing 1X HBSS (Invitrogen, Carlsbad, CA), was inserted through the cervical membrane between the head and the thorax. HBSS was slowly injected, and only the first drop of perfusate from each mosquito was collected into a microfuge tube containing cell lysis buffer (10% SDS, 1 M Tris pH 7.5, 5 mM EDTA), mixed well, and kept on ice. Each remaining carcass after perfusion was collected in parallel to the hemolymph sample by immediately freezing it in a tube on dry ice. Carcasses were stored at -80°C.

tag: strain

value: Liverpool

value: hemolymph

tag: infection

value: E. coli

tag: replicate


title: carcass-naive-cy5-rep4

description:
Sample name: Cy5.NC4
raw data file: 251642810048_BLOCK1.gpr

source_name: Naive, carcass, Cy5, replicate 4

value: carcass

value: Naive


title: hemocyte-mlut-cy5-rep3

description:
Sample name: Cy5.MH4
raw data file: 251642810047_BLOCK4.gpr

source_name: M. luteus-challenged, hemocyte, Cy5, replicate 3

value: M. luteus


title: carcass-ecoli-cy5-rep2

description:
Sample name: Cy5.EC3
raw data file: 251642810043_BLOCK1.gpr

source_name: E. coli-challenged, carcass, Cy5, replicate 2


title: carcass-ecoli-cy5-rep3

description:
Sample name: Cy5.EC4
raw data file: 251642810047_BLOCK1.gpr

source_name: E. coli-challenged, carcass, Cy5, replicate 3


title: hemocyte-naive-cy5-rep3

description:
Sample name: Cy5.NH3
raw data file: 251642810044_BLOCK2.gpr

source_name: Naive, hemocyte, Cy5, replicate 3


title: hemocyte-ecoli-cy5-rep2

description:
Sample name: Cy5.EH3
raw data file: 251642810043_BLOCK2.gpr

source_name: E. coli-challenged, hemocyte, Cy5, replicate 2


title: carcass-mlut-cy5-rep2

description:
Sample name: Cy5.MC3
raw data file: 251642810043_BLOCK3.gpr

source_name: M. luteus-challenged, carcass, Cy5, replicate 2


title: carcass-mlut-cy5-rep3

description:
Sample name: Cy5.MC4
raw data file: 251642810047_BLOCK3.gpr

source_name: M. luteus-challenged, carcass, Cy5, replicate 3


title: carcass-naive-cy5-rep3

description:
Sample name: Cy5.NC3
raw data file: 251642810044_BLOCK1.gpr

source_name: Naive, carcass, Cy5, replicate 3


title: carcass-mlut-cy5-rep1

description:
Sample name: Cy5.MC2
raw data file: 251642810042_BLOCK4.gpr

source_name: M. luteus-challenged, carcass, Cy5, replicate 1


title: health control151


title: health control150


title: hemocyte-mlut-cy5-rep2

description:
Sample name: Cy5.MH3
raw data file: 251642810043_BLOCK4.gpr

source_name: M. luteus-challenged, hemocyte, Cy5, replicate 2


title: health control148


title: hemocyte-naive-cy5-rep4

description:
Sample name: Cy5.NH4
raw data file: 251642810048_BLOCK2.gpr


title: hemocyte-mlut-cy5-rep1

description:
Sample name: Cy5.MH2
raw data file: 251642810042_BLOCK2.gpr

source_name: M. luteus-challenged, hemocyte, Cy5, replicate 1


title: carcass-naive-cy5-rep2

description:
Sample name: Cy5.NC2
raw data file: 251642810042_BLOCK3.gpr

source_name: Naive, carcass, Cy5, replicate 2


title: health control147


title: health control146


title: health control145


title: health control144


title: health control143


title: health control142


title: health control141


title: health control140


title: hemocyte-naive-cy5-rep2

description:
Sample name: Cy5.NH2
raw data file: 251642810042_BLOCK1.gpr

source_name: Naive, hemocyte, Cy5, replicate 2


title: hemocyte-naive-cy5-rep1

description:
Sample name: Cy5.NH1
raw data file: 251642810038_BLOCK1.gpr

source_name: Naive, hemocyte, Cy5, replicate 1


title: carcass-ecoli-cy5-rep1

description:
Sample name: Cy5.EC1
raw data file: 251642810038_BLOCK4.gpr

source_name: E. coli-challenged, carcass, Cy5, replicate 1


title: health control139

source_name: health control


title: carcass-naive-cy5-rep1

description:
Sample name: Cy5.NC1
