title: CHC441T

description: Hepatocellular carcinoma


title: CHC469N

status: Public on Feb 27 2012

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: Paired normal sample for tumor CHC469T

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from 3 mm3 frozen samples from tumor and nontumoral liver tissue using high salt precipitation (as described in PMID: 3344216).

tag: sample

tag: tissue

value: Paired normal


title: Parkinson's Disease serum (PD vs. MS) sample 23

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

country: USA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum (PD vs. AD) results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

label: Alexa Fluor 647

molecule: other

label_protocol: standard Invitrogen protocol

extract_protocol: All serum (PD vs. AD) samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: age

tag: gender

value: Male

tag: mini mental state exam (mmse) score

tag: sample type

value: serum

tag: disease state

value: Parkinson's Disease


title: Parkinson's Disease serum (PD vs. MS) sample 20

value: Female


title: Parkinson's Disease serum (PD vs. MS) sample 22


title: CHC438T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma

tag: hbv infection

value: no

tag: hcv infection

tag: alcool intake

tag: age (year)

tag: gender (m=male; f=female)

value: M

tag: tumor diameter (mm)


title: Parkinson's Disease serum (PD vs. MS) sample 19


title: Parkinson's Disease serum (PD vs. MS) sample 21


title: CHC438N

description: Paired normal sample for tumor CHC438T


title: Parkinson's Disease serum (PD vs. MS) sample 18


title: CHC441N

description: Paired normal sample for tumor CHC441T


title: CHC437N

description: Paired normal sample for tumor CHC437T


title: CHC434T

description: Hepatocellular carcinoma

value: F


title: CHC437T

description: Hepatocellular carcinoma

value: yes


title: CHC405T

description: Hepatocellular carcinoma


title: CHC433N

description: Paired normal sample for tumor CHC433T


title: CHC405N

description: Paired normal sample for tumor CHC405T


title: CHC433T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 16

value: UNK


title: Parkinson's Disease serum (PD vs. MS) sample 14


title: CHC398T

description: Hepatocellular carcinoma


title: CHC430N

description: Paired normal sample for tumor CHC430T


title: CHC339T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 17


title: CHC399T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 12


title: Parkinson's Disease serum (PD vs. MS) sample 11


title: Parkinson's Disease serum (PD vs. MS) sample 10


title: CHC434N

description: Paired normal sample for tumor CHC434T


title: Parkinson's Disease serum (PD vs. MS) sample 9


title: CHC398N

description: Paired normal sample for tumor CHC398T


title: CHC335N

description: Paired normal sample for tumor CHC335T


title: CHC361N

description: Paired normal sample for tumor CHC361TB


title: CHC335T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 8


title: Parkinson's Disease serum (PD vs. MS) sample 15


title: CHC430T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 13


title: Parkinson's Disease serum (PD vs. MS) sample 7


title: CHC333T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 6


title: CHC361TB

description: Hepatocellular carcinoma


title: CHC339N

description: Paired normal sample for tumor CHC339T


title: Parkinson's Disease serum (PD vs. MS) sample 3


title: Parkinson's Disease serum (PD vs. MS) sample 5


title: CHC327T

description: Hepatocellular carcinoma


title: CHC326T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. MS) sample 2


title: Parkinson's Disease serum (PD vs. MS) sample 4


title: CHC333N

description: Paired normal sample for tumor CHC333T


title: Younger Control serum (PD vs. CY) sample 20

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

extract_protocol: All serum samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

value: Younger Control


title: CHC322T

description: Hepatocellular carcinoma


title: CHC402T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. CY) sample 18


title: Younger Control serum (PD vs. CY) sample 17


title: Younger Control serum (PD vs. CY) sample 14


title: CHC322N

description: Paired normal sample for tumor CHC322T


title: Younger Control serum (PD vs. CY) sample 15


title: Younger Control serum (PD vs. CY) sample 19


title: Younger Control serum (PD vs. CY) sample 13


title: Younger Control serum (PD vs. CY) sample 12


title: Parkinson's Disease serum (PD vs. MS) sample 1


title: CHC314T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. CY) sample 11


title: CHC309N

description: Paired normal sample for tumor CHC309T


title: Younger Control serum (PD vs. CY) sample 16


title: Younger Control serum (PD vs. CY) sample 10


title: Younger Control serum (PD vs. CY) sample 9


title: CHC313T

description: Hepatocellular carcinoma


title: CHC314N

description: Paired normal sample for tumor CHC314T


title: CHC307T

description: Hepatocellular carcinoma


title: CHC309T

description: Hepatocellular carcinoma


title: CHC304T

description: Hepatocellular carcinoma


title: CHC306N

description: Paired normal sample for tumor CHC306T


title: CHC304N

description: Paired normal sample for tumor CHC304T


title: CHC313N

description: Paired normal sample for tumor CHC313T


title: Younger Control serum (PD vs. CY) sample 8


title: Younger Control serum (PD vs. CY) sample 6


title: Younger Control serum (PD vs. CY) sample 4


title: Younger Control serum (PD vs. CY) sample 7


title: CHC317T

description: Hepatocellular carcinoma


title: CHC306T

description: Hepatocellular carcinoma


title: CHC301T

description: Hepatocellular carcinoma


title: CHC302N

description: Paired normal sample for tumor CHC302T


title: CHC258T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. CY) sample 5


title: CHC302T

description: Hepatocellular carcinoma


title: CHC258N

description: Paired normal sample for tumor CHC258T


title: CHC254T

description: Hepatocellular carcinoma


title: CHC307N

description: Paired normal sample for tumor CHC307T


title: CHC303N

description: Paired normal sample for tumor CHC303T


title: Younger Control serum (PD vs. CY) sample 1


title: Younger Control serum (PD vs. CY) sample 2


title: Parkinson's Disease serum (PD vs. CY) sample 27


title: CHC301N

description: Paired normal sample for tumor CHC301T


title: Parkinson's Disease serum (PD vs. CY) sample 28


title: Parkinson's Disease serum (PD vs. CY) sample 29


title: CHC326N

description: Paired normal sample for tumor CHC326T


title: Parkinson's Disease serum (PD vs. CY) sample 26


title: Parkinson's Disease serum (PD vs. CY) sample 25


title: Younger Control serum (PD vs. CY) sample 3


title: CHC303T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 23


title: Parkinson's Disease serum (PD vs. CY) sample 24


title: Parkinson's Disease serum (PD vs. CY) sample 20


title: Parkinson's Disease serum (PD vs. CY) sample 22


title: Parkinson's Disease serum (PD vs. CY) sample 21


title: CHC253T

description: Hepatocellular carcinoma


title: CHC252T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 19


title: CHC253N

description: Paired normal sample for tumor CHC253T


title: Parkinson's Disease serum (PD vs. CY) sample 18


title: Parkinson's Disease serum (PD vs. CY) sample 16


title: Parkinson's Disease serum (PD vs. CY) sample 14


title: Parkinson's Disease serum (PD vs. CY) sample 15


title: CHC245N

description: Paired normal sample for tumor CHC245T


title: CHC252N

description: Paired normal sample for tumor CHC252T


title: Parkinson's Disease serum (PD vs. CY) sample 17


title: Parkinson's Disease serum (PD vs. CY) sample 13


title: Parkinson's Disease serum (PD vs. CY) sample 12


title: CHC254N

description: Paired normal sample for tumor CHC254T


title: CHC241N

description: Paired normal sample for tumor CHC241T


title: Parkinson's Disease serum (PD vs. CY) sample 11


title: CHC245T

description: Hepatocellular carcinoma


title: CHC250T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 10


title: CHC239T

description: Hepatocellular carcinoma


title: CHC229T

description: Hepatocellular carcinoma


title: CHC241T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 9


title: CHC242T

description: Hepatocellular carcinoma


title: CHC235T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 8


title: Parkinson's Disease serum (PD vs. CY) sample 7


title: Parkinson's Disease serum (PD vs. CY) sample 6


title: Parkinson's Disease serum (PD vs. CY) sample 4


title: CHC230N

description: Paired normal sample for tumor CHC230T


title: CHC226N

description: Paired normal sample for tumor CHC226T


title: CHC230T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 2


title: CHC228N

description: Paired normal sample for tumor CHC228T


title: CHC228T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 5


title: CHC237N

description: Paired normal sample for tumor CHC237T


title: CHC229N

description: Paired normal sample for tumor CHC229T


title: CHC210N

description: Paired normal sample for tumor CHC210T


title: CHC226T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CY) sample 3


title: Parkinson's Disease serum (PD vs. CY) sample 1


title: Older Control serum (PD vs. CO) sample 20

value: Older Control


title: CHC210T

description: Hepatocellular carcinoma


title: CHC237T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 19


title: Older Control serum (PD vs. CO) sample 15


title: Older Control serum (PD vs. CO) sample 17


title: CHC211N

description: Paired normal sample for tumor CHC211T


title: Older Control serum (PD vs. CO) sample 14


title: CHC208T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 18


title: CHC206T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 13


title: Older Control serum (PD vs. CO) sample 16


title: CHC218T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 11


title: CHC203T

description: Hepatocellular carcinoma


title: CHC206N

description: Paired normal sample for tumor CHC206T


title: Older Control serum (PD vs. CO) sample 12


title: Older Control serum (PD vs. CO) sample 8


title: Older Control serum (PD vs. CO) sample 10


title: CHC205N

description: Paired normal sample for tumor CHC205T


title: CHC205T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 7


title: CHC196T

description: Hepatocellular carcinoma


title: CHC218N

description: Paired normal sample for tumor CHC218T


title: CHC197T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 6


title: Older Control serum (PD vs. CO) sample 9


title: CHC196N

description: Paired normal sample for tumor CHC196T


title: Older Control serum (PD vs. CO) sample 5


title: Older Control serum (PD vs. CO) sample 4


title: CHC208N

description: Paired normal sample for tumor CHC208T


title: CHC211T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. CO) sample 3


