title: Cf_T101

value: male

value: 9 yr old

value: mast cell tumor case T101

value: mast cell tumor (MCT)


title: Cf_T92

status: Public on May 06 2014

type: RNA

city: Agripolis - Legnaro (PD)

first: Mery

last: Giantin

state: Padova

address: Viale Università, 16

department: Dip. Biomedicina Comparata e Alimentazione

country: Italy

institute: University of Padova

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

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software

molecule: total RNA

organism: Canis lupus familiaris

source_name: mast cell tumour sample

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

extract_protocol:
Aliquot from the central part of the mast cell tumor mass aseptically collected during surgical intervention, submerged in RNAlater solution and stored at –20°C until extraction
Mast cell tumor total RNA was extracted using Trizol reagent according to manufacturer instruction and purified according to Qiagen RNeasy Mini Kit protocol for tissue samples

tag: breed

value: Boston Terrier

tag: gender

value: female

tag: age

value: 7 yr old

tag: tumor case id

value: mast cell tumor case T92

tag: tissue


title: I106

type: genomic

city: St Lucia

first: Allan

middle: F

last: McRae

state: QLD

address: QBI Building (#79)

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using an Illumina bead array reader

data_processing:
GenomeStudio Methylation Module v1.8
Raw data file: raw_data_signal_intensities.txt contains Unmethylated and methylated signal intensities
Processed data file: average_beta.txt:  Normalised Average Beta (Normalised to internal controls, background subtraction) and the Detection P-value

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood, healthy

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood lymphocytes by the salt precipitation method

value: peripheral blood lymphocytes

value: M

tag: twin

value: MZ


title: I107


title: Cf_T103

value: Crossbred

value: 13 yr old

value: mast cell tumor case T103


title: Cf_T112

value: Boxer

value: 5 yr old

value: mast cell tumor case T112


title: Human_BTH_51-Z159-33265T

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

country: China

institute: astrazeneca

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Hu133Plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Expression Console. RMA algorithm provided by software ExpressionConsole was used to call gene level expression values from raw signals.

label: biotin

source_name: gastric cancer frozen tumor tissues

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: Tumor tissues were collected after surgical resection and frozed for total RNA extraction

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

value: gastric

tag: phenotype

value: gastric cancer


title: I103

value: F

value: DZ


title: I105


title: Human_BTH_415-9541385T


title: Human_BTH_163-Z37-25762T


title: Human_BTH_469-9542538T


title: Cf_T100

value: Dalmatian

value: 4 yr old

value: mast cell tumor case T100

value: mast cell tumor (MCT)


title: I102

value: peripheral blood lymphocytes


title: Human_BTH_467-9542415T


title: Human_BTH_449-9541701T


title: Cf_T91

value: Labrador retriever

value: female

value: 10 yr old

value: mast cell tumor case T91


title: Human_BTH_171-N35-23553T


title: Human_BTH_357-9539681T


title: Cf_T88

value: 8 yr old

value: mast cell tumor case T88


title: I101

value: M

value: MZ


title: I100


title: Human_BTH_85-A69-26043T

value: gastric


title: Human_BTH_517-9544005T

value: gastric cancer


title: Human_BTH_303-9538803T


title: Cf_T90

value: Crossbred

value: male

value: 13 yr old

value: mast cell tumor case T90


title: Human_BTH_317-9538998T


title: Cf_T89

value: not available

value: 6 yr old

value: mast cell tumor case T89


title: Human_BTH_307-9538826T


title: Human_BTH_69-N37-23830T


title: Cf_T84

value: Boxer

value: 3 yr old

value: mast cell tumor case T84

value: mast cell tumor (MCT)


title: Cf_T87

value: female

value: 8 yr old

value: mast cell tumor case T87


title: I098

value: peripheral blood lymphocytes

value: M


title: I099

value: F

value: MZ


title: Human_BTH_169-N33-22820T

value: gastric

value: gastric cancer


title: Human_BTH_111-Z77-26914T


title: Cf_T83

value: Labrador Retriever

value: mast cell tumor case T83


title: I097


title: Human_BTH_511-9544004T


title: Human_BTH_57-Z85-28072T


title: I096


title: Human_BTH_507-9532687T


title: Cf_T82

value: Golden Retriever

value: male

value: 4 yr old

value: mast cell tumor case T82


title: Human_BTH_165-Z17-24876T


title: Human_BTH_559-9546067T


title: Human_BTH_513-9544112T


title: Human_BTH_167-A41-23993T


title: Human_BTH_501-9532666T


title: I095


title: Cf_T80

value: 6 yr old

value: mast cell tumor case T80


title: Human_BTH_525-9544427T


title: I094


title: Human_BTH_131-Z59-26277T


title: Human_BTH_203-N1-15388T


title: Cf_T77

value: Bouvier des Flandres

value: female

value: 12 yr old

value: mast cell tumor case T77

value: mast cell tumor (MCT)


title: Cf_T73

value: 9 yr old

value: mast cell tumor case T73


title: Human_BTH_13-Z123-28886T

value: gastric


title: Human_BTH_503-9532669T

value: gastric cancer


title: Cf_T81

value: Crossbred

value: 10 yr old

value: mast cell tumor case T81


title: Cf_T64

value: Dogo Argentino

value: male

value: mast cell tumor case T64


title: Human_BTH_575-9547496T


title: I093

value: peripheral blood lymphocytes

value: F

value: DZ


title: Human_BTH_15-A21-19605T


title: I092

value: M


title: Human_BTH_573-9546266T


title: I091


title: I090


title: I089


title: Human_BTH_209-Z65-26284T


title: I088


title: I087


title: Human_BTH_593-9547050T


title: Cf_T62

value: female

value: mast cell tumor case T62


title: Human_BTH_423-9541535T


title: Cf_T61

value: 12 yr old

value: mast cell tumor case T61

value: mast cell tumor (MCT)


title: Cf_T57.1

value: mast cell tumor case T57


title: Human_BTH_191-Z9-24758T

value: gastric

value: gastric cancer


title: Human_BTH_215-A15-18920T


title: Cf_T56

value: Crossbred

value: mast cell tumor case T56


title: Human_BTH_37-Z111-28681T


title: I086

value: MZ


title: Cf_T58

value: Labrador Retriever

value: 10 yr old

value: mast cell tumor case T58


title: Cf_T53

value: Cocker Spaniel

value: gender not available

value: 8 yr old

value: mast cell tumor case T53


title: Human_BTH_153-Z39-25765T


title: needles-Tree number 9-Resistant-Right

city: Quebec

first: Isabelle

last: Giguere

state: Quebec

address: 1030, avenue de la Medecine

country: Canada

institute: Universite Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next, the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution on a PowerScanner (Tecan Group Ltd., Männedorf, Switzerland) microarray scanner at 50% laser power with the autogain funtion on to automatically adjust PMT level. Image analysis was carried out using ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA).

data_processing: Mean intensity and local background were obtained for each spot on the array. Bad spots resulting from dust, high local background or saturation were flagged.  Net intensity was calculated by subtracting trimmed background from mean intensity. Data analysis was carried out using the FlexArray 1.6 software package (http://genomequebec.mcgill.ca/FlexArray). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background-subtracted data were log2-transformed and quantile normalization was used to normalize intensity distributions between arrays.

label: Alexa 647

organism: Picea glauca

source_name: Picea glauca needles, Tree number 9, Resistant

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground using a Mixer Mill MM 300 (Retsch, Haan, Germany) and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008).