raw data file: 251642810038_BLOCK3.gpr

source_name: Naive, carcass, Cy5, replicate 1


title: health control136


title: hemocyte-naive-cy3-rep4

description:
Sample name: Cy3.NH4
raw data file: 251642810048_BLOCK1.gpr

source_name: Naive, hemocyte, Cy3, replicate 3


title: health control138


title: carcass-mlut-cy3-rep3

description:
Sample name: Cy3.MC4
raw data file: 251642810047_BLOCK4.gpr

source_name: M. luteus-challenged, carcass, Cy3, replicate 3


title: health control137


title: health control133


title: health control132


title: health control134


title: carcass-ecoli-cy3-rep3

description:
Sample name: Cy3.EC4
raw data file: 251642810047_BLOCK2.gpr

source_name: E. coli-challenged, carcass, Cy3, replicate 3


title: carcass-naive-cy3-rep3

description:
Sample name: Cy3.NC3
raw data file: 251642810044_BLOCK2.gpr

source_name: Naive, carcass, Cy3, replicate 3


title: health control131


title: hemocyte-mlut-cy3-rep3

description:
Sample name: Cy3.MH4
raw data file: 251642810047_BLOCK3.gpr

source_name: M. luteus-challenged, hemocyte, Cy3, replicate 3


title: hemocyte-ecoli-cy3-rep3

description:
Sample name: Cy3.EH4
raw data file: 251642810047_BLOCK1.gpr

source_name: E. coli-challenged, hemocyte, Cy3, replicate 3


title: health control135


title: health control129


title: hemocyte-ecoli-cy3-rep2

description:
Sample name: Cy3.EH3
raw data file: 251642810043_BLOCK1.gpr

source_name: E. coli-challenged, hemocyte, Cy3, replicate 2


title: health control128


title: hemocyte-mlut-cy3-rep2

description:
Sample name: Cy3.MH3
raw data file: 251642810043_BLOCK3.gpr

source_name: M. luteus-challenged, hemocyte, Cy3, replicate 2


title: carcass-mlut-cy3-rep2

description:
Sample name: Cy3.MC3
raw data file: 251642810043_BLOCK4.gpr

source_name: M. luteus-challenged, carcass, Cy3, replicate 2


title: health control127


title: health control126


title: hemocyte-mlut-cy3-rep1

description:
Sample name: Cy3.MH2
raw data file: 251642810042_BLOCK4.gpr

source_name: M. luteus-challenged, hemocyte, Cy3, replicate 1


title: carcass-ecoli-cy3-rep2

description:
Sample name: Cy3.EC3
raw data file: 251642810043_BLOCK2.gpr

source_name: E. coli-challenged, carcass, Cy3, replicate 2


title: hemocyte-naive-cy3-rep2

description:
Sample name: Cy3.NH2
raw data file: 251642810042_BLOCK3.gpr

source_name: Naive, hemocyte, Cy3, replicate 2


title: hemocyte-naive-cy3-rep3

description:
Sample name: Cy3.NH3
raw data file: 251642810044_BLOCK1.gpr


title: carcass-naive-cy3-rep2

description:
Sample name: Cy3.NC2
raw data file: 251642810042_BLOCK1.gpr

source_name: Naive, carcass, Cy3, replicate 2


title: health control130


title: carcass-mlut-cy3-rep1

description:
Sample name: Cy3.MC2
raw data file: 251642810042_BLOCK2.gpr

source_name: M. luteus-challenged, carcass, Cy3, replicate 1


title: hemocyte-ecoli-cy3-rep1

description:
Sample name: Cy3.EH1
raw data file: 251642810038_BLOCK4.gpr

source_name: E. coli-challenged, hemocyte, Cy3, replicate 1


title: health control125

source_name: health control


title: hemocyte-naive-cy3-rep1

description:
Sample name: Cy3.NH1
raw data file: 251642810038_BLOCK3.gpr

source_name: Naive, hemocyte, Cy3, replicate 1


title: health control124


title: carcass-naive-cy3-rep1

description:
Sample name: Cy3.NC1
raw data file: 251642810038_BLOCK1.gpr

source_name: Naive, carcass, Cy3, replicate 1


title: health control119


title: health control117


title: health control118


title: health control116


title: carcass-ecoli-cy3-rep1

description:
Sample name: Cy3.EC1
raw data file: 251642810038_BLOCK2.gpr

source_name: E. coli-challenged, carcass, Cy3, replicate 1


title: hemocyte-ecoli-cy5-rep1

description:
Sample name: Cy5.EH1
raw data file: 251642810038_BLOCK2.gpr