title: Older Control serum (PD vs. CO) sample 2


title: Older Control serum (PD vs. CO) sample 1


title: CHC191T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 28


title: Parkinson's Disease serum (PD vs. CO) sample 29


title: Parkinson's Disease serum (PD vs. CO) sample 26


title: CHC168T

description: Hepatocellular carcinoma


title: CHC168N

description: Paired normal sample for tumor CHC168T


title: CHC195N

description: Paired normal sample for tumor CHC195T


title: Parkinson's Disease serum (PD vs. CO) sample 25


title: CHC164T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 24


title: CHC158T

description: Hepatocellular carcinoma


title: CHC155N

description: Paired normal sample for tumor CHC155T


title: Parkinson's Disease serum (PD vs. CO) sample 23


title: CHC154T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 22


title: Parkinson's Disease serum (PD vs. CO) sample 21


title: CHC152T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 20


title: Parkinson's Disease serum (PD vs. CO) sample 18


title: Parkinson's Disease serum (PD vs. CO) sample 27


title: CHC141T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 19


title: Parkinson's Disease serum (PD vs. CO) sample 17


title: CHC152N

description: Paired normal sample for tumor CHC152T


title: CHC141N

description: Paired normal sample for tumor CHC141T


title: CHC137T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 16


title: CHC154N

description: Paired normal sample for tumor CHC154T


title: CHC129T

description: Hepatocellular carcinoma


title: CHC129N

description: Paired normal sample for tumor CHC129T


title: Parkinson's Disease serum (PD vs. CO) sample 14


title: CHC130N

description: Paired normal sample for tumor CHC130T


title: Parkinson's Disease serum (PD vs. CO) sample 15


title: Parkinson's Disease serum (PD vs. CO) sample 13


title: CHC130T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 12


title: CHC126N

description: Paired normal sample for tumor CHC126T


title: Parkinson's Disease serum (PD vs. CO) sample 11


title: Parkinson's Disease serum (PD vs. CO) sample 10


title: CHC1185T

description: Hepatocellular carcinoma


title: CHC121T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 8


title: CHC123T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 7


title: Parkinson's Disease serum (PD vs. CO) sample 9


title: CHC126T

description: Hepatocellular carcinoma


title: CHC121N

description: Paired normal sample for tumor CHC121T


title: CHC1196T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. CO) sample 6


title: Parkinson's Disease serum (PD vs. CO) sample 5


title: Parkinson's Disease serum (PD vs. CO) sample 4


title: Parkinson's Disease serum (PD vs. CO) sample 3


title: CHC115N

description: Paired normal sample for tumor CHC115T


title: CHC1185N

description: Paired normal sample for tumor CHC1185T


title: CHC203N

description: Paired normal sample for tumor CHC203T


title: CHC197N

description: Paired normal sample for tumor CHC197T


title: Parkinson's Disease serum (PD vs. CO) sample 1


title: Younger Control serum (PD vs. NDC) sample 12


title: CHC097T

description: Hepatocellular carcinoma


title: CHC100N

description: Paired normal sample for tumor CHC100T


title: Younger Control serum (PD vs. NDC) sample 11


title: CHC115T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. NDC) sample 10


title: CHC097N

description: Paired normal sample for tumor CHC097T


title: CHC1196N

description: Paired normal sample for tumor CHC1196T


title: CHC060N

description: Paired normal sample for tumor CHC060T


title: Younger Control serum (PD vs. NDC) sample 9


title: CHC191N

description: Paired normal sample for tumor CHC191T


title: Older Control serum (PD vs. NDC) sample 4


title: Parkinson's Disease serum (PD vs. CO) sample 2


title: CHC195T

description: Hepatocellular carcinoma


title: CHC081N

description: Paired normal sample for tumor CHC081T


title: CHC081T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. NDC) sample 16


title: CHC155T

description: Hepatocellular carcinoma


title: CHC158N

description: Paired normal sample for tumor CHC158T


title: CHC164N

description: Paired normal sample for tumor CHC164T


title: CHC100T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. NDC) sample 3


title: Younger Control serum (PD vs. NDC) sample 15


title: CHC046T

description: Hepatocellular carcinoma


title: CHC051N

description: Paired normal sample for tumor CHC051T


title: CHC059T

description: Hepatocellular carcinoma


title: Older Control serum (PD vs. NDC) sample 1


title: Younger Control serum (PD vs. NDC) sample 13


title: Older Control serum (PD vs. NDC) sample 6


title: Older Control serum (PD vs. NDC) sample 2


title: Older Control serum (PD vs. NDC) sample 8


title: Older Control serum (PD vs. NDC) sample 7


title: CHC060T

description: Hepatocellular carcinoma


title: Younger Control serum (PD vs. NDC) sample 8


title: CHC043N

description: Paired normal sample for tumor CHC043T


title: CHC051T

description: Hepatocellular carcinoma


title: CHC037N

description: Paired normal sample for tumor CHC037T


title: BC 47 N 581 TH17 PI

type: RNA

city: Napoli

first: Raffaele

last: De Palma

address: via Pansini 5

department: Clinical & Experimental Medicine

country: Italy

institute: Second University of Naples

description: BC 47 N 581 TH17 PI

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: Culture

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

growth_protocol: See Cosmi et al J Exp Med. 2008 Aug 4;205(8):1903-16

extract_protocol: RNA was prepared using the Trizol RNA Purification kit (Prodotti Gianni, Milano) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: Human Th17 cell clone

tag: donor

value: Healthy Donor UPN 47

tag: clone

value: clone 581

tag: treatment

value: stimulated with PMA and Ionomycin


title: Younger Control serum (PD vs. NDC) sample 20


title: CHC059N

description: Paired normal sample for tumor CHC059T

tag: sample

value: Paired normal


title: BC 47 N 523 TH17 PI

description: BC 47 N 523 TH17 PI

treatment_protocol: See Cosmi et al J Exp Med. 2008 Aug 4;205(8):1903-16

value: clone 523


title: Younger Control serum (PD vs. NDC) sample 14

value: Male

value: serum


title: CHC037T

description: Hepatocellular carcinoma

tag: tissue


title: CHC034T

description: Hepatocellular carcinoma


title: CHC034N

description: Paired normal sample for tumor CHC034T


title: CHC043T

description: Hepatocellular carcinoma


title: CHC032N

description: Paired normal sample for tumor CHC032T


title: Younger Control serum (PD vs. NDC) sample 7

tag: age

value: Female


title: CHC033T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma


title: BC 36 N 281 TH1 PI

description: BC 36 N 281 TH1 PI

value: Human Th1 cell clone

value: Healthy Donor UPN 36

value: clone 281


title: BC 36 N 281 TH1

description: BC 36 N 281 TH1

value: unstimulated


title: Older Control serum (PD vs. NDC) sample 5

tag: gender


title: CHC046N

description: Paired normal sample for tumor CHC046T


title: Younger Control serum (PD vs. NDC) sample 18

tag: mini mental state exam (mmse) score


title: Older Control serum (PD vs. NDC) sample 10

tag: sample type


title: Older Control serum (PD vs. NDC) sample 12

tag: disease state


title: BC 36 N 333 TH1

description: BC 36 N 333 TH1

value: clone 333


title: Younger Control serum (PD vs. NDC) sample 19

value: Younger Control


title: Older Control serum (PD vs. NDC) sample 9

value: Older Control


title: CHC031N

description: Paired normal sample for tumor CHC031T


title: Younger Control serum (PD vs. NDC) sample 17


title: BC 36 N 333 TH1 PI

description: BC 36 N 333 TH1 PI


title: Older Control serum (PD vs. NDC) sample 20


title: BC 47 N 581 TH17

description: BC 47 N 581 TH17

value: Human Th17 cell clone


title: U937-shGSK3A-Construct6-rep1

city: Boston

first: Kimberly

last: Stegmaier

state: MA

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

description:
U937 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: U937_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D06_596676.CEL

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing:
Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
The ABS_CALL values were generated in R with the MAS5 algorithm.

label: biotin

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.

extract_protocol: RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).

treatment_protocol: The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.