value: needles

tag: slide batch

tag: resistance to budworm

value: Resistant

tag: position of sample in tree

value: Right

tag: tree number


title: needles-Tree number 7-Non-resistant-Right

source_name: Picea glauca needles, Tree number 7, Non-resistant

value: Non-resistant


title: Human_BTH_585-9547182T


title: Human_BTH_453-9541959T


title: Negative control strain with empty plasmid

city: Taipei

first: Chia-Wei

last: Hu

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

description: Gene expression of R. palustris with empty plasmid (negative control)

hyb_protocol: 1.0 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was mixed with 10x Agilent blocking agent and 2x HI-RPM GE hybridization buffer following the manufacturers instructions.Tha mixed samples were hybridized to Agilent Whole Agilent R.palustris Custom Microarray GE 8x15k for 17 hours at 65°C in a rotating Agilent hybridization oven rotating at 10 rpm.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1minute and 1 minute for GE Wash buffer 2 (Agilent) at 37°C, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505B using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Red and Green PMT is set to 100%).

data_processing: The scanned images were analyzed withFeature Extraction (FE) 10.7.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rhodopseudomonas palustris

source_name: Negative control bacteria with empty plasmid

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Spike-In 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: Bacteria were kept in anaerobic photoheterotrophic condition, and grown in PMSC medium supplemented with succinate and added with 40ug/ml gentamycin

extract_protocol: RNA was prepared using the RNA mini kit (QIAGEN) following the manufacturer's recommendations.  The protocol includes cell lysis by sonication and RNA stabilization by RNAprotectTM Bacteria Reagent (QIAGEN)

treatment_protocol: Bacteria with successfully transformed plasmid were incubated at 30℃ with light, and harvested at OD660=1.5

tag: strain

tag: optical density

tag: genotype/variation


title: I085

value: peripheral blood lymphocytes

value: M

value: DZ


title: cbbT1 over-expressing strain replicate 1

description: Gene expression of R. palustris with cbbT1 overexpression

source_name: cbbT1 over-expressing R.palustris bacteria

value: cbbT1 over-expression


title: cbbT2 over-expressing strain replicate 1

description: Gene expression of R. palustris with cbbT2 overexpression

source_name: cbbT2 over-expressing R.palustris bacteria

value: cbbT2 over-expression


title: Wild type strain

description: Gene expression of R. palustris010 (wild type)

source_name: Wild type bacteria Rpa010

value: Wild type strain


title: I104

value: F


title: I083

value: MZ


title: Cf_T55

value: English Setter

value: male

value: mast cell tumor case T55

value: mast cell tumor (MCT)


title: needles-Tree number 7-Non-resistant-Top

value: Top


title: needles-Tree number 7-Non-resistant-Left

value: needles

value: Left


title: Cf_T50

value: pit bull

value: female

value: 7 yr old

value: mast cell tumor case T50


title: needles-Tree number 9-Resistant-Top

value: Resistant


title: I082

value: peripheral blood lymphocytes

value: M

value: DZ


title: Cf_T51

value: Crossbred

value: 6 yr old

value: mast cell tumor case T51


title: needles-Tree number 6-Resistant-Right

source_name: Picea glauca needles, Tree number 6, Resistant

value: Right


title: needles-Tree number 9-Resistant-Left


title: I084


title: I081

value: MZ


title: needles-Tree number 4-Non-resistant-Right

source_name: Picea glauca needles, Tree number 4, Non-resistant

value: Non-resistant


title: I080


title: I079

value: F


title: needles-Tree number 3-Non-resistant-Right

source_name: Picea glauca needles, Tree number 3, Non-resistant

value: needles


title: I078


title: needles-Tree number 4-Non-resistant-Top

value: Top


title: Cf_T49

value: male

value: 14 yr old

value: mast cell tumor case T49

value: mast cell tumor (MCT)


title: I077


title: Cf_T14

value: female

value: not available

value: mast cell tumor case T14


title: needles-Tree number 4-Non-resistant-Left

value: Left


title: Cf_T47

value: Boxer

value: 11 yr old

value: mast cell tumor case T47


title: needles-Tree number 6-Resistant-Left

value: Resistant


title: needles-Tree number 3-Non-resistant-Top


title: needles-Tree number 1-Resistant-Left

source_name: Picea glauca needles, Tree number 1, Resistant


title: I076

value: peripheral blood lymphocytes

value: DZ


title: needles-Tree number 2-Resistant-Right

source_name: Picea glauca needles, Tree number 2, Resistant

value: Right


title: Cf_T12.1

value: 10 yr old

value: mast cell tumor case T12


title: needles-Tree number 6-Resistant-Top

value: needles

value: Top


title: Cf_T48

value: Dogo Argentino

value: mast cell tumor case T48


title: needles-Tree number 2-Resistant-Top


title: Cf_T30

value: Golden Retriever

value: female

value: 5 yr old

value: mast cell tumor case T30

value: mast cell tumor (MCT)


title: I075

value: F


title: needles-Tree number 2-Resistant-Left

value: Left


title: needles-Tree number 19-Resistant-Right

source_name: Picea glauca needles, Tree number 19, Resistant

value: Resistant


title: Cf_T6.2

value: Cane Corso

value: male

value: 8 yr old

value: mast cell tumor case T6


title: Cf_T9.1

value: Cocker Spaniel

value: 10 yr old

value: mast cell tumor case T9


title: I073

value: peripheral blood lymphocytes

value: M

value: MZ


title: I074

value: DZ


title: needles-Tree number 19-Resistant-Left

value: needles


title: needles-Tree number 3-Non-resistant-Left

value: Non-resistant


title: needles-Tree number 17-Non-resistant-Top

source_name: Picea glauca needles, Tree number 17, Non-resistant

value: Top


title: needles-Tree number 17-Non-resistant-Left


title: needles-Tree number 1-Resistant-Top


title: I072


title: needles-Tree number 16-Non-resistant-Right

source_name: Picea glauca needles, Tree number 16, Non-resistant

value: Right


title: I071


title: needles-Tree number 19-Resistant-Top


title: needles-Tree number 16-Non-resistant-Left

value: Left


title: needles-Tree number 17-Non-resistant-Right


title: needles-Tree number 16-Non-resistant-Top


title: I070

value: F


title: needles-Tree number 12-Non-resistant-Right

source_name: Picea glauca needles, Tree number 12, Non-resistant


title: DP_rep3

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

country: USA

institute: Yale University

description:
SAMPLE 12
DP

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi in R

organism: Mus musculus

source_name: B Cell

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA samples was extracted using the RNeasy mini kit (Qiagen, CA)

tag: cell type

value: splenic memory B cells

tag: surface markers

value: CD80+ PDL2+


title: I069

source_name: whole blood, healthy


title: needles-Tree number 12-Non-resistant-Left


title: needles-Tree number 15-Resistant-Left

source_name: Picea glauca needles, Tree number 15, Resistant

value: Resistant


title: needles-Tree number 15-Resistant-Right


title: DP_rep2

description:
SAMPLE 11
DP


title: I067


title: needles-Tree number 12-Non-resistant-Top


title: DP_rep1

description:
SAMPLE 10
DP


title: I066


title: needles-Tree number 11-Resistant-Left

source_name: Picea glauca needles, Tree number 11, Resistant


title: needles-Tree number 10-Non-resistant-Right

source_name: Picea glauca needles, Tree number 10, Non-resistant


title: I065


title: needles-Tree number 10-Non-resistant-Top


title: I068


title: needles-Tree number 11-Resistant-Top


title: DN_rep3

description:
SAMPLE 6
DN

value: CD80- PDL2-


title: SP_rep2

description:
SAMPLE 8
SP

value: CD80- PDL2+


title: SP_rep1

description:
SAMPLE 7
SP


title: needles-Tree number 10-Non-resistant-Left


title: I064


title: DN_rep2

description:
SAMPLE 5
DN


title: needles-Tree number 11-Resistant-Right


title: SP_rep3

description:
SAMPLE 9
SP


title: I061


title: I060


title: I059


title: I062


title: I055


title: I056


title: I054


title: I053


title: I052


title: I063


title: I050


title: I057


title: Exosomes from Pooled Healthy donors serum

city: Guangzhou

first: ping

last: lan

address: 651 Dongfend East Road

institute: Sun Yat-sen University Cancer Center

description: Control

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering.
The corrected value is the signal of the probe after background correction =Foreground-Background Intensity. If the corrected value is a negative number ,then the final normalized value is defined as null.