source_name: E. coli-challenged, hemocyte, Cy5, replicate 1


title: health control115


title: carcass-naive-cy3-rep4

description:
Sample name: Cy3.NC4
raw data file: 251642810048_BLOCK2.gpr

source_name: Naive, carcass, Cy3, replicate 4


title: health control114


title: health control121


title: health control113


title: health control122


title: health control110


title: health control112


title: health control105


title: health control108


title: health control106


title: health control107


title: health control109


title: health control103


title: health control104


title: health control111


title: ankylosing spondylitis57

source_name: ankylosing spondylitis


title: health control97


title: health control98


title: health control102


title: ankylosing spondylitis54


title: ankylosing spondylitis56


title: ankylosing spondylitis55


title: ankylosing spondylitis53


title: ankylosing spondylitis52


title: ankylosing spondylitis50


title: ankylosing spondylitis48


title: health control101


title: ankylosing spondylitis47


title: ankylosing spondylitis46


title: ankylosing spondylitis45


title: ankylosing spondylitis51


title: health control149


title: ankylosing spondylitis44


title: ankylosing spondylitis41


title: ankylosing spondylitis40


title: ankylosing spondylitis42


title: ankylosing spondylitis38


title: ankylosing spondylitis39


title: wild-type mouse exposed to cigarette smoke, biological replicate 2

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent 4X44K whole mouse gene expression array (014868). Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters.

source_name: Lung_wild-type_cigarette smoke exposure

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cigarette smoke exposure was performed in a stainless steel chamber (71 cm x 61 cm x 61 cm) using a smoking machine (Model TE-10, Teague Enterprises). The smoking machine puffs each 1R3F cigarette for 2 seconds, for a total of 9 puffs prior to ejection, at a flow rate of 1.05 l/min, providing a standard puff of 35 cm3. The smoke machine was adjusted to deliver 5 cigarettes at one time. Mice were exposed 5 days/week for 4 months.

tag: background strain

tag: genotype/variation

value: wild type

value: 12 weeks

value: whole lung


title: ankylosing spondylitis37

value: female

value: peripheral blood


title: wild-type mouse exposed to cigarette smoke, biological replicate 1

value: male


title: wild-type mouse exposed to cigarette smoke, biological replicate 4


title: wild-type mouse exposed to cigarette smoke, biological replicate 3


title: ankylosing spondylitis43


title: ankylosing spondylitis35


title: Rora mutant mouse exposed to cigarette smoke, biological rep 4

source_name: Lung_Rora mutant_cigarette smoke exposure

value: Rora (Retinoic acid related orphan receptor) mutant


title: Rora mutant mouse exposed to cigarette smoke, biological rep 2


title: Rora mutant mouse exposed to cigarette smoke, biological rep 1


title: wild-type mouse exposed to room air, biological replicate 3

source_name: Lung_wild-type_room air exposure


title: wild-type mouse exposed to room air, biological replicate 2


title: ankylosing spondylitis34


title: ankylosing spondylitis32


title: ankylosing spondylitis33


title: Rora mutant mouse exposed to cigarette smoke, biological rep 3


title: ankylosing spondylitis31


title: ankylosing spondylitis30


title: EA 2018_30

city: Shanghai

first: Shiyuan

last: Hu

address: 300# fenglin road

institute: Institute of plant physiology and ecology, Shanghai institutes for biological sciences, Chinese academy of sciences

hyb_protocol: The purified Cy3-labeled cRNA was hybridized to Agilent 60-mer oligo-chips (Agilent Technologies, Palo Alto, CA, USA) in a rotary oven (0.011×g, 60°C, 17 h).