tag: cell line

tag: shRNA construct

value: GSK3A Construct 6


title: Older Control serum (PD vs. NDC) sample 11


title: Older Control serum (PD vs. NDC) sample 19


title: CHC033N

description: Paired normal sample for tumor CHC033T


title: BC 47 N 523 TH17

description: BC 47 N 523 TH17

value: Healthy Donor UPN 47


title: CHC018N

description: Paired normal sample for tumor CHC018T


title: Older Control serum (PD vs. NDC) sample 17


title: U937-shGSK3A-Construct6-rep2

description:
U937 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: U937_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D11_596666.CEL


title: expt. 2 mammary gland_four times daily milking 5 d_rep 3

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

department: Medicine

institute: University of Vermont

hyb_protocol: The biotinylated cRNAs were fragmented into 50- to 200-base fragments and then hybridized to GeneChip Bovine Genome Arrays for 16h at 45°C in a rotating Affymetrix GeneChip Hybridization Oven 320.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin on an automated Affymetrix GeneChip Fluidic Station F450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 2700 and the images quantified using Affymetrix GeneChip Operating Software.

data_processing: The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org).  Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003).  An alternative normalization method based on housekeeping genes did not significantly change the results.  The false discovery rate (FDR) was calculated by performing distinct permutations of the sample labels (Benjamini et al., 2001; Storey and Tibshirani, 2003; Storey et al., 2005).  In experiment 1, probe sets were considered differentially expressed when the signed fold change (4X vs. 2X) was ≥ 2, the P-value was < 0.05, and the FDR was < 0.20.  In experiment 2, probe sets were considered differentially expressed when the signed fold change was ≥ 1.2 and the P-value was < 0.10.  The less stringent signed fold change and P-value cutoffs for experiment 2 were used to allow for identification of genes that were differentially expressed in experiment 1 and may have been differentially expressed in experiment 2, but to a lesser degree.  To protect against false positives, the results of experiment 1 were used as a filter and only those genes differentially expressed in that experiment were investigated for differential expression in experiment 2.

organism: Bos taurus

source_name: bovine mammary gland, 4X milking

label_protocol: RNA amplification and microarray analysis for both experiments was performed at the University of Vermont microarray core facility using previously described protocols (Affymetrix, 2005-2006).  Briefly, 2 ug of total RNA from each tissue sample were reverse transcribed to the single stranded cDNA using a T7-oligo(dT) primer.  T4 DNA polymerase was used to synthesize double-stranded cDNA, which served as a template for in vitro transcription using T7 RNA polymerase to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated from each biopsy sample using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  The RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: Lactating mammary gland

value: 4X milking


title: Older Control serum (PD vs. NDC) sample 15


title: Older Control serum (PD vs. NDC) sample 18


title: expt. 2 mammary gland_control_rep7

source_name: bovine mammary gland, control

value: 2X milking


title: CHC018T

description: Hepatocellular carcinoma

tag: hbv infection

value: yes

tag: hcv infection

value: no

tag: alcool intake

value: F


title: Older Control serum (PD vs. NDC) sample 16

value: Male

value: serum


title: Younger Control serum (PD vs. NDC) sample 4


title: U937-shGSK3B-Construct2-rep2

description:
U937 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: U937_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D09_596680.CEL

value: GSK3B Construct 2


title: U937-shGSK3A-Construct5-rep1

description:
U937 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: U937_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D05_596632.CEL

value: GSK3A Construct 5


title: Older Control serum (PD vs. NDC) sample 13


title: U937-shGSK3A-Construct5-rep2

description:
U937 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: U937_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D10_596608.CEL


title: expt. 2 mammary gland_four times daily milking 5 d_rep 2


title: Younger Control serum (PD vs. NDC) sample 2

value: Female


title: Younger Control serum (PD vs. NDC) sample 1


title: U937-shGSK3B-Construct1-rep2

description:
U937 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: U937_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D08_596716.CEL

value: GSK3B Construct 1


title: Younger Control serum (PD vs. NDC) sample 3

value: Younger Control


title: U937-shGSK3B-Construct2-rep1

description:
U937 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: U937_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D04_596654.CEL


title: expt. 2 mammary gland_four times daily milking 5 d_rep 1


title: expt. 2 mammary gland_control_rep6


title: CHC031T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma

tag: age (year)

tag: gender (m=male; f=female)

value: M

tag: tumor diameter (mm)


title: Younger Control serum (PD vs. NDC) sample 6


title: CHC028T

description: Hepatocellular carcinoma


title: CHC032T

description: Hepatocellular carcinoma


title: expt. 2 mammary gland_control_rep5


title: Parkinson's Disease serum (PD vs. NDC) sample 29

value: Parkinson's Disease


title: U937-shControl-rep3

description:
U937 cell line infected with scrambled control shRNA, biological rep3
Sample name: U937_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D07_596720.CEL

value: Scrambled Control


title: U937-shGSK3B-Construct1-rep1

description:
U937 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: U937_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D03_596708.CEL


title: Younger Control serum (PD vs. NDC) sample 5


title: Older Control serum (PD vs. NDC) sample 14

value: Older Control


title: Parkinson's Disease serum (PD vs. NDC) sample 28


title: U937-shControl-rep2

description:
U937 cell line infected with scrambled control shRNA, biological rep2
Sample name: U937_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D02_596628.CEL


title: Parkinson's Disease serum (PD vs. NDC) sample 26


title: expt. 1 mammary gland_milk removed 3.5h_rep4

source_name: bovine mammary gland, 4X milking plus milk removal

value: Lactating mammary gland

value: 4X milking plus milk removal


title: Parkinson's Disease serum (PD vs. NDC) sample 27


title: CHC013N

description: Paired normal sample for tumor CHC013T

value: Paired normal


title: CHC013T

description: Hepatocellular carcinoma

value: no

value: yes


title: MOLM14-shGSK3A-Construct6-rep2

description:
MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: MOLM14_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C11_596726.CEL

value: GSK3A Construct 6


title: U937-shControl-rep1

description:
U937 cell line infected with scrambled control shRNA, biological rep1
Sample name: U937_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D01_596638.CEL


title: CHC014T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. NDC) sample 24

value: Male

value: serum


title: Parkinson's Disease serum (PD vs. NDC) sample 23


title: Parkinson's Disease serum (PD vs. NDC) sample 22


title: Parkinson's Disease serum (PD vs. NDC) sample 18


title: Parkinson's Disease serum (PD vs. NDC) sample 17


title: Parkinson's Disease serum (PD vs. NDC) sample 16

value: UNK


title: Parkinson's Disease serum (PD vs. NDC) sample 15


title: MOLM14-shGSK3A-Construct5-rep1

description:
MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: MOLM14_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C05_596604.CEL

value: GSK3A Construct 5


title: MOLM14-shGSK3B-Construct2-rep2

description:
MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: MOLM14_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C09_596558.CEL

value: GSK3B Construct 2


title: Parkinson's Disease serum (PD vs. NDC) sample 20

value: Female


title: expt. 1 mammary gland_milk removed 3.5h_rep3


title: Parkinson's Disease serum (PD vs. NDC) sample 25


title: Parkinson's Disease serum (PD vs. NDC) sample 14


title: MOLM14-shGSK3A-Construct6-rep1

description:
MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: MOLM14_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C06_596630.CEL


title: expt. 1 mammary gland_milk removed 3.5h_rep1


title: expt. 1 mammary gland_milk removed 3.5h_rep2


title: expt. 1 mammary gland_control_rep3

value: 2X milking


title: Parkinson's Disease serum (PD vs. NDC) sample 19


title: expt. 1 mammary gland_control_rep2


title: MOLM14-shGSK3B-Construct2-rep1

description:
MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: MOLM14_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C04_596732.CEL


title: expt. 1 mammary gland_control_rep4


title: Parkinson's Disease serum (PD vs. NDC) sample 13


title: CHC012T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma

value: M


title: expt. 1 mammary gland_control_rep1


title: CHC008N

description: Paired normal sample for tumor CHC008T


title: Parkinson's Disease serum (PD vs. NDC) sample 21

value: Parkinson's Disease


title: Parkinson's Disease serum (PD vs. NDC) sample 11


title: Parkinson's Disease serum (PD vs. NDC) sample 12


title: BALB/cCrl biological replicate 4

city: Edmonton

first: Heather

middle: E

last: McDermid

state: Alberta

address: University of Alberta

department: Biological Sciences

country: Canada

institute: University of Alberta

description:
BALBGT E304
Gene expression data from embryos 11-14 somites, before neural tube closure.

hyb_protocol: Hybridization and scanning of Affymetrix MOE430 2.0 chips were processed by The Center of Applied Genomics (Hospital for Sick Children, Toronto) in May of 2008. Protocol EukGE-WS2v5 with 15 ug cRNA.

scan_protocol: Hybridization and scanning of chips were processed by The Center of Applied Genomics (Hospital for Sick Children, Toronto) in May of 2008. Machine used was Affymetrix GeneChip Scanner 3000 with a 150 target scaling

data_processing: Two methods were used and reported. The first was normalization and analysis by the R/gcRMA statistical package, while the second more stringent analysis used Arraystar 4.0 (DNASTAR) with RMA for calculating signal strength and normalization.