source_name: exosomes from human serum

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: source


title: I049


title: I051


title: I048


title: I047


title: CDM-LSRLUXS-30-B2b

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

institute: Drexel University College of Medicine

description:
552781A12_43021_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

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

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

data_processing: Raw data (.pair file) was edited to remove subclusters (genes) that are not present in Haemophilus influenzae CZ4126/02 by merging it with a list of subclusters known to be present in CZ4126/02. In addition, to analyze data from two different gene expression platforms together the data were modified to match each other (averaging intensity values from sets of probes on the 144K array platform and removing certain control probes from the 72K array platform). These modified data (.pair files) were 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.).

organism: Haemophilus influenzae

source_name: Haemophilus influenzae CZ4126/02 ΔluxS::Specr,Δlsr::Cmr

label_protocol: Labeling of cDNA was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Haemophilus influenzae CZ4126/02ΔluxS::Specr and Haemophilus influenzae CZ4126/02ΔluxS::Specr,ΔLsr::Cmr were grown in CDM (Coleman et al. J Clin Microbiol. 41 (9), 4408-10.) with or without the addition of 3µM synthetic AI-2 to log phase and stationary phase using an inoculum from an overnight culture grown in BHI. 40 mL cultures incubated at 37°C and shaking at 200 rpm.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Plus kit with the standard protocol with gDNA eliminator columns. Eluted RNA (~85 µL) was DNased by adding 10 µL 10X TurboDNase buffer and 5 µL TurboDNase (2 units/µL) (Ambion) and incubating at 37 °C for 1.5 hours. 2 µL more TurboDNase was added and incubation continued for an additional 1.5 hours. DNased RNA samples were cleaned by passing the samples through the RNeasy protocol a second time (with gDNA eliminator steps). Samples were eluted in nuclease free (n.f.) water, quantitated on a Nanodrop 1000 spectrophotometer and stored at -80 °C. First and second-strand cDNA synthesis was performed using a SuperScript® One-Cycle cDNA Kit (Invitrogen) as outlined in the NimbleGen Microarray Experienced User’s Guide including RNaseA and cDNA precipitation steps.

treatment_protocol: 2 mL of culture was diluted in 4 mL RNAProtect (Qiagen) and stored at RT for 10 minutes, then 4 °C overnight. Samples were pelleted, the supernatant removed and the cell pellets resuspended in 100 µL of 1X Tris-EDTA (TE) + 1 mg/mL lysozyme (Worthington Biochemical) and 1 mg/mL proteinase K (Qiagen).

tag: genotype

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time

value: 30 minutes after ODA600 0.75

tag: biological replicate

tag: technical replicate

tag: probe set


title: CDM-LSRLUXS-30-B1b

description:
552715A12_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Naïve_rep2

description:
SAMPLE 2
Naïve

value: Naïve control


title: Naïve_rep3

description:
SAMPLE 3
Naïve


title: CDM-LSRLUXS-30-B2a

description:
552781A12_43021_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: I046

tag: tissue

value: peripheral blood lymphocytes

tag: gender

tag: twin

tag: age


title: I058

value: M


title: I045


title: I044


title: I043

value: DZ


title: CDM-LUXS-30-B2b

description:
552781A11_43021_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: Haemophilus influenzae CZ4126/02 ΔluxS::Specr


title: CDM-LSRLUXS-30-A2a

description:
558764A08_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: CDM-LSRLUXS-30-B1a

description:
552715A12_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Exosomes from Pooled NPC Patients serum

description: Patient

value: Exosomes from Pooled NPC Patients serum


title: CDM-LSRLUXS-30-A2b

description:
558764A08_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Blood CD8 Tem cells - patient 6

city: Cambridge

first: Tim

last: Raine

address: Addenbrooke's Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

description: Gene expression data from T effector memory cells sorted by flow cytometry

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer’s instructions

scan_protocol: GeneChips scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing:
Microarray data was preprocessed using RMA implemented in R with affy package
log2 RMA signal after batch correction according to the methods ofJohnson et al. Biostatistics 8, 118-127 (2007). Presence/absence calls are based upon the Affymetrix Power Tools Detection Above BackGround (DABG) algorithm: Every probeset is assigned a p value representing the probability of the signal representing background noise, based upon the comparison of the signal from each of the probes in a given probeset and from non-expressed control probes matched for GC-content. We define a transcript ID as detected in any given sampe if ≥50% of probesets mapped to a given transcript ID have a DABG p value ≤0.01. Presence/absence calls are not made (left blank) for transcript IDs mapping to control or cross-hybridising probesets, or those not mapped to an either an autosome or to chromosome X.

source_name: Peripheral blood, healthy control

label_protocol: Amplified RNA was biotinylated using the Encore Biotin Module (NuGen) according to standard manufacturer's protocol

extract_protocol: RNA extraction was performed using RNeasy micro kits (Qiagen) in an automated manner on the QIAcube platform (Qiagen). Extracted RNA was subject to quantification and quality assurance using an Agilent 2100 Bioanalyzer (Agilent Technologies) and samples checked for a RNA Integrity Value (RIN) >7 prior to further analysis. RNA amplification was performed using the Ovation Pico system (NuGen Technologies) with 1ng starting material from all samples.

treatment_protocol: Subjects received a standardised bowel preparation and underwent the procedure in the morning. 8 pinch biopsies were collected pairwise from the terminal ileum, within 10cm of the ileocaecal valve and with visual avoidance of Peyer’s patches as well as of previously sampled areas. Biopsies were collected into RPMI medium (Invitrogen) on ice and processed immediately. 10ml of peripheral blood was also collected into tubes containing 15mg EDTA (Sigma).    Terminal ileal biopsies were suspended in calcium and magnesium free medium with 2mM EDTA and 1mM DTT (Sigma) and agitated for 30 minutes with 3 changes of media. At each stage, supernatants (containing the IEL fraction) were separated off using a 70μm cell strainer (Greiner Bio-One). After the last media change, the remaining fragments were dissociated through incubation with 200U/ml collagenase IV (Sigma) for 1 hour, prior washing through a 70μm cell strainer. PBMC were separated by centrifugation over a Nycodenz density gradient (Axis-Shield). All isolation steps with the exception of enzymatic digestion were performed at 4C. Cells were stained with an antibody cocktail comprising monoclonal antibodies (mAb) to CD19 (HIB19), CD326 (9C4), TCRab (IP26), CD62L (DREG-56), CD45RO (UCHL1), CD8a (HIT8a), CD4 (RPA-T4) (all from Biolegend), mAb to CD3 (SK7, from eBioscience), and mAb to CD8b (2ST8.5H7, from BD Biosciences). After the final antibody wash step, 4',6-diamidino-2-phenylindole (DAPI, Sigma) was added to washed cells, to enable live/dead discrimination. Cell separation was performed using a BD Facs Aria III cell sorter (BD Biosciences) with cells sorted directly into chilled cell lysis and RNA stabilisation buffer (Buffer RLT, Qiagen) prior to storage at -80C. Sort purity was verified to >99% prior to and after each sort. To minimise cellular perturbation, sorting was performed using a 100µm nozzle at the low sorting pressures using chilled, preservative free PBS.