scan_protocol: Agilent scan G2565BA; Resolution:5μm.

data_processing:
Feature extraction software provided by Agilent (version 7.5, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity
of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.

organism: Clostridium acetobutylicum EA 2018

source_name: Clostridium acetobutylicum EA 2018, P2 media 30 hours

label_protocol: Agilent oligonucleotide microarrays technology was used for monochromic analysis, in which probes (size: 60bp; three replicates for each ORF) from the two groups were labeled by incorporation of cyanine 3 (Cy3) (Agilent Technologies, Palo Alto, CA, USA).

extract_protocol: Total RNA was extracted and purified by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy cleanup kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s protocol. The total RNA yield was quantified by spectrophotometric analysis (NanoDrop Technology, Cambridge, UK) and the quality was verified by gel electrophoresis.

tag: fermentation time

tag: medium


title: ankylosing spondylitis29


title: ankylosing spondylitis27


title: ankylosing spondylitis26


title: EA 2018_24

source_name: Clostridium acetobutylicum EA 2018, P2 media 24 hours


title: ankylosing spondylitis28


title: wild-type mouse exposed to room air, biological replicate 4


title: ankylosing spondylitis23


title: EA 2018_13

source_name: Clostridium acetobutylicum EA 2018, P2 media 13 hours


title: ATCC 824_30

organism: Clostridium acetobutylicum ATCC 824

source_name: Clostridium acetobutylicum ATCC 824, P2 media 30 hours

value: ATCC 824


title: ankylosing spondylitis24


title: ATCC 824_21

source_name: Clostridium acetobutylicum ATCC 824, P2 media 21 hours


title: EA 2018_09

source_name: Clostridium acetobutylicum EA 2018, P2 media 9 hours


title: ankylosing spondylitis22


title: ankylosing spondylitis21


title: EA 2018_17

source_name: Clostridium acetobutylicum EA 2018, P2 media 17 hours


title: ATCC 824_17

source_name: Clostridium acetobutylicum ATCC 824, P2 media 17 hours


title: ankylosing spondylitis20


title: wild-type mouse exposed to room air, biological replicate 1


title: EA 2018_21

source_name: Clostridium acetobutylicum EA 2018, P2 media 21 hours


title: ATCC 824_24

source_name: Clostridium acetobutylicum ATCC 824, P2 media 24 hours


title: ATCC 824_09

source_name: Clostridium acetobutylicum ATCC 824, P2 media 9 hours


title: ankylosing spondylitis16


title: ankylosing spondylitis17


title: ankylosing spondylitis18


title: ankylosing spondylitis19


title: ATCC 824_13

source_name: Clostridium acetobutylicum ATCC 824, P2 media 13 hours


title: ankylosing spondylitis13


title: ankylosing spondylitis15


title: ankylosing spondylitis14


title: ankylosing spondylitis12


title: Wt Fetal liver cells engrafted in BM of an irradiated mice, biological rep2

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

description:
Gene expression data
WTB220+tg+_Rep2

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays  chip according to manufacturer instructions

scan_protocol: Chips  were scanned  using  a  GeneChip TM Scanner  3000

data_processing: The data were Normalized using RMA method by dCHIP, Limma and GCRMA. unsupervised clustering and other analyses been done in dCHIP

source_name: Bone marrow of C57Bl6 mice

label_protocol: RNA was labelled  and  amplified  according  to  Affymetrix TM GeneChip Expression  Analysis Technical Manual 2011

growth_protocol: Cells obtained fresh from the bone marrow of wild type mice either after transplanting Pax5KO or wild type fetal liver or without transplantation

extract_protocol: MicroRNeasy kit from qiagene has been used to extract the RNA according to manufacturer instruction

treatment_protocol: No treatment has been used

tag: tissue [transplant]

value: Adult 8-12weeks old

value: B220+ cells sorted out from bone marrow after 4 weeks


title: Tonsil 1

city: Marseille

first: Emilie

last: Mamessier

address: case 906

institute: CIML

description: Gene expression data from child's tonsil

hyb_protocol: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.intensity of each array was arbitrarily set to 100.