organism: Mus musculus

source_name: BALB/cCrl

label_protocol: Labeled samples were prepared from 1 ug of RNA according to standard Affymetrix protocols

growth_protocol: All experiments were approved by the Animal Care and Use Committee of the University of Alberta. Mice were housed in a 14 hour light/10 hour dark cycle at 22±2 degrees Celsius and were fed Laboratory Rodent Diet 5001 (LabDiet), except for breeding females who received Mouse Diet 9F 5020 (LabDiet). Wildtype mouse strains used for this study were BALB/cAnNCrl (“BALB/cCrl”) (a University of Alberta colony originally from Charles River Laboratories) and FVB/N (Jackson Laboratories). Two congenic Cecr2Gt45Bic mouse mutant lines were previously generated by backcrossing the allele onto a BALB/cCrl or FVB/N genetic background for over 10 generations. BALB/cCrl Cecr2Gt45Bic heterozygotes were crossed to generate embryos for microarray analysis, while FVB/N Cecr2Gt45Bic homozygotes were crossed for embryo collection.

extract_protocol: Frozen embryos were thawed on ice and RNA extracted by the Qiagen Lipid RNA Extraction Kit (Invitrogen) following manufacturer's protocol and eluted in 30 ul DEPC-treated water. RNA quality and quantity tested via Agilent 2100 Bioanalyzer RNA 6000 Nano or Pico chips.

treatment_protocol: Embryos were collected through CO2 culling of pregnant dam followed by dissection of embryos in DEPC-PBS on ice. Embryos were photographed to assess progression of neural closure and somite number. Extraembryonic membranes were collected for genotyping and embryos flash frozen to -80 degrees awaiting RNA extraction.

value: Mouse embryo just prior to cranial neural closure

value: 11-14 somites

tag: strain background

value: BALB/cCrl

tag: genotype

value: Wildtype


title: MOLM14-shGSK3B-Construct1-rep1

description:
MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: MOLM14_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C03_596594.CEL

value: GSK3B Construct 1


title: LA+HYP_3

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

institute: Duke University

description: gene expression data from MCF7 cells

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Expression Console (Affymetrix) was used to generate the RMA file. Cluster 3.0 was used for hierarhical clustering.

source_name: MCF7 cells

label_protocol: Affymetrix standard protocol

growth_protocol: MCF7 breast cancer cells were cultured in DMEM (GIBCO-11995) supplemented with 10% fetal bovine serum and 1× antibiotics (penicillin, 10000UI/ml and streptomycin, 10000UI/ml).

extract_protocol: RNA were extracted by miRVana kits (Ambion) with standard protocol.

treatment_protocol: MCF7 cells were exposed to control condition (ambient air ~21% O2, no lactate and neutral pH), lactic acidosis (ambient air, 10 mM Lactate and pH 6.7), hypoxia (1% pO2, no lactate and neutral pH) and the combined lactic acidosis and hypoxia (1% pO2, 10 mM Lactate and pH 6.7) condition for 24 hours.

tag: growth conditions

value: media with 10 mM lactic acid (pH 6.7) in hypoxia (1% pO2)


title: CHC008T

description: Hepatocellular carcinoma

tag: sample

tag: tissue

value: yes

value: no

value: F


title: LA+HYP_2

description: gene expression data from MCF7 cells


title: Parkinson's Disease serum (PD vs. NDC) sample 6

tag: age

tag: gender

value: Male

value: serum


title: Parkinson's Disease serum (PD vs. NDC) sample 5

tag: mini mental state exam (mmse) score

tag: sample type


title: Parkinson's Disease serum (PD vs. NDC) sample 9

tag: disease state


title: Parkinson's Disease serum (PD vs. NDC) sample 10


title: Parkinson's Disease serum (PD vs. NDC) sample 4


title: MOLM14-shControl-rep3

description:
MOLM-14 cell line infected with scrambled control shRNA, biological rep3
Sample name: MOLM14_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C07_596588.CEL

tag: cell line

tag: shRNA construct

value: Scrambled Control


title: BALB/cCrl biological replicate 2

description:
BALBGT E254
Gene expression data from embryos 11-14 somites, before neural tube closure.

value: Female


title: Parkinson's Disease serum (PD vs. NDC) sample 8


title: LA+HYP_1

description: gene expression data from MCF7 cells


title: MOLM14-shControl-rep2

description:
MOLM-14 cell line infected with scrambled control shRNA, biological rep2
Sample name: MOLM14_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C02_596656.CEL


title: LA_3

description: gene expression data from MCF7 cells

value: media with 10 mM lactic acid (pH 6.7)


title: MOLM14-shGSK3A-Construct5-rep2

description:
MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: MOLM14_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C10_596704.CEL

value: GSK3A Construct 5


title: BALB/cCrl biological replicate 3

description:
BALBGT E316
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: Cecr2Gt45Bic BALB/cCrl biological replicate 4

description:
BALBGT E181
Gene expression data from embryos 11-14 somites, before neural tube closure.

source_name: Cecr2Gt45Bic BALB/cCrl


title: MOLM14-shGSK3B-Construct1-rep2

description:
MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: MOLM14_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C08_596612.CEL


title: Cecr2Gt45Bic BALB/cCrl biological replicate 1

description:
BALBGT E237
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: MOLM14-shControl-rep1

description:
MOLM-14 cell line infected with scrambled control shRNA, biological rep1
Sample name: MOLM14_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C01_596616.CEL


title: Cecr2Gt45Bic BALB/cCrl biological replicate 3

description:
BALBGT E189
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: HYP_2

description: gene expression data from MCF7 cells

value: control media in hypoxia (1% pO2)


title: HYP_1

description: gene expression data from MCF7 cells


title: Parkinson's Disease serum (PD vs. NDC) sample 7

value: Parkinson's Disease


title: BALB/cCrl biological replicate 1

description:
BALBGT E180
Gene expression data from embryos 11-14 somites, before neural tube closure.

value: Mouse embryo just prior to cranial neural closure


title: Parkinson's Disease serum (PD vs. NDC) sample 3

value: UNK


title: Cecr2Gt45Bic BALB/cCrl biological replicate 2

description:
BALBGT E264
Gene expression data from embryos 11-14 somites, before neural tube closure.

value: 11-14 somites

value: BALB/cCrl


title: THP1-shGSK3A-Construct6-rep1

description:
THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: THP1_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B06_596642.CEL

value: GSK3A Construct 6


title: LA_2

description: gene expression data from MCF7 cells


title: HYP_3

description: gene expression data from MCF7 cells


title: Parkinson's Disease serum (PD vs. NDC) sample 1


title: LA_1

description: gene expression data from MCF7 cells


title: Parkinson's Disease serum (PD vs. NDC) sample 2


title: THP1-shGSK3A-Construct6-rep2

description:
THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: THP1_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B11_596554.CEL


title: THP1-shGSK3A-Construct5-rep2

description:
THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: THP1_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B10_596686.CEL


title: THP1-shGSK3B-Construct1-rep2

description:
THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: THP1_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B08_596590.CEL

value: GSK3B Construct 1


title: Ctrl_3

description: gene expression data from MCF7 cells

value: control media


title: THP1-shGSK3B-Construct1-rep1

description:
THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: THP1_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B03_596576.CEL


title: Oct4 Lif+ 24h, rep2

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Oct4 Lif+ 24h

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data were extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.

The data were normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 18 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.

More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Oct4 Lif+ 24h

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit, according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using Trizol according to Invitrogen's protocol.  Cells were pelleted and 1mL Trizol reagent was added to the cell pellet.

treatment_protocol: Oct4 (5) cell line. These cells were plated at 200000 cells/75 cm flask in the presence of LIF. 24h after plating, total RNA was extracted.

tag: strain

value: derived from ZHBTc4

tag: cell type

value: embryonic stem (ES) cells

tag: lif

value: present

tag: time

tag: genetic modification

value: gene knock-in

tag: individual identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using the Agilent Fluorescent Linear Amplification kit, according to the manufacturer's instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using the Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts.

value: reference


title: THP1-shGSK3B-Construct2-rep2

description:
THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: THP1_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B09_596702.CEL

value: GSK3B Construct 2


title: ZHBTc4 Lif- 120h, rep2

description: ZHBTc4 Lif- 120h

source_name: ZHBTc4 Lif- 120h

treatment_protocol: ZHBTc4 cell line. These cells were plated at 200000 cells/75 cm flask in the presence of LIF. 24h after plating, medium was changed to the no LIF condition, and changed again after 2 days of LIF withdrawal. After 5 days of LIF withdrawal, total RNA was extracted.

value: absent


title: Ctrl_1

description: gene expression data from MCF7 cells


title: THP1-shControl-rep3

description:
THP-1 cell line infected with scrambled control shRNA, biological rep3
Sample name: THP1_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B07_596722.CEL

value: Scrambled Control


title: THP1-shGSK3A-Construct5-rep1

description:
THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: THP1_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B05_596730.CEL

value: GSK3A Construct 5


title: Oct4 Lif+ 24h, rep1

description: Oct4 Lif+ 24h

treatment_protocol: Oct4 (4) cell line. These cells were plated at 200000 cells/75 cm flask in the presence of LIF. 24h after plating, total RNA was extracted.