value: Female

value: Blood

value: CD8+ T effector memory cell


title: CDM-LUXS-30-B2a

description:
552781A11_43021_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: I041


title: I040


title: I039


title: I042


title: CDM-LUXS-30-B1b

description:
552715A11_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: I038


title: CDM-LUXS-30-B1a

description:
552715A11_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: I037


title: CDM-LUXS-30-A2a

description:
558764A07_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: needles-Tree number 1-Resistant-Right

value: needles

tag: slide batch

tag: resistance to budworm

tag: position of sample in tree

value: Right

tag: tree number


title: I035

value: F


title: I036

value: MZ


title: CDM-LSRLUXS-B2a

description:
552781A08_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: CDM-LSRLUXS-B2b

description:
552781A08_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: CDM-LSRLUXS-B1b

description:
552715A08_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: needles-Tree number 15-Resistant-Top

value: Resistant

value: Top


title: Kiidney Yin deficiency_After treatment 1

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

institute: Fujian Academy of Traditional Chinese Medicine

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA),Scan region Scan Area (61 x 21.6 mm),Scan resolution:5μm,scanning mode Single Pass.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Add the images (.tif) to be extracted to the Agilent Feature Extraction (FE) software Project. Select Project > Start Extracting and export data to txt.Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity genes were filtered (Genes that at least 5 out of 15 samples have flags in Detected were chosen for further analysis).

source_name: human peripheral blood

label_protocol: if the yield is <1.65μg and the specific activity is <9.0 pmol Cy3 or Cy5 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: Five (5) ml of peripheral blood was taken from each patient. Mononuclear cells were isolated via lymphocyte lysing.And then add 1 ml trizol reagents.

tag: disease

value: kidney Yin deficiency

tag: time point

value: After treatment

tag: Sex


title: I033


title: I034


title: Kiidney Yin deficiency_After treatment 2


title: DN_rep1

description:
SAMPLE 4
DN

tag: cell type

value: splenic memory B cells

tag: surface markers

value: CD80- PDL2-


title: Kiidney Yin deficiency_Before treatment 3

value: Before treatment


title: Kiidney Yin deficiency_Before treatment 1


title: Kiidney Yin deficiency_After treatment 3


title: CDM-LSRLUXS-B1a

description:
552715A08_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: genotype

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time


title: Kiidney Yin deficiency_Before treatment 2


title: RAD21 Replicate 1

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

description:
.wig file containing MA2C signals normalized for the replicate is provided (Cohesin_MA2Cscore.wig).
.wig files containing normalized signals for each duplicate are also provided

hyb_protocol: Hybridization was performed by NimbleGen Systems (Services, Reykjavic), following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Standard NimbleGen protocols (scanned at NimbleGen services, Reykjavic). See www.nimblegen.com.

data_processing: Model-based Analysis of 2 Color Arrays (MA2C; Song JS et al., 2007) on the ChIP duplicate. MA2C parameters were: robust normalization (C=1), peak calling for a minimum of 4 probes (maximum gap set at 250 bp) in a sliding window of 300 bp half-width.

source_name: RAD21 ChIP from MDA::ER cells treated for 50' with 10-8M estradiol

label_protocol: Labeling was performed by NimbleGen Systems (Services, Reykjavic), following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were maintained in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS, BioWest), antibiotics (Roche), and 0.8 mg/ml Hygromycin (Calbiochem) for continuous selection of the clone, at 37°C under 5% CO2.

extract_protocol: MDA::ER cells were fixed for 10 min at room temperature in a PBS solution containing 1.5% formaldehyde (ACROS). After a 5 min quenching with 0.125M glycine, cells were washed twice in ice-cold PBS and collected in 1 ml of cold buffer (100 mM Tris-HCl [pH 9.4] and 100 mM DTT). Cells were then pelleted and lysed for 10 min in ice in 300 µl of lysis buffer [10 mM EDTA, 50 mM Tris-HCl (pH 8.0), 1% SDS, 0.5% Empigen BB (Sigma)]. Crosslinked chromatin was sheared to an average size of 500 bp by sonication for 15 min with 30secs on/off cycles at full power in a BioRuptor apparatus (Diagenode). Following 10 minutes of centrifugation at 10,000 x g, 30 µl were kept as input fraction and the remainder diluted 5 fold in IP buffer (2 mM EDTA, 100 mM NaCl, 20 mM Tris-HCl [pH 8.1], and 0.5%Triton X-100) for a 3h pre-clearing incubation at 4°C under rocking with 10 µg of yeast tRNAs and 100 µl of a 50% protein A/Protein G-Sepharose beads slurry (Amersham Pharmacia Biosciences) slurry. Immunoprecipitation was then carried out overnight at 4°C under rocking using 2 µg of antibodies. Complexes were recovered after 3 hr incubation at 4°C with 10 µg of yeast tRNAs and 100 µl of a 50% protein A/Protein G-Sepharose beads slurry. Precipitates were then serially washed, using 500 µl of Washing Buffers (WB) I [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 150 mM NaCl], WB II [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl], WB III [1 mM EDTA, 10 mM Tris-HCl (pH 8.1), 1% NP-40, 1% Deoxycholate, 0.25 M LiCl] and then twice with 1 mM EDTA, 10 mM Tris-HCl (pH 8.1). Precipitated complexes were removed from the beads through three sequential incubations of 10 min with 50 µl of 1% SDS, 0.1 M NaHCO3. Crosslink was reversed by an overnight incubation at 65°C with 50 µg of Proteinase K (Sigma). Following a subsequent incubation of the samples with 2.5 µg RNAse (Sigma) for 1h at 37°C, the DNA was then purified on NucleoSpin™ columns (Macherey-Nagel) using NTB buffer and eluted in 40 µl of elution buffer. Efficiency of the ChIP assay was evaluated using qPCR positive and negative controls before proceeding to the amplification of 11 µl of pooled triplicate ChIP and input samples using the WGA whole genome amplification kit (Sigma).

treatment_protocol: MDA::ER cells were plated at 2x106 cells per 9cmØ dishes in DMEM/10% FCS complemented with 0.8 mg/ml hygromycin for 16h. Following two washes with PBS, cells were then cultivated for 3 days in DMEM/2.5% charcoal-stripped serum (BioWest) complemented with Hygromycin. Confluent cells were then treated with Estradiol (E2, Sigma) at a final concentration of 10-8 M for 50 min.

value: female

tag: cell line

value: MDA-MB231 breast cancer cells

tag: integrated vector

tag: er status

value: Positive

tag: chip antibody

value: ChIP performed using a mix of  antibodies:anti-RAD21 (ab992, Abcam) and anti-Scc3 (gift from Dr. JM Peters).