source_name: Tonsil from age-matched child

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Microarray Tissue Mini Kit  (Qiagen)

value: tonsil

value: M


title: ProB cell sorted from BM of B57Bl6 mice, biological rep1

description:
Gene expression data
ProB_Rep1

value: Bone marrow

tag: age

value: ProB cell


title: PSC27_BLEO_3, PSC27 cells treated with bleomycin, replicate #3

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid, extract, and LOWESS normalize data (default protocol). Spots of poor quality were replaced by NA (null) values.

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: cell line

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA was purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: PSC27 cells

tag: treatment group

value: treated with bleomycin


title: Tonsil 2

tag: gender


title: PreB cell sorted from BM of B57Bl6 mice, biological rep2

description:
Gene expression data
PreB_Rep1

tag: tissue

tag: cell type

value: PreB cell


title: CLP Ly6D- CLP cell sorted from BM of B57Bl6 mice, biological rep1

description:
Gene expression data
WT Ly6D-CLP_Rep1

value: CLP Ly6D- CLP cell


title: CLP Ly6D+ CLP cell sorted from BM of B57Bl6 mice, biological rep1

description:
Gene expression data
WT Ly6D+CLP_Rep1

value: CLP Ly6D+ CLP cell


title: PSC27_H2O2_3, PSC27 cells treated with hydrogen peroxide, replicate #3

value: treated with hydrogen peroxide


title: CLP Ly6D- CLP cell sorted from BM of B57Bl6 mice, biological rep2

description:
Gene expression data
WT Ly6D-CLP_Rep2


title: Wt Fetal liver cells engrafted in BM of an irradiated mice, biological rep1

description:
Gene expression data
WTB220+tg+_Rep1


title: ProB cell sorted from BM of B57Bl6 mice, biological rep2

description:
Gene expression data
ProB_Rep2


title: ankylosing spondylitis10

source_name: ankylosing spondylitis

value: female

value: peripheral blood


title: Wt Fetal liver cells engrafted in BM of an irradiated mice, biological rep3

description:
Gene expression data
WTB220+tg+_Rep3


title: P4-Blood

description: Gene expression data from IL10R2-/- patients with a DLBCL

source_name: peripheral blood from IL10R2-/- patient

value: blood


title: ankylosing spondylitis11

value: male


title: ankylosing spondylitis9


title: P3-Biopsy

source_name: lymph node biopsy from IL10R2-/- patient

value: lymph node


title: P3-Blood


title: PSC27_Pre_3, untreated PSC27 cells, replicate #3

value: untreated


title: P4-Biopsy


title: PreB cell sorted from BM of B57Bl6 mice, biological rep3

description:
Gene expression data
PreB_Rep2

value: Adult 8-12weeks old


title: Pax5KO Fetal liver cells engrafted in BM of an irradiated mice, biological rep2

description:
Gene expression data
PAXB220+tg+_Rep2

value: B220+ cells sorted out from bone marrow after 4 weeks


title: Pax5KO Fetal liver cells engrafted in BM of an irradiated mice, biological rep3

description:
Gene expression data
PAXB220+tg+_Rep3


title: ankylosing spondylitis6


title: ankylosing spondylitis5


title: ankylosing spondylitis3


title: PSC27_RAD_1, PSC27 cells treated with gamma-irradiation, replicate #2

value: treated with gamma-irradiation


title: PSC27_RAD_1, PSC27 cells treated with gamma-irradiation, replicate #3


title: ankylosing spondylitis2


title: PSC27_BLEO_2, PSC27 cells treated with bleomycin, replicate #2


title: 14269101 - Wild type 1 Repet2 vs SAIL 4 Repet2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level.

hyb_protocol: SAIL 4 Repet2 Cy5 / Wild type 1 Repet2 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.