title: THP1-shGSK3B-Construct2-rep1

description:
THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: THP1_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B04_596688.CEL


title: Cecr2Gt45Bic FVB/N biological replicate 4

description:
FVBGT E39
Gene expression data from embryos 11-14 somites, before neural tube closure.

source_name: Cecr2Gt45Bic FVB/N

tag: strain background

value: FVB/N

tag: genotype

value: Female


title: ZHBTc4 Lif- 48h, rep2

description: ZHBTc4 Lif- 48h

source_name: ZHBTc4 Lif- 48h

treatment_protocol: ZHBTc4 cell line. These cells were plated at 200000 cells/75 cm flask in the presence of LIF. 24h after plating, medium was changed to the minus LIF condition. Total RNA was extracted 48h after LIF withdrawal.


title: Ctrl_2

description: gene expression data from MCF7 cells

tag: growth conditions


title: FVB/N biological replicate 4

description:
FVB E137
Gene expression data from embryos 11-14 somites, before neural tube closure.

source_name: FVB/N

tag: tissue

value: Mouse embryo just prior to cranial neural closure

value: Wildtype


title: Cecr2Gt45Bic FVB/N biological replicate 2

description:
FVBGT E44
Gene expression data from embryos 11-14 somites, before neural tube closure.

tag: age

value: 11-14 somites


title: FVB/N biological replicate 3

description:
FVB E72
Gene expression data from embryos 11-14 somites, before neural tube closure.

tag: gender


title: Cecr2Gt45Bic FVB/N biological replicate 1

description:
FVBGT E50
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: Cecr2Gt45Bic FVB/N biological replicate 3

description:
FVBGT E60
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: THP1-shControl-rep2

description:
THP-1 cell line infected with scrambled control shRNA, biological rep2
Sample name: THP1_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B02_596660.CEL


title: FVB/N biological replicate 2

description:
FVB E59
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: FVB/N biological replicate 1

description:
FVB E67
Gene expression data from embryos 11-14 somites, before neural tube closure.


title: ZHBTc4 Lif+ 24h, rep1

description: ZHBTc4 Lif+ 24h

source_name: ZHBTc4 Lif+ 24h

treatment_protocol: ZHBTc4 cell line. These cells were plated at 200000 cells/75 cm flask in the presence of LIF. 24h after plating, total RNA was extracted.


title: Y73 mock inoculation at 24 hpi, biological rep3

city: Hangzhou

first: Xuming

last: Wang

state: Zhejiang

address: Shiqiao Road 198#

department: Institute of Virology and Biotechnology

country: China

institute: Zhejiang Academy of Agricultural Sciences

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ºC on GeneChip Rice Genome Array. GeneChips were then washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The data were analyzed with Agilent Genesping 11 using default analysis settings and global scaling as normalization method.

organism: Oryza sativa

source_name: japonica rice(Y73) leaf  mock inoculation with H2O 24 hpi

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

growth_protocol: Rice seeds were germinated at 37 ºC for 1 d. After germination, the plants were grown in a growth room under a photosynthetic photon flux density of approximately 200 μmol photons m-2s-1 with a 12 h light (32 ºC)/12 h dark (28 ºC) photoperiod. Humidity was controlled at 60%.

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

treatment_protocol: For the evaluation of bacterial blight resistance, rice plants at the tillering stage were inoculated with Philippine Xoo strains by the leaf-clipping method, plants inoculated with Philippine Xoo strain PXO341 (race 10) were used for RNA extraction from three independent treatments.

value: leaf

value: japonica cv Y73

value: max tilling stage

tag: infection

value: control


title: THP1-shControl-rep1

description:
THP-1 cell line infected with scrambled control shRNA, biological rep1
Sample name: THP1_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B01_596662.CEL


title: ZHBTc4 Lif- 120h, rep1

description: ZHBTc4 Lif- 120h

value: embryonic stem (ES) cells

tag: sample type


title: ZHBTc4 Lif- 48h, rep1

description: ZHBTc4 Lif- 48h


title: HL60-shGSK3A-Construct6-rep1

description:
HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: HL60_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A06_596738.CEL

value: GSK3A Construct 6


title: HL60-shGSK3A-Construct5-rep2

description:
HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: HL60_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A10_596670.CEL


title: Y73 mock inoculation at 24 hpi, biological rep2


title: ZHBTc4 Lif+ 24h, rep2

description: ZHBTc4 Lif+ 24h

value: present

value: gene knock-in


title: Oct4 Lif- 120h, rep1

description: Oct4 Lif- 120h

source_name: Oct4 Lif- 120h

treatment_protocol: Cells were derived from the ZHBTc4 cell line, grown in the presence of tetracycline to switch off transcription from the tet-regulatable oct4 transgene and electroporated with the moct4 construct. The cell line derived is under puromycin selection. These cells were plated at 200000 cells/75 cm flask in the presence of LIF, TET, and puromycin (2ug/ml). Medium was changed at 24 h after plating to the minus LIF condition. Medium was changed again at 72h. Total RNA was extracted 120h after LIF withdrawal.

value: derived from ZHBTc4

value: random integration by electroporation

value: reference


title: Y73 Xoo inoculation at 24 hpi, biological rep3

source_name: japonica rice(Y73) leaf inoculated with Xoo 24 hpi

value: Xanthomonas oryzae pv. Oryzae (Xoo)-inoculation


title: HL60-shGSK3A-Construct6-rep2

description:
HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: HL60_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A11_596684.CEL


title: Y73 Xoo inoculation at 24 hpi, biological rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: Y73 Xoo inoculation at 24 hpi, biological rep1


title: Y73 mock inoculation at 24 hpi, biological rep1


title: Oct4 VP2 Lif- 120h, rep1

description: Oct4 VP2 Lif- 120h

source_name: Oct4 VP2 Lif- 120h

treatment_protocol: Cells were derived from the ZHBTc4 cell line, grown in the presence of tetracycline to switch off transcription from the tet-regulatable oct4 transgene and electroporated with the moct4-vp16 construct. The cell line derived is under puromycin selection. These cells were plated at 250000 cells/75 cm flask in the presence of LIF, TET, and puromycin (2ug/ml). Medium was changed at 24 h after plating to the minus LIF condition. Medium was changed again at 72h. Total RNA was extracted 120h after LIF withdrawal.

value: absent


title: Oct4 VP2 Lif- 120h, rep2

description: Oct4 VP2 Lif- 120h


title: Oct4 Lif- 120h, rep2

description: Oct4 Lif- 120h


title: HL60-shGSK3A-Construct5-rep1

description:
HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: HL60_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A05_596562.CEL

value: GSK3A Construct 5


title: 50 pg Universal Human Reference RNA + T30 2-phase PCR rep2

city: San Diego

first: Craig

last: April

state: CA

address: 9885 Towne Centre Drive

institute: Illumina, Inc.

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was analyzed using GenomeStudio v2.0

label_protocol: Standard Illumina labelling protocol

extract_protocol: WA09 (H9) RNA was extracted using TRIzol

tag: group

value: low input

value: 50 pg Universal Human Reference RNA + H9 T30 2-phase PCR


title: HL60-shGSK3B-Construct2-rep1

description:
HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: HL60_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A04_596674.CEL

tag: cell line

value: GSK3B Construct 2


title: 50 pg Universal Human Reference RNA + T30 2-phase PCR rep1

description: replicate 1


title: HL60-shGSK3B-Construct2-rep2

description:
HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: HL60_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A09_596622.CEL

tag: shRNA construct


title: 50 pg Universal Human Reference RNA + T30 1-phase PCR rep2

description: replicate 2

value: 50 pg Universal Human Reference RNA + H9 T30 1-phase PCR


title: HL60-shGSK3B-Construct1-rep2

description:
HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: HL60_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A08_596694.CEL

value: GSK3B Construct 1


title: Oct4 Lif- 48h, rep2

description: Oct4 Lif- 48h

source_name: Oct4 Lif- 48h

treatment_protocol: Cells were derived from the ZHBTc4 cell line, grown in the presence of tetracycline to switch off transcription from the tet-regulatable oct4 transgene and electroporated with the moct4 construct. The cell line derived is under puromycin selection. These cells were plated at 200000 cells/75 cm flask in the presence of LIF, TET, and puromycin (2ug/ml). Medium was changed at 24 h after plating to the minus LIF condition. Total RNA was extracted 48h after LIF withdrawal.

tag: strain


title: HL60-shGSK3B-Construct1-rep1

description:
HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: HL60_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A03_596652.CEL


title: 50 pg Universal Human Reference RNA + T30 1-phase PCR rep1

description: replicate 1


title: Oct4 Lif- 48h, rep1

description: Oct4 Lif- 48h

tag: cell type


title: Oct4 VP2 Lif- 48h, rep1

description: Oct4 VP2 Lif- 48h

source_name: Oct4 VP2 Lif- 48h

treatment_protocol: Cells were derived from the ZHBTc4 cell line, grown in the presence of tetracycline to switch off transcription from the tet-regulatable oct4 transgene and electroporated with the moct4-vp16 construct. The cell line derived is under puromycin selection. These cells were plated at 250000 cells/75 cm flask in the presence of LIF, TET, and puromycin (2ug/ml). The medium was changed at 24 h after plating to the minus LIF condition. Total RNA was extracted 48h after LIF withdrawal.