tag: chip antibody 1

tag: chip antibody 1 manufacturer

value: Abcam

tag: chip antibody 1 catalog #

tag: chip antibody 2

tag: chip antibody 2 manufacturer

value: Dr. JM Peters

tag: treatment

value: estrogen

source_name: Input DNA from MDA::ER cells treated for 50' with 10-8M estradiol

extract_protocol: MDA::ER cells were fixed for 10 min at room temperature in a PBS solution containing 1.5% formaldehyde (ACROS). After a 5 min quenching with 0.125M glycine, cells were washed twice in ice-cold PBS and collected in 1 ml of cold buffer (100 mM Tris-HCl [pH 9.4] and 100 mM DTT). Cells were then pelleted and lysed for 10 min in ice in 300 µl of lysis buffer [10 mM EDTA, 50 mM Tris-HCl (pH 8.0), 1% SDS, 0.5% Empigen BB (Sigma)]. Crosslinked chromatin was sheared to an average size of 500 bp by sonication for 15 min with 30secs on/off cycles at full power in a BioRuptor apparatus (Diagenode). Following 10 minutes of centrifugation at 10,000 x g, 30 µl were kept as input fraction. Crosslink was reversed by an overnight incubation at 65°C with 50 µg of Proteinase K (Sigma). Following a subsequent incubation of the samples with 2.5 µg RNAse (Sigma) for 1h at 37°C, the DNA was then purified on NucleoSpin™ columns (Macherey-Nagel) using NTB buffer and eluted in 40 µl of elution buffer. Efficiency of the ChIP assay was evaluated using qPCR positive and negative controls before proceeding to the amplification of 11 µl of pooled triplicate ChIP and input samples using the WGA whole genome amplification kit (Sigma).

value: Input DNA


title: I032

tag: tissue

value: peripheral blood lymphocytes

tag: gender

value: M

tag: twin

tag: age


title: CDM-LSRLUXS-A2b

description:
558764A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype

tag: biological replicate

tag: technical replicate

tag: probe set


title: RAD21 Replicate 2

tag: cell line

tag: integrated vector


title: ER Replicate 2

description:
Wig file containing MA2C signals normalized for the replicate is provided (ER_MA2Cscore.wig).
.wig files containing normalized signals for each duplicate are also provided

source_name: ER ChIP from MDA::ER cells treated for 50' with 10-8M estradiol

tag: er status

tag: chip antibody

value: ChIP performed using a mix of anti-estrogen receptor antibodies:HC20 (Santa Cruz) and ERAb-10/TE111.SD11 (NeoMarkers).

value: anti-estrogen receptor

value: Santa Cruz

value: NeoMarkers

tag: chip antibody 2 catalog #


title: I030

value: MZ


title: CDM-LSRLUXS-A2a

description:
558764A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: growth medium

tag: sampling time


title: I028

value: F

value: DZ


title: CDM-LUXS-B2b

description:
552781A07_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

value: chemically-defined media (CDM)


title: RNA Pol II Replicate 2

description:
.wig file containing MA2C signals normalized for the replicate is provided (Pol_MA2Cscore.wig).
.wig files containing normalized signals for each duplicate are also provided

source_name: RNA Polymerase II ChIP from MDA::ER cells treated for 50' with 10-8M estradiol

value: female

value: MDA-MB231 breast cancer cells

value: ChIP performed using a mix of anti-RNA Polymerase antibodies:anti-Pol II (C-21, SantaCruz) and Anti-RNA polymerase II (CTDH48, Millipore).

tag: chip antibody 1

value: anti-PolII

tag: chip antibody 1 manufacturer

tag: chip antibody 1 catalog #

tag: chip antibody 2

value: anit-PolII

tag: chip antibody 2 manufacturer

value: Millipore


title: I029

tag: tissue

tag: gender

tag: twin

tag: age


title: CDM-LUXS-B2a

description:
552781A07_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype

tag: biological replicate

tag: technical replicate

tag: probe set


title: CDM-LUXS-B1b

description:
552715A07_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: I027


title: CDM-LUXS-30-A2b

description:
558764A07_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

value: 30 minutes after ODA600 0.75


title: I026

value: peripheral blood lymphocytes


title: CDM-LUXS-A2b

description:
558764A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: I024


title: I025


title: RNA Pol II Replicate 1

tag: cell line

tag: integrated vector

tag: er status

value: Positive

tag: chip antibody

tag: treatment

value: estrogen

value: Input DNA


title: CDM-LUXS-A2a

description:
558764A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: growth medium

tag: sampling time


title: CTCF Replicate 2

description:
.wig file containing MA2C signals normalized for the replicate is provided (CTCF_MA2Cscore.wig).
.wig files containing normalized signals for each duplicate are also provided

source_name: CTCF ChIP from MDA::ER cells treated for 50' with 10-8M estradiol

value: ChIP performed using the #07-729 antibody (Millipore).

tag: chip antibody 1

value: anti-CTCF

tag: chip antibody 1 manufacturer

tag: chip antibody 1 catalog #


title: I023

tag: tissue

tag: gender


title: AI2+CDM-LSRLUXS-30-B2b

description:
552781A10_44022_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

value: chemically-defined media (CDM) with 3uM AI-2 added


title: AI2+CDM-LSRLUXS-30-B2a

description:
552781A10_44022_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: CTCF Replicate 1


title: I021

value: M

tag: twin

tag: age


title: Naïve_rep1

description:
SAMPLE 1
Naïve

tag: cell type

value: splenic memory B cells

tag: surface markers

value: Naïve control


title: I022


title: AI2+CDM-LSRLUXS-30-B1a

description:
552715A10_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: genotype

tag: biological replicate

tag: technical replicate

tag: probe set


title: AI2+CDM-LSRLUXS-30-A2b

description:
558764A06_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Lola-N replicate 3

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

description: Dam-Lola-N / Dam-control in stage 17 embryos

hyb_protocol: Hybridisation has been done with HX1 mixer following Nimblegen's procedures

scan_protocol: Arrays were scanned by Nimblegen

data_processing: The  Dam-fusion/Dam log2 ratios were median normalised using NimbleScan software (Nimblegen)

organism: Drosophila melanogaster

source_name: Dam-Lola-N processed DNA from stage 10-11 embryos

label_protocol: Labeling has been done using the Nimbelgen Dual-Color Labeling Kit based on a Klenow enzymatic reaction following manufacturer's protocol

growth_protocol: Embryos were collected for 3 hours and allowed to develop for a further 4 hours (at 25oC).

extract_protocol: Tissues were dissected and placed n 180ul of PBS with 100mM EDTA before samples were processed as previously described (Choksi et al., 2006)

treatment_protocol: Embryos were collected, washed and frozen on dry ice.

value: w-; + ; UAS-Dam-Lola-N

value: stage 10-11 embryos

source_name: Dam processed DNA from stage 10-11 embryos

value: w-; + ; UAS-Dam


title: ER Replicate 1

description:
.wig file containing MA2C signals normalized for the replicate is provided (ER_MA2Cscore.wig).
.wig files containing normalized signals for each duplicate are also provided

value: female

tag: cell line

value: MDA-MB231 breast cancer cells

tag: integrated vector

tag: er status

tag: chip antibody

value: ChIP performed using a mix of anti-estrogen receptor antibodies:HC20 (Santa Cruz) and ERAb-10/TE111.SD11 (NeoMarkers).

value: anti-estrogen receptor

value: Santa Cruz

tag: chip antibody 2

tag: chip antibody 2 manufacturer

value: NeoMarkers

tag: chip antibody 2 catalog #


title: I019

tag: tissue

value: peripheral blood lymphocytes

value: F

value: MZ


title: CDM-LUXS-B1a

description:
552715A07_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time


title: I020

tag: gender

tag: twin

tag: age


title: AI2+CDM-LSRLUXS-30-A2a

description:
558764A06_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype

value: chemically-defined media (CDM) with 3uM AI-2 added

value: 30 minutes after ODA600 0.75


title: Lola-N replicate 1


title: I018

value: M

value: DZ


title: AI2+CDM-LUXS-30-B2b

description:
552781A09_44022_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: biological replicate


title: I017


title: I016


title: AI2+CDM-LUXS-30-B1b

description:
552715A09_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

tag: technical replicate


title: AI2+CDM-LUXS-30-B2a

description:
552781A09_44022_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: AI2+CDM-LUXS-30-B1a

description:
552715A09_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: MCF7, siCTRL ,biological replicate 3

city: Lyon

first: Didier

last: Auboeuf

address: 28 rue Laennec

institute: INSERM - CNRS [CRCL]