source_name: SAIL 4 Repet2

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=Arabidopsis compost  hygrometry=glasshouse condition  Temperature=glasshouse condition  Light=LD glasshouse condition

extract_protocol: SAIL 4 Repet2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: SAIL 4

tag: ecotype

value: columbia

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:1.02

value: whole plant

source_name: Wild type 1 Repet2

extract_protocol: Wild type Repet2:10ug. (Qiagen_RNeasy.pdf)

value: Wild type


title: TLR2KO-BMDC-WT-OMV

city: Pasadena

first: Yue

last: Shen

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

hyb_protocol: Microarray (AgilentWhole Mouse Genome chip) hybridizations (65°C for 16 hours) and washes were performed with Agilent reagents following standard protocols.

scan_protocol: Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1.

data_processing:
The normalized/processed data are included in the LogRatio column of the Agilent Feature Extraction files.
Significant genes were selected based on p< 0.01 and fold change >2.0. For enrichment analysis of biological process ontology, probe lists were analyzed in DAVID (The Database for Annotation, Visualization and Integrated Discovery annotation tools (http://david.abcc.ncifcrf.gov/)) and selected based on p< 0.01.

source_name: TLR2-/- CD11c+ BMDCs treated with OMVs from wild type B.fragilis

label_protocol: RNA samples (1ug total RNA) from BMDCs were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).

growth_protocol: BMDCs were differentiated from BM in the presence of 20ng/ml GM-CSF in vitro, from which CD11c+ BMDC were sorted.

extract_protocol: RNA was collected either from BMDCs using RNeasy Mini Kit (Qiagen).

treatment_protocol: 10µg/ml OMVs from either wild type or ∆PSA B.fragilis were added into BMDC culture.

value: BMDC

tag: treatment protocol

value: OMVs from wild type B.fragilis

tag: length of treatment

source_name: vehicle treated TLR2-/- CD11c+ BMDCs

value: vehicle


title: ankylosing spondylitis1

value: female


title: TLR2KO-BMDC-∆PSA-OMV

source_name: TLR2-/- CD11c+ BMDCs treated with OMVs from ∆PSA B.fragilis

tag: strain

value: OMVs from ∆PSA B.fragilis


title: WT-BMDC-WT-OMV

source_name: wild type CD11c+ BMDCs treated with OMVs from wild type B.fragilis

value: wild type

source_name: vehicle treated wild type CD11c+ BMDCs


title: 14269102 - SAIL 4 Repet2 vs Wild type 1 Repet2

hyb_protocol: Wild type 1 Repet2 Cy5 / SAIL 4 Repet2 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: WT-BMDC-∆PSA-OMV

source_name: wild type CD11c+ BMDCs treated with OMVs from ∆PSA B.fragilis


title: PSC27_H2O2_1, PSC27 cells treated with hydrogen peroxide, replicate #1

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: PSC27 cells

value: treated with hydrogen peroxide


title: 14269067 - SAIL 1 Repet2 vs Wild type 1 Repet2

hyb_protocol: Wild type 1 Repet2 Cy5 / SAIL 1 Repet2 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.

source_name: SAIL 1 Repet2

extract_protocol: SAIL 1 Repet2:10ug. (Qiagen_RNeasy.pdf)

value: SAIL 1


title: 14269069 - SAIL 4 Repet1 vs Wild type 1 Repet1

hyb_protocol: Wild type 1 Repet1 Cy5 / SAIL 4 Repet1 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.

source_name: Wild type 1 Repet1

extract_protocol: Wild type Repet1:10ug. (Qiagen_RNeasy.pdf)

source_name: SAIL 4 Repet1

extract_protocol: SAIL 4 Repet1:10ug. (Qiagen_RNeasy.pdf)


title: 14269066 - Wild type 1 Repet2 vs SAIL 1 Repet2

hyb_protocol: SAIL 1 Repet2 Cy5 / Wild type 1 Repet2 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: 14269068 - Wild type 1 Repet1 vs SAIL 4 Repet1

hyb_protocol: SAIL 4 Repet1 Cy5 / Wild type 1 Repet1 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: PSC27_H2O2_2, PSC27 cells treated with hydrogen peroxide, replicate #2