tag: lif


title: Oct4 VP2 Lif+ 24h, rep1

description: Oct4 VP2 Lif+ 24h

source_name: Oct4 VP2 Lif+ 24h

treatment_protocol: Cells were derived from the ZHBTc4 cell line, grown in the presence of tetracycline to switch off transcription from the tet-regulatable oct4 transgene and electroporated with the oct4-vp16 construct. The cell line derived is under puromycin selection. These cells were plated at 250000 cells/75 cm flask in the presence of LIF, TET, and puromycin (2ug/ml). Total RNA was extracted 24h after plating.

tag: time


title: 50 pg H9 T30+N9 1-phase PCR rep2

description: replicate 2

source_name: 50 pg H9 T30+N9 1-phase PCR

value: 50 pg H9 T30+N9 1-phase PCR

value: H9 sublcone T30


title: Oct4 VP2 Lif+ 24h, rep2

description: Oct4 VP2 Lif+ 24h

value: embryonic stem (ES) cells

tag: genetic modification


title: 50 pg H9 T30+N6 1-phase PCR rep1

description: replicate 1

source_name: 50 pg H9 T30+N6 1-phase PCR

value: 50 pg H9 T30+N6 1-phase PCR


title: HL60-shControl-rep2

description:
HL-60 cell line infected with scrambled control shRNA, biological rep2
Sample name: HL60_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A02_596668.CEL

value: Scrambled Control


title: 50 pg H9 T30+N9 1-phase PCR rep1

description: replicate 1


title: HL60-shControl-rep3

description:
HL-60 cell line infected with scrambled control shRNA, biological rep3
Sample name: HL60_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A07_596570.CEL


title: HL60-shControl-rep1

description:
HL-60 cell line infected with scrambled control shRNA, biological rep1
Sample name: HL60_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A01_596706.CEL


title: 1 ng Universal Human Reference RNA + T30 1-phase PCR

description: replicate 1

value: high input

value: 1 ng Universal Human Reference RNA + H9 T30 1-phase PCR


title: 6p (43831002)

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Microarray scanning, data acquisition and identification of probe sets showing a significant difference (p=0.05) in expression level between the two culture conditions considered were performed by Roche-NimbleGen as in previous studies (Samolski et al., 2009). Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Background correction, normalization, and expression analysis from the data were performed using the RMA algorithm (Irizarry et al., 2003). The significance of the differential expression under each two conditions compared was determined by statistical analysis performed with the T-test algorithm (Baldi and Long, 2001). Transcripts showing significantly differential expression (FC≥2) were annotated Gene Ontology (GO) terms, and analyzed using the Genespring GX program. All the values (34,149) unfiltered are provided in this record.

organism: Trichoderma reesei

source_name: mycelium

label_protocol: High quality purified RNAs were submitted to Roche-NimbleGene (40 μg per 3-microarray set) where cDNAs were synthesized, amplified and labeled and then used for subsequent hybridization. Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Tomato-Trichoderma spp. hydroponic cultures were used. First, tomato seeds were placed inside phytatray II boxes (Sigma) (30 seeds per box), on a sterile gauze sheet over a sterile stainless steel screen, which held them 1 cm above 100 mL of MS medium, and maintained at 24ºC in a plant growth chamber with controlled light and humidity conditions as described above, for 2 weeks. Spores of Trichoderma spp. (107 spores) were used to inoculate 250-mL flasks containing 100 mL of minimal medium (MM, Penttilä et al., 1987), supplemented with 2% glucose. Each strain (T6, T7, T34 and T87) was was indiviually cultured at 28°C and 200 rpm in darkness for 48 h. Then, mycelia were harvested by filtration, washed with sterile water, and use to inoculate phytatray II boxes that contained 2-weeks old tomato plants.  Tomato-Trichoderma hydroponic cultures were maintained at 25°C and 80 rpm for 20 h. Finally, Trichoderma mycelia were harvested by filtration (the mycelium on the plant roots was recovered with a direct water jet), washed twice with sterile distilled water, frozen in liquid nitrogen and lyophilized. In parallel, Trichoderma strains were cultured without tomato plants.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Freeze-dried mycelia from Trichoderma spp.-tomato plant interactions and Trichoderma spp. cultures were ground in liquid nitrogen using a mortar and pestle.

tag: culture conditions

value: Trichoderma T6-Tomato plant

value: mycelium


title: 50 pg H9 T30+N6 1-phase PCR rep2

description: replicate 2


title: Oct4 VP2 Lif- 48h, rep2

description: Oct4 VP2 Lif- 48h

value: derived from ZHBTc4

value: random integration by electroporation

tag: individual identifier

value: reference


title: 6p (43821702)


title: 6 (43830802)

value: Trichoderma T6


title: 1 ng H9 T30 1-phase PCR rep2

description: replicate 2

source_name: 1 ng H9 T30 1-phase PCR

value: 1 ng H9 T30 1-phase PCR


title: 6p (43831502)


title: 87p (43831702)

organism: Trichoderma virens

value: Trichoderma T87-Tomato plant


title: 87p (43809102)


title: F-CA-52 rep2

city: Cleveland

first: Gurkan

last: Bebek

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Univ.

hyb_protocol: All samples were hybridized to the Illumina Sentrix Human-6_v3 Expression BeadChip by manufacturer defined protocols.

scan_protocol: Illumina standard protocols are followed.

data_processing: Normalization is done using average normalization algorithm of BeadStudio Gene Expression Module v3.4 (Illumina Inc.).

source_name: Stromal cells cultured from tumors; passages 4-5

growth_protocol: Cells are grown as previously described in Peehl et al. (2000).

extract_protocol: Total RNAs were extracted from semi-confluent cells (passages 4-5) one day after feeding fresh medium using RNeasy Mini Kit (Qiagen) is used according to the manufacturer’s instructions and treated with TURBO DNA-free kit (Ambion).

value: prostate cancer stroma


title: 6 (43809202)


title: 1 ng H9 T30 1-phase PCR rep1

description: replicate 1


title: 6 (43809002)


title: F-CA-67 rep2

label_protocol: Illumina standard protocols are followed.


title: 87p (43808502)


title: F-CA-39 rep2


title: CD20- RPMI-8226 REPLICATE 3

first: Teresa

last: Paíno

address: Campus Miguel de Unamuno

institute: Centro de investigación del cáncer

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Gene 1.0 ST array (Affymetrix), after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: Expression value for each probe set was calculated using dCHip program that normalize arrays using probes of 'Invariant set' and 'Running median' smoothing and obtains expression/signal values using 'Model-based expression' modelling method and '5th percentile of region (PM-only)' as background subtraction

label: BIOTIN

source_name: RPMI-8226 MULTIPLE MYELOMA CELL LINE

label_protocol: Labeling were performed according to protocols from Affymetrix. Briefly,100 ng of total RNA was labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

value: NEGATIVE


title: 87 (43831902)

value: Trichoderma T87


title: CD20- RPMI-8226 REPLICATE 2


title: 87 (43830702)


title: HUVEC_control antisense_48hr_rep3

city: London

first: Graeme

middle: Miles

last: Birdsey

address: Hammersmith Hospital, Du Cane Road

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

hyb_protocol: 15µg of fragmented cRNA was made up into a hybridisation cocktail in accordance with the Affymetrix technical manual corresponding to a 49 format (standard)/64 format array. The hybridisation cocktail was added to the appropriate array and hybridised for 16hrs at 45°C. The array is washed and stained on the GeneChip® fluidics station 450 using the appropriate fluidics script.

scan_protocol: The array was inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

data_processing: Differential gene expression analysis was carried out using Rosetta Resolver Data Analysis System (version 7.1, Rosetta Biosoftware). Statistical analysis was performed using false discovery rate (FDR)–corrected P values, following Benjamin-Hochberg Multiple Test Correction.