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Exon-level analyses were obtained using the Affymetrix Power Tools software, the RMA-sketch algorithm, core probesets, and antigenomic probes for background correction
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.mps

source_name: MCF7 cells

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

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% fetal bovine serum, MCF10A cells were cultured in 1:1 (DMEM)/HAM-F12 medium supplemented with 5% horse serum (Cambrex), 10 ng/ml human epidermal growth factor (PromoCell), 0.5 μg/ml hydrocortisone (Sigma), 10 μg/ml insulin (Sigma) and 100 ng/ml cholera toxin (Sigma).

extract_protocol: Total RNA was extracted using Tripure isolation reagent (Roche) according to the manufacturer's protocol

treatment_protocol: MCF7 and MCF10A were transfected for 48 h with either a control siRNA or with a single siRNA targeting a conserved region in both DDX5 and DDX17 transcripts; siRNA were used at a final concentration of 26.6 nM

tag: cell type

value: ER+ breast cancer

tag: cell line

tag: transfection

value: CTRL

tag: replicate


title: Muscle_old_control_983

city: Berlin

first: Jens

last: Fielitz

address: Augustenburger Platz 1

department: Cardiology

country: Germany

institute: Charité Universitätsmedizin Berlin

hyb_protocol: Fluidic station 450 protocol FS450_0001

scan_protocol: Scanning was performed using the the AFFYMETRIX GeneChip Scanner 3000 7G and the Affymetrix Genechip Command Console 2.0.0.1029

data_processing:
Date were quantile normalized using Partek Genomic Suite 6.5, RMA background correction and pre background adjustment for GC content
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: not applicable

source_name: skeletal muscle, orthopedic control

extract_protocol: Total RNA extracted with Trizol.

tag: individual

tag: group

value: old control

tag: disease

value: orthopedic control

tag: critical illness myopathy

value: skeletal muscle


title: I031

source_name: whole blood, healthy

tag: tissue


title: I014


title: AI2+CDM-LUXS-30-A2b

description:
558764A05_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: growth medium

tag: sampling time


title: Lola-N replicate 2

value: w-; + ; UAS-Dam-Lola-N

value: stage 10-11 embryos

value: w-; + ; UAS-Dam


title: AI2+CDM-LSRLUXS-30-B1b

description:
552715A10_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Muscle_old_control_964

tag: gender

value: female


title: I013

value: peripheral blood lymphocytes

tag: twin

tag: age


title: AI2+CDM-LUXS-30-A2a

description:
558764A05_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype

tag: biological replicate


title: Muscle_IPmnsCIM_IP_786

source_name: skeletal muscle, No Critical illness myopathy

value: IPmnsCIM

value: male

value: critically ill patient

value: No Critical illness myopathy


title: Muscle_old_control_987


title: MCF7, siDDX5 and DDX17,biological replicate 1

value: DDX5 and DDX17


title: MCF7, siCTRL ,biological replicate 2


title: AI2+CDM-LSRLUXS-B2b

description:
552781A06_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

value: chemically-defined media (CDM) with 3uM AI-2 added

tag: technical replicate

tag: probe set


title: I011

value: F

value: DZ


title: I012

value: M


title: AI2+CDM-LSRLUXS-B2a

description:
552781A06_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: Muscle_old_control_357

value: old control


title: AI2+CDM-LSRLUXS-B1b

description:
552715A06_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: I009


title: I010


title: I008


title: AI2+CDM-LSRLUXS-A2b

description:
558764A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Muscle_old_control_984

value: orthopedic control


title: I007


title: AI2+CDM-LSRLUXS-B1a

description:
552715A06_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: AI2+CDM-LSRLUXS-A2a

description:
558764A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: MCF7, siDDX5 and DDX17,biological replicate 3

tag: cell type

value: ER+ breast cancer

tag: cell line


title: AI2+CDM-LUXS-B2b

description:
552781A05_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Muscle_IPplsCIM_IP_743

source_name: skeletal muscle, Critical illness myopathy

value: IPplsCIM

value: Critical illness myopathy

value: skeletal muscle


title: MCF10A, siCTRL ,biological replicate 2

source_name: MCF10A cells

value: non-tumorigenic mammary epithelial cell lines

tag: transfection

value: CTRL

tag: replicate


title: I005

value: peripheral blood lymphocytes

value: MZ


title: I015


title: I004


title: Muscle_IPplsCIM_IP_739

tag: individual

tag: group

value: female

value: critically ill patient


title: caNFATc1 MKC, Rep.3

first: Valerie

last: Horsley

address: 266 Whitney Avenue

department: Department of Molecular, Cellular and Developmental Biology

description: Primary mouse keratinocytes infected with caNFATc1 retroviruses.

hyb_protocol: 2.5 ug of biotinylated, fragmented cDNA was hybridized at 45oC for 17 hours to the Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Processed chips were read using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Probe-level analyses were performed on the CEL files using the RMA algorithm and log2 transformations of the data were performed, both using the Agilent GeneSpring GX11 software.
Probe group file: MoEX-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Mouse keratinocytes, caNFATc1

label_protocol: RNAs were labeled using the Ovation Exon Module, Ovation Pico WT Asystem and Encore Biotin Module (Nugen) to generate biotinylated cDNA.

growth_protocol: Primary mouse keratinocytes were grown in low calcium keratinocyte growth media at 37oC and 7.5% CO2.

extract_protocol: Total RNA was extracted using Trizol LS and the Qiagen RNeasy Kit according to the manufacturer's protocol.

treatment_protocol: Keratinocytes were infected with retroviruses encoding a caNFATc1 or an empty vector (MSCV) control.

tag: strain/background

tag: genotype/variation

value: wild type

value: keratinocytes

tag: transgene expression

value: constitutively active NFATc1 (caNFATc1)


title: Muscle_IPplsCIM_IP_725

tag: disease

tag: critical illness myopathy

tag: tissue


title: I003

tag: gender

tag: twin

value: DZ

tag: age


title: MCF7, siDDX5 and DDX17,biological replicate 2

value: DDX5 and DDX17


title: AI2+CDM-LUXS-B1a

description:
552715A05_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

source_name: Haemophilus influenzae CZ4126/02 ΔluxS::Specr

tag: genotype

tag: growth medium

value: chemically-defined media (CDM) with 3uM AI-2 added

tag: sampling time

tag: biological replicate

tag: technical replicate


title: AI2+CDM-LUXS-A2b

description:
558764A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: I001

value: F


title: caNFATc1 MKC, Rep.2

tag: cell type


title: MCF7, siCTRL ,biological replicate 1

value: ER+ breast cancer

tag: cell line

tag: transfection

tag: replicate


title: Control MKC, Rep.2

description: Primary mouse keratinocytes infected with MSCV control retroviruses.