label: Biotin

source_name: HUVEC treated with control antisense for 48 hours

label_protocol: 2ug of total RNA is converted to cDNA via first and second strand synthesis using the GeneChip® Expression 3’-Amplification One-Cycle cDNA Synthesis kit, in conjunction with the GeneChip® Eukaryotic PolyA RNA Control Kit. Biotin labelled cRNA is synthesised from the double-stranded cDNA using the GeneChip® Expression 3’-Amplification IVT Labelling Kit

growth_protocol: HUVEC were maintained in EGM-2 media

extract_protocol: Total RNA was isolated from cells using the Rneasy kit (Qiagen) according to the manufacturer's  instructions

treatment_protocol: HUVEC were treated with either Erg-specific or control antisense (known as GeneBloc) for either 24 hr or 48 hr

value: Umbilical vein endothelial cells


title: F-CA-93 rep2


title: CD20dim+ RPMI-8226 REPLICATE 3

value: POSITIVE


title: F-PZ-105 rep2

source_name: Stromal cells cultured from normal peripheral zone tissues; passages 4-5

value: normal stroma


title: F-CA-31 rep2


title: HUVEC_control antisense_48hr_rep1


title: F-PZ-102 rep2


title: 87 (43828702)


title: F-PZ-64 rep2


title: F-PZ-79 rep2


title: HUVEC_control antisense_48hr_rep2


title: CD20dim+ RPMI-8226 REPLICATE 2


title: 7p (43831102)

organism: Trichoderma hamatum

value: Trichoderma T7-Tomato plant


title: CD20- RPMI-8226 REPLICATE 1

value: negative


title: HUVEC_Erg antisense_48hr_rep2

source_name: HUVEC treated with Erg antisense for 48 hours


title: HUVEC_Erg antisense_48hr_rep3


title: CD20dim+ RPMI-8226 REPLICATE 1

value: positive


title: 7p (43831802)


title: F-PZ-82 rep2


title: 7 (43821502)

organism: Trichoderma harzianum

value: Trichoderma T7


title: 7p (44836202)

value: mycelium


title: F-CA-67 rep1


title: HUVEC_Erg antisense_48hr_rep1


title: ESEP Differentiating B

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

description: RMA expression value derived from GeneSpring GX software

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST by the AECOM microarray facility following Affymetrix guidelines.

scan_protocol: Samples were scanned by the AECOM microarray facility as suggested by Affymetrix.

data_processing: The raw data (CEL files) from each microarray was normalized by RMA methods in GeneSpring GX software. The log2 transformed signal intensities were averaged for biological replicates, and the mean value was used to compute the fold expression change.

source_name: ES-EP cells

label_protocol: Labeling was performed as suggested by Affymetrix by the AECOM microarray facility.

growth_protocol: MEL cells were grown in DMEM supplemented with 10% FBS (Gemini), 2mM L-glutamine, and 5mg/ml puromycin. ES-EPs were cultured in StemPro34 media (Invitrogen) supplmented with 2u/ml Epogen (Amgen), 40ng/ml hIGF-1 (Sigma), 10-6M dexamethosone (Sigma), 100ng/ml murine SCF (R&D Systems/Invitrogen), and 0.1% b-mercaptoethanol (Gibco). ES-EP were maintained between 1-6x106 cells/ml by adding fresh media daily.

extract_protocol: RNA was isolated from >1x106 cells using the RNeasy RNA isolation kit (Qiagen).

treatment_protocol: MEL cells were differentiated by the addition of 0.1 mM 17b-estradiol for 48 hours.  ES-EP cells were differentiated for 24 hours by culturing in StemPro34 media supplemented with 10u/ml Epogen, 10mg/ml insulin (Sigma), 3mM mifepristone (Sigma), and 0.1% b-mercaptoethanol.

value: ES cell derived erythroid progenitor cells

tag: cell state

value: differentiating

value: ES-EP


title: HUVEC_control antisense_24hr_rep3

source_name: HUVEC treated with control antisense for 24 hours


title: ESEP Differentiating A


title: F-CA-52 rep1


title: 7 (43808902)


title: 7 (43808602)


title: 34p (43809902)

value: Trichoderma T34-Tomato plant


title: 34p (45385902)


title: HUVEC_control antisense_24hr_rep2


title: F-CA-93 rep1


title: F-CA-39 rep1


title: WT_d8_1

city: Geneva

first: Sandra

last: Kallert

address: 1, rue Michel-Servet

department: Pathology and Immunology

country: Switzerland

institute: University of Geneva

hyb_protocol: Following fragmentation, 5.5 ug of biotinylated RNA were hybridized for 16 hr at 45C to individual Affymetrix Gene Mouse Arrays 1.0 ST. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual (Affymetrix) instructions.

scan_protocol: Microarrays were scanned in a GeneChip Scanner 3000 7G (Affymetrix), and quality control was evaluated by Affymetrix software (Expression Console).

data_processing: The data were preprocessed (RMA) using the Expression Console from Affymetrix.

source_name: spleen, day 8 after intravenous infection with 200 pfu LCMV-WE, wt

label_protocol: Labeling protocol was carried out with 300 ng of purified RNA, with biotin, according to the Affymetrix Gene Mouse Arrays 1.0 ST protocol.

extract_protocol: Trizol (Invitrogen) isolation according to the manufacturer's standard protocol, with subsequent DNase I treatment.

value: spleen

value: FACS-sorted P14 CD8+ T cells

tag: genotype

value: wt

tag: recipient mice


title: MEL Differentiating B

source_name: MEL cells

value: erythroleukemia cells


title: T1_d8_3

source_name: spleen, day 8 after intravenous infection with 200 pfu LCMV-WE, ST2 -/-

tag: tissue


title: WT_d8_2


title: HUVEC_Erg antisense_24hr_rep3

source_name: HUVEC treated with Erg antisense for 24 hours


title: 34p (43810302)


title: MEL Differentiating A


title: WT_d8_3


title: HUVEC_untreated_0 hr_rep3

source_name: HUVEC untreated


title: 34 (43810202)

value: Trichoderma T34


title: F-CA-31 rep1

value: prostate cancer stroma


title: F-PZ-105 rep1


title: HUVEC_control antisense_24hr_rep1

value: Umbilical vein endothelial cells


title: F-PZ-102 rep1

value: normal stroma


title: T1_d8_2


title: 34 (43821602)


title: 34 (43809802)


title: F-PZ-82 rep1


title: HUVEC_Erg antisense_24hr_rep2


title: HUVEC_untreated_0 hr_rep2


title: HUVEC_Erg antisense_24hr_rep1


title: F-PZ-79 rep1


title: T1_d8_1


title: HUVEC_untreated_0 hr_rep1


title: F-PZ-64 rep1


title: ATP-treated AML 14 blasts

status: Public on Feb 25 2012

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: Gene expression data from ATP-treated AML blasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: ATP-treated AML blasts

label_protocol: Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Primary leukemic cells were obtained from  the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.

extract_protocol: Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.

value: AML blasts

tag: fab classification


title: ATP-treated AML 13 blasts


title: ATP-treated AML 10 blasts


title: untreated AML 14 blasts

description: Gene expression data from untreated AML blasts

source_name: untreated AML blasts


title: untreated AML 7C blasts


title: untreated AML 13 blasts


title: ATP-treated AML 3 blasts


title: ATP-treated AML 7C blasts


title: ATP-treated AML 12 blasts


title: x803

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description:
GRHL2_3
HMLE+Twist-ER+GRHL2-rep3

hyb_protocol: Affymetrix GeneChip wt terminal hybridization protocol using Affymetrix GeneChip® WT Terminal Hybridization, Wash and Stain Kit cat# 900720 and Affymetrix GeneChip® Hybridization Control Kit cat# 900454.

scan_protocol: Scanned on the Affymetrix GeneChip® 3000 7G Plus scanner with AutoLoader using 532 nm light.

data_processing:
Gene-level RMA normalization using Expression Console software.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.core.mps
Exons included in analysis: core
Genome build: hg19

source_name: HMLE+Twist-ER cells, GRHL2/pMIG

label_protocol: Affymetrix GeneChip wt terminal labeling protocol using Affymetrix GeneChip® WT Terminal Labeling Kit cat# 900671.

growth_protocol: DME/F12 (Gibco) + 5% horse serum + 1X penicillin-streptomycin-glutamine (PSG) + 10 μg/ml insulin, 10 ng/ml EGF, 0.5 mg/ml hydrocortisone, 4-hydroxytamoxifen (4-OHT; 10ng/ml).

extract_protocol: Qiagen RNeasy Plus kit.

value: human mammary epithelial cells (HMLE)+Twist-ER

tag: retroviral expression vector


title: untreated AML 8 blasts


title: untreated AML 2B blasts


title: ATP-treated AML 9 blasts


title: untreated AML 3 blasts


title: x801

description:
GRHL2_1
HMLE+Twist-ER+GRHL2-rep1


title: untreated AML 11 blasts


title: untreated AML 6B blasts


title: ATP-treated AML 6B blasts


title: x802

description:
GRHL2_2
HMLE+Twist-ER+GRHL2-rep2


title: ATP-treated AML 11 blasts


title: x763

description:
pMIG_3
HMLE+Twist-ER+pMIG-rep3

source_name: HMLE+Twist-ER cells, pMIG

value: pMIG


title: untreated AML 10 blasts


title: ATP-treated AML 2B blasts


title: x762

description:
pMIG_2
HMLE+Twist-ER+pMIG-rep2


title: untreated AML 4B blasts


title: ATP-treated AML 8 blasts


title: ATP-treated AML 4B blasts


title: x761

description:
pMIG_1
HMLE+Twist-ER+pMIG-rep1


title: untreated AML 9 blasts


title: Normoxic cells with non-targeting siRNA replicate 3

city: Houston

first: Mei Yee

last: Koh

state: TX

address: 1515 Holcombe Blvd

department: Experimental Therapeutics

institute: U.T. M.D. Anderson Cancer Center

description: LN229 cells transfected with siRNA and placed in normoxia

hyb_protocol: Hybridizations were performed using a GeneChip® Hybridization Oven, while array washing and staining was performed using a GeneChip® Fluidics Station 450.