source_name: Mouse keratinocytes, MSCV control

tag: strain/background

tag: genotype/variation

tag: transgene expression

value: vector control


title: MCF10A, siDDX5 and DDX17,biological replicate 1


title: Muscle_IPmnsCIM_IP_785

tag: individual

tag: group

value: IPmnsCIM

tag: disease

tag: critical illness myopathy

value: No Critical illness myopathy

tag: tissue


title: I002

tag: gender

value: M

tag: twin

tag: age


title: AI2+CDM-LUXS-A2a

description:
558764A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype

tag: growth medium

tag: sampling time

tag: biological replicate

tag: technical replicate


title: Control MKC, Rep.3

tag: cell type


title: MCF10A, siDDX5 and DDX17,biological replicate 3

value: non-tumorigenic mammary epithelial cell lines

tag: cell line

tag: transfection

tag: replicate


title: Muscle_IPmnsCIM_IP_813

tag: individual

value: skeletal muscle


title: Control MKC, Rep.1

tag: strain/background

tag: genotype/variation

tag: transgene expression


title: AI2+CDM-LUXS-B2a

description:
552781A05_45023_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: AI2+CDM-LUXS-B1b

description:
552715A05_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Ep-PC-3

status: Public on May 05 2014

city: Notre Dame

first: Jessica

last: Hellmann

state: IN

address: 100 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

description: Nimblegen one-color microarray results for subpooled individual samples from peripheral populations exposed to a central climate regime

hyb_protocol: cDNA synthesis, sample labeling, hybridization, and microarray scanning were carried out following manufacturer’s instructions.  Briefly, 10 μg of total RNA was converted into double-stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Quality and quantity of cDNA was assessed using a 2100 Bioanalyzer (Agilent) and a NanoDrop. One μg of cDNA was labeled using with a NimbleGen One-Color DNA labeling kit (Roche NimbleGen, Inc.).  Six μg of labeled product was hybridized to each array for 16 h at 42 C. Arrays were washed with a NimbleGen Wash Buffer Kit and dried for 1 min in a Microarray High-Speed Centrifuge (Arrayit Corp).

scan_protocol: Microarrays were scanend at 2-μm resolution with a NimbleGen MS 200 Microarray Scanner. Hybridization and scanning were performed in the University of Notre Dame Genomics Core Facility. Array image data quality was assessed, and raw fluorescence intensity values for each probe were obtained using NimbleScan v2.5 software (Roche NimbleGen).

data_processing: Probes showing expression higher than background in more than half of the 12 microarrays were kept for statistical test. Raw gene expression data were log2 transformed and normalized using quintile normalization method (Bolstad et al. 2003). Array image data were processed using NimbleScan. For each species, probes showing expression higher than background in more than half of the 12 microarrays were kept for statistical test and constituted the set of “.”a were log2 transformed and normalized using quantile normalization method. Multiply-corrected two-way ANOVAs identified 6 (possibly overlapping) subsets of transcripts: those showing (1) up or (2) down regulation by source population (peripheral relative to central), those showing (3) up or (4) down regulation by treatment (peripheral relative to central), and those showing (5) up or (6) down-regulated interactions (“s). Up (down)-regulated interaction transcripts were defined as those whose expression in natal (non-natal) conditions was higher than in non-natal (natal) conditions. P-values were adjusted using Storey's FDR method within each species.

organism: Gesta propertius

source_name: Erynnis propertius, multiple late-instar larvae about to enter diapause, peripheral source, central treatment

label_protocol: Total RNA was fluorescently labeled using a Cy3 NimbleGen One-Color DNA Labeling Kit.

growth_protocol: Adult females were captured from southern Oregon (Central source population) and Vancouver Island, British Columbia (Peripheral source population) and housed in oviposition cages in portable greenhouses in each region. For Erynnis propertius between one and five mothers were housed per cage. Eggs from each female were transported to greenhouses at the University of Notre Dame and allowed to hatch under native climate conditions. Larvae from each mother were divided equally between two climate treatments representing 10-year average climate regimes for Medford, OR and Victoria, BC, as used in a previous phenotype experiment performed by Pelini et al. 2009. Climate treatments were carried out in Conviron MTR30 growth chambers throughout the larval growth period. E. propertius larvae were fed native hostplant (Quercus garryana) shipped from field sites; just before diapause, larvae were collected and frozen at -80C.

extract_protocol: Whole-body RNA from frozen individuals was extracted using an RNeasy kit (QIAGEN Inc.) over a period of two months. Extracted RNA from each experimental group was subpooled for biological replicates, transcribed into cDNA (Invitrogen Superscript).

treatment_protocol: Eggs were hatched in conditions representing their source population, then moved to Conviron MTR30 where they were raised in treatment conditions representative of 10-year averages for Medford OR, or Vancourver, WA.

tag: developmental stage

value: Larvae immediately pre-diapuase

tag: number of individuals pooled

tag: population

value: peripheral populations

tag: treatment

value: exposed to a central climate regime


title: Ep-CP-2

description: Nimblegen one-color microarray results for subpooled individual samples from central populations exposed to a peripheral climate regime

source_name: Erynnis propertius, multiple late-instar larvae about to enter diapause, central source, peripheral treatment

value: central populations

value: exposed to a peripheral climate regime


title: Ep-CC-1

description: Nimblegen one-color microarray results for subpooled individual samples from central populations exposed to a central climate regime

source_name: Erynnis propertius, multiple late-instar larvae about to enter diapause, central source, central treatment


title: EP-CC-2


title: Ep-CP-1


title: EP-CC-3


title: Ep-CP-3


title: Ep-PC-2


title: Ep-PC-1


title: Ep-PP-3

description: Nimblegen one-color microarray results for subpooled individual samples from peripheral populations exposed to a peripheral climate regime

source_name: Erynnis propertius, multiple late-instar larvae about to enter diapause, peripheral source, peripheral treatment


title: Pz-CP-3

organism: Papilio zelicaon

source_name: Papilio zelicaon, multiple late-instar larvae about to enter diapause, central source, peripheral treatment

growth_protocol: Adult females were captured from southern Oregon (Central source population) and Vancouver Island, British Columbia (Peripheral source population) and housed in oviposition cages in portable greenhouses in each region. Exactly one Paplio zelicaon mother was housed per cage. Eggs from each female were transported to greenhouses at the University of Notre Dame and allowed to hatch under native climate conditions. Larvae from each mother were divided equally between two climate treatments representing 10-year average climate regimes for Medford, OR and Victoria, BC, as used in a previous phenotype experiment performed by Pelini et al. 2009. Climate treatments were carried out in Conviron MTR30 growth chambers throughout the larval growth period. P. zelicaon were fed Petroselinum crispum, a suitable non-native host, propagated in the greenhouse; just before diapause, larvae were collected and frozen at -80C.


title: Pz-CC-2

source_name: Papilio zelicaon, multiple late-instar larvae about to enter diapause, central source, central treatment


title: Pz-PC-2

source_name: Papilio zelicaon, multiple late-instar larvae about to enter diapause, peripheral source, central treatment


title: Pz-PC-1


title: Muscle_IPmnsCIM_IP_846

tag: group

tag: gender

value: female

tag: age

tag: disease

value: critically ill patient

tag: critical illness myopathy

tag: tissue


title: Ep-PP-1


title: MCF10A, siDDX5 and DDX17,biological replicate 2

tag: cell type

tag: cell line

tag: transfection

value: DDX5 and DDX17


title: Pz-CC-3


title: Pz-CP-2


title: Ep-PP-2


title: Pz-CP-1


title: Pz-CC-1


title: Pz-PC-3


title: PZ-PP-2

source_name: Papilio zelicaon, multiple late-instar larvae about to enter diapause, peripheral source, peripheral treatment


title: 800uM Proline Pulse t=15 min

city: New York

first: David

last: Gresham

state: NY

address: 12 Waverly Place, Rm 203

department: Biology

institute: New York University

description: gene expression in nitrogen limited chemostats

hyb_protocol: Cy3 and Cy5 labeled cRNA was co-hybridized to an Agilent 60-mer DNA microarray at 65C for 16 hours.  DNA microarrays were washed using the standard Agilent wash protocol.

scan_protocol: DNA microarrays were scanned using an Agilent Technologies Scanner G2505B

data_processing: Probe intensities were determined using the Agilent Feature Exractor software and normalized between the Cy5 and Cy3 channel using a linear-loess normalization

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast nitrogen-limited chemostat

label_protocol: cDNA from each sample was generated using MMLV reverse transcriptase primed with a poly-dT primer containing the promoter sequence for T7 RNA polymerase.  Labeled cRNA was generated using T7 RNA polymerase and UTPs labeled with either Cy3 or Cy5.

growth_protocol: Chemostat cultures were maintained in aerobic Sixfors fermentors (Infors) at 30°C using constant stirring at 400rpm

extract_protocol: mRNA was prepared using hot acid phenol exatraction followed by purification using a QIAGEN RNeasy mini kit

treatment_protocol: All nitrogen-limiting media contained 800µM nitrogen regardless of the molecular form of the nitrogen and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins

tag: nutrient limitation or pulse

value: 800uM Proline

tag: steady-state or pulse

value: pulse

source_name: Ammonium limited chemostat D=0.12

tag: nutrient limitation

value: ammonium

value: steady-state


title: 800uM Proline Pulse t=30 min


title: Pz-PP-1

source_name: Papilio zelicaon multiple late-instar larvae about to enter diapause, peripheral source, peripheral treatment


title: 800uM Proline Pulse t=0 min


title: Pz-PP-3


title: 800uM Proline Pulse t=240 min


title: 800uM Proline Pulse t=5 min


title: 800uM Proline Pulse t=10 min


title: I006

source_name: whole blood, healthy

extract_protocol: genomic DNA was extracted from peripheral blood lymphocytes by the salt precipitation method

value: peripheral blood lymphocytes

tag: twin


title: 800uM Proline Pulse t=60 min


title: 800uM Proline Pulse t=180 min


title: 800uM Proline Pulse t=120 min


title: caNFATc1 MKC, Rep.1

tag: strain/background

tag: genotype/variation

value: wild type

value: keratinocytes

tag: transgene expression

value: constitutively active NFATc1 (caNFATc1)


title: 400uM Glutamine Pulse t=10 min

value: 400uM Glutamine


title: 400uM Glutamine Pulse t=120 min


title: 400uM Glutamine Pulse t=240 min


title: 400uM Glutamine Pulse t=5 min


title: 400uM Glutamine Pulse t=15 min


title: 400uM Glutamine Pulse t=30 min


title: 400uM Glutamine Pulse t=0 min

value: Glutamate


title: 400uM Glutamine Pulse t=180 min


title: Glutamate D=0.21


title: Urea D=0.2

value: Urea


title: Glutamate D=0.168


title: Glutamate D=0.068


title: 400uM Glutamine Pulse t=60 min


title: Glutamate D=0.13


title: MCF10A, siCTRL ,biological replicate 3

value: non-tumorigenic mammary epithelial cell lines

value: CTRL

tag: replicate


title: Proline D=0.16

value: Proline


title: Glutamine D=0.16

value: Glutamine


title: Proline D=0.12


title: Glutamine D=0.21


title: MCF10A, siCTRL ,biological replicate 1


title: Urea D=0.06


title: Urea D=0.13


title: Urea D=0.16


title: Glutamine D=0.06


title: Allantoin D=0.12

value: Allantoin


title: Allantoin D=0.06


title: Glutamine D=0.12


title: Arginine D=0.06

value: Arginine


title: Arginine D=0.12


title: Arginine D=0.21


title: Arginine D=0.16


title: Proline D=0.06


title: Proline D=0.21


title: Allantoin D=0.21


title: Allantoin D=0.16


title: Reverted hepatic stellate cells rHSC2

first: Robert

last: Schwabe

address: 1150 St. Nicholas Ave, Room 415

institute: Columbia University

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

source_name: Hepatic stellate cells isolated from Balb/c mice following 4 injections of CCl4 and a 45 day rest period

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Hepatic stellate cells were isolated from 2 groups of 18 week old male Balb/c mice using density centrifugation and subsequent retinoid autofluorescence-based FACS sorting:  Group 1: Quiescent HSCs were isolated from 18 week old normal Balb/c mice and lysed immediately after FACS sorting. Group 2: Hepatic stellate cells were isolated from 16 week old Balb/c mice that had previously been treated with 4 injections of CCl4 (0.5 ul/g body weight, two injections per week) followed by a rest period of 45 days. Hepatic stellate cells were lysed immediately after FACS sorting.

value: male

tag: strain

value: Balb/c

value: Hepatic stellate cells


title: Quiescent control hepatic stellate cells qHSC3

source_name: Quiescent hepatic stellate cells isolated from Balb/c mice

tag: gender

value: Quiescent hepatic stellate cells


title: Reverted hepatic stellate cells rHSC3


title: PDAC_Patient:GEO-PC-107_rep1

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

institute: Garvan Institute of Medical Research

description: PDAC tumour RNA, Patient:GEO-PC-107, replicate 1

hyb_protocol: Amplified cRNA (750ng) was hybridized onto Illumina human HT-12 arrays (V4) as per manufacturer's instructions

scan_protocol: Arrays were scanned on a Bead Array Reader (Illumina)

data_processing: Expression measurements were extracted using the GenomeStudio (version 2009.1) software (Illumina Inc), using no background correction or normalisation, and exported in one batch. This unnormalised data was Background corrected, log2 transformed, and quantile normalized, using lumi package in R.

label_protocol: mRNA samples (150ng/sample) were amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) as per manufacturer’s instructions. Amplified RNA was quantified using a NanoDrop (Thermo Scientific) and distribution of the amplified material was analysed in an 2100 Bioanalyzer (Agilent)

growth_protocol: Pancreas tissue was surgically removed from PDAC patients undergoing Whipple surgical resection.

extract_protocol: RNA was extracted from primary tissue using the Qiagen Allprep kit in accordance with the manufacturers instructions.

treatment_protocol: Tissue was immediately snap frozen in liquid nitrogen (for full protocol see APGI website: http://www.pancreaticcancer.net.au/).

value: Pancreas

value: PDAC


title: Reverted hepatic stellate cells rHSC1


title: Quiescent control hepatic stellate cells qHSC1


title: Reverted hepatic stellate cells rHSC4


title: PDAC_Patient:GEO-PC-105_rep1

description: PDAC tumour RNA, Patient:GEO-PC-105, replicate 1


title: Quiescent control hepatic stellate cells qHSC2


title: PDAC_Patient:GEO-PC-099_rep1

description: PDAC tumour RNA, Patient:GEO-PC-099, replicate 1


title: PDAC_Patient:GEO-PC-104_rep1

description: PDAC tumour RNA, Patient:GEO-PC-104, replicate 1


title: PDAC_Patient:GEO-PC-108_rep1

description: PDAC tumour RNA, Patient:GEO-PC-108, replicate 1


title: PDAC_Patient:GEO-PC-098_rep1

description: PDAC tumour RNA, Patient:GEO-PC-098, replicate 1


title: PDAC_Patient:GEO-PC-106_rep1

description: PDAC tumour RNA, Patient:GEO-PC-106, replicate 1


title: PDAC_Patient:GEO-PC-102_rep1

description: PDAC tumour RNA, Patient:GEO-PC-102, replicate 1


title: PDAC_Patient:GEO-PC-100_rep1

description: PDAC tumour RNA, Patient:GEO-PC-100, replicate 1