scan_protocol: Arrays were scanned using a GeneChipScanner 3000 7G.

data_processing:
Data were processed using Partek software
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dtl.hg18.core.mps

source_name: Normoxic LN229 with non-targeting siRNA replicate 3

label_protocol: Samples were processed using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay

growth_protocol: LN229 cells grown in DMEM/F-12 and 10% FBS. Seeded, transfected with siRNA 24 hours after seeding. Cells placed in hypoxia 48 hours after transfection, harvested after a further 16 hours hypoxia or normoxia

extract_protocol: RNAeasy kit (Qiagen)

value: glioblastoma

tag: oxygen tension

value: Normoxic (20% O2)


title: Normoxic cells with non-targeting siRNA replicate 2

source_name: Normoxic LN229 with non-targeting siRNA replicate 2


title: Hypoxic cells with HIF-2A siRNA replicate 1

description: LN229 cells transfected with siRNA and placed in hypoxia

source_name: Hypoxic LN229 with HIF-2A siRNA replicate 1

value: Hypoxic (1%O2)


title: Normoxic cells with non-targeting siRNA replicate 1

source_name: Normoxic LN229 with non-targeting siRNA replicate 1


title: Hypoxic cells with HIF-2A siRNA replicate 2

source_name: Hypoxic LN229 with HIF-2A siRNA replicate 2


title: Hypoxic cells with non-targeting siRNA replicate 2

source_name: Hypoxic LN229 with non-targeting siRNA replicate 2


title: Hypoxic cells with HIF-1A siRNA replicate 1

source_name: Hypoxic LN229 with HIF-1A siRNA replicate 1


title: Hypoxic cells with HIF-1A siRNA replicate 3

source_name: Hypoxic LN229 with HIF-1A siRNA replicate 3


title: Hypoxic cells with HIF-1A siRNA replicate 2

source_name: Hypoxic LN229 with HIF-1A siRNA replicate 2


title: Hypoxic cells with HIF-2A siRNA replicate 3

source_name: Hypoxic LN229 with HIF-2A siRNA replicate 3


title: Hypoxic cells with non-targeting siRNA replicate 3

source_name: Hypoxic LN229 with non-targeting siRNA replicate 3


title: LPS_Genipin_Liver3

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArrayTM and scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by genepix 4.1 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 1 or control probes. Spots that passed these criteria were normalized by the limma package of the R program (http://www.r-project.org/).

source_name: Liver

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: Total RNAs were extracted according to RNeasy kit.

tag: treatment group

value: LPS+Genipin

value: Liver

value: FVB


title: Mock_Liver1

value: Mock


title: LPS_Liver1

value: LPS


title: LPS_Kidney1

source_name: Kidney

value: Kidney


title: LPS_Liver3


title: Hypoxic cells with non-targeting siRNA replicate 1

source_name: Hypoxic LN229 with non-targeting siRNA replicate 1

tag: cell line


title: Mock_Liver3


title: Mock_Liver2


title: untreated AML 12 blasts

source_name: untreated AML blasts


title: LPS_Genipin_Kidney2


title: LPS_Genipin_Kidney3


title: LPS_Kidney3


title: LPS_Liver2


title: LPS_Genipin_Liver1


title: LPS_Genipin_Liver2


title: LPS_Kidney2


title: LPS_Genipin_Kidney1


title: Mock_Kidney2


title: Mock_Kidney3


title: Mock_Kidney1


title: LPS_Genipin_Heart2

source_name: Heart

value: Heart


title: LPS_Genipin_Heart3


title: Mock_Heart2


title: LPS_Heart3


title: LPS_Heart1


title: LPS_Heart2


title: Mock_Heart1


title: LPS_Genipin_Brain2

source_name: Brain

value: brain


title: Mock_Heart3


title: LPS_Genipin_Heart1


title: LPS_Genipin_Brain3


title: LPS_Brain3


title: LPS_Brain1


title: Mock_Brain1


title: Mock_Brain2


title: Naïve CD4 anti-CD3 + anti-CD28 rep2

city: San Francisco

first: Dimitri

last: de Kouchkovsky

address: 513 Parnassus Ave HSW 1102 Box 0540

department: Diabetes Center

institute: UCSF

hyb_protocol: The SureHyb chamber kit and Gasket slide kit (Agilent) were used to hybridize the labeled RNA for 18 h at 56°C to Exiqon miRCURY LNA miRNA array V.11.0, lot# 31043.03 according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on Axon GenePix 4000B scanner, and GPR files containing fluorescent ratios (sample/control or vice versa ) were generated using GenePix Pro 6.0 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GeneSpring software was used.

source_name: Anti-CD3+anti-CD28 activated naïve CD4 T cell

label_protocol: Total RNA was labeled with Cy5/Cy3 using miRCURY LNA microRNA array Power Labeling kit (Exiqon) according to the manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI + 5% FCS from the time of isolation until RNA harvest

extract_protocol: RNA samples for microarray were prepared with Trizol (Invitrogen, Carlsbad CA) according to the manufacturer’s instructions. RNA integrity was confirmed with a Bioanalyzer 2100 (Agilent, Santa Clara CA); only samples with a RIN ≥7.5 were processed further.

treatment_protocol: For microarray analysis, CD4+CD45RA+ T cells were isolated on a BD FACSAria II cell sorter (BD Biosciences, San Jose, CA) using anti-CD4 (BD, clone SK3) and CD45RA (BD, clone HI100). Cells with >99% purity were seeded at a density of 1x106 cells/mL of RMPI-1640 supplemented with 5% human heat-inactivated pooled AB serum (Valley Biomedical, Winchester, VA). Cells were activated with latex beads conjugated to control antibody (BD, clone MPC-11) or antibodies specific for anti-CD3 (clone OKT3) or to both anti-CD3 and anti-CD28 (clone 9.3).

value: CD4+CD45RA+ T cells

tag: treatment

value: Anti-CD3 + anti-CD28 conjugated to latex beads

source_name: Unactivated PBMC

value: PBMC


title: Naïve CD4 no activation rep1

source_name: Unactivated naïve CD4 T cell


title: Naïve CD4 no activation rep2


title: Naïve CD4 anti-CD3 rep3

source_name: Anti-CD3 activated naïve CD4 T cell

value: Anti-CD3 conjugated to latex beads


title: Naïve CD4 anti-CD3 rep2


title: Naïve CD4 no activation rep3


title: Naïve CD4 anti-CD3 + anti-CD28 rep3


title: LPS_Brain2

tag: strain


title: LPS_Genipin_Brain1


title: Mock_Brain3


title: Naïve CD4 anti-CD3 rep1

tag: cell type


title: Forskolin treated smooth muscle cells replicate 3

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

department: Pediatrics

institute: University of Virginia

description: Biological replicate 3 of 3 treated

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between sample groups C and “T”. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.1) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: kidney aSMCs derived from the renin cell lineage (Pentz et al, Am J Physiol Heart Circ Physiol 294: H699-H707, 2008)

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 or Cy5 dye staining.

growth_protocol: Cells were grown to ~ 80% confluence and then treated.

extract_protocol: Total RNA extracted using mirVana™ miRNA isolation kit following manufacturer's instructions.

treatment_protocol: 10µM forskolin + 100 µM IBMX for 24 hrs plus an additional treatment with 10µM forskolin for 30 min. before harvest.

tag: primary cell line

tag: passage

value: mixed 129Sv/C57Bl6

value: Forskolin


title: Naïve CD4 anti-CD3 + anti-CD28 rep1


title: Placebo, no lice, fish 4

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: Control, biological replicate 4 of 4

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Mixture of all samples

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Salmon post smolts were kept in tanks with sea water

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)

treatment_protocol: Salmon were injected with cortisol or placebo and infected with lice

value: skin

source_name: Placebo, no lice, fish 4


title: miR-1 up-regulated group vs. control group, replicate 1

city: Beibei

first: GAO

last: Song

state: Chongqing

address: tiansheng road 2#

department: ISSB

institute: Southwest University

hyb_protocol: The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
LOWESS normalized, data obtained from processed cy3 signal intensity/ processed cy5 signal intensity.The software from CapitalBio Crop was used.
Ratio>=2.0 or Ratio<=0.5 were consideried to be up-regulated and down-regulated genes, respectively

organism: Bombyx mori

source_name: non-treated control

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

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

tag: gender

value: mixed

value: whole organism

tag: developmental stage

value: 1 day after finishing spinning

value: control

source_name: miR-1 mimics injected larvae

value: miR-1 mimics


title: miR-1 up-regulated group vs. control group, replicate 2


title: Forskolin treated smooth muscle cells replicate 2

description: Biological replicate 2 of 3 treated

value: kidney aSMCs derived from the renin cell lineage


title: Control smooth muscle cells replicate 2

description: Biological replicate 2 of 3 Control

treatment_protocol: no treatment

value: Control


title: Control smooth muscle cells replicate 3

description: Biological replicate 3 of 3 Control

treatment_protocol: untreated