title: Stem_83DAT_24:00_rep3

source_name: Stem, 83 days after transplanting, 24:00, replicate 3

value: Stem


title: Root_76DAT_24:00_rep3

status: Public on Jan 13 2011

type: RNA

city: Tsukuba

first: Baltazar

last: Antonio

state: Ibaraki

address: Kannondai 2-1-2

department: Genome and Biodiversity Research

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression of root at nighttime 76 days after transplanting

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA (or entire labeled cRNA for samples with low yield) were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Root, 76 days after transplanting, 24:00, replicate 3

label_protocol: One-color spike-mix was added to the RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2008.

extract_protocol: For leaf blade, leaf sheath, root, stem, inflorescence, pistil, anther, lemma, palea, ovary and embryo samples, total RNA was extracted using RNeasy plant minikit (QIAGEN). For endosperm samples, total RNA was extracted with phenol and purified using the RNeasy mini spin column of the RNeasy plant mini kit. The extracted RNA was quantified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: synonym

value: Oryza sativa L. ssp. japonica

tag: cultivar

value: Nipponbare

tag: organ/tissue

value: Root

tag: growth/development stage

value: 76 days after transplanting

tag: sampling time

value: Nighttime 24:00


title: Stem_90DAT_12:00_rep3

description: Gene expression of stem at daytime 90 days after transplanting

source_name: Stem, 90 days after transplanting, 12:00, replicate 3

value: 90 days after transplanting

value: Daytime 12:00


title: Stem_83DAT_24:00_rep1

description: Gene expression of stem at nighttime 83 days after transplanting

source_name: Stem, 83 days after transplanting, 24:00, replicate 1

value: 83 days after transplanting


title: Root_76DAT_12:00_rep3

description: Gene expression of root at daytime 76 days after transplanting

source_name: Root, 76 days after transplanting, 12:00, replicate 3


title: Septic Shock_biological rep35 01-0062A

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Avenue

department: Pediatrics

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from septic shock patient

hyb_protocol: Standard Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Gene expression was measured using one patient sample per chip. Image files were captured using an Affymetrix GeneChip Scanner 3000. CEL files were subsequently preprocessed using Robust Multiple-Array Average (RMA) normalization and GeneSpring GX 7.3 software (Agilent Technologies, Palo Alto, CA). All signal intensity-based data were used after RMA normalization, which specifically suppresses all but significant variation among lower intensity probe sets. All chips representing patient samples were then normalized to the respective median values of controls.

label: biotin

organism: Homo sapiens

source_name: Children ≤ 10 years old

label_protocol: WT-Ovation Pico (NuGen)

extract_protocol: Qiagen extraction from PaxGene whole blood RNA collection tubes

treatment_protocol: standard ICU care for septic shock

tag: tissue

value: whole blood

tag: disease state

value: septic shock patient

tag: age (years)

tag: outcome

value: Survivor

tag: group

value: B


title: Septic Shock_biological rep32 01-0059A


title: Root_27DAT_12:00_rep3

description: Gene expression of root at daytime 27 days after transplanting

source_name: Root, 27 days after transplanting, 12:00, replicate 3

value: 27 days after transplanting


title: Septic Shock_biological rep36 05-0007


title: Root_27DAT_24:00_rep1

description: Gene expression of root at nighttime 27 days after transplanting

source_name: Root, 27 days after transplanting, 24:00, replicate 1


title: Root_27DAT_24:00_rep3

source_name: Root, 27 days after transplanting, 24:00, replicate 3


title: LeafSheath_76DAT_24:00_rep3

description: Gene expression of leaf sheath at nighttime 76 days after transplanting

source_name: Leaf sheath, 76 days after transplanting, 24:00, replicate 3

value: Leaf sheath


title: Root_76DAT_12:00_rep1

source_name: Root, 76 days after transplanting, 12:00, replicate 1


title: Root_27DAT_12:00_rep2

source_name: Root, 27 days after transplanting, 12:00, replicate 2


title: Root_27DAT_24:00_rep2

source_name: Root, 27 days after transplanting, 24:00, replicate 2


title: Root_27DAT_12:00_rep1

source_name: Root, 27 days after transplanting, 12:00, replicate 1


title: Septic Shock_biological rep29 01-0044A

value: Nonsurvivor

value: A


title: LeafSheath_76DAT_12:00_rep3

description: Gene expression of leaf sheath at daytime 76 days after transplanting

source_name: Leaf sheath, 76 days after transplanting, 12:00, replicate 3


title: LeafSheath_76DAT_24:00_rep1

source_name: Leaf sheath, 76 days after transplanting, 24:00, replicate 1


title: Septic Shock_biological rep31 01-0058A


title: Septic Shock_biological rep27 01-0034A

value: C


title: LeafSheath_27DAT_12:00_rep2

description: Gene expression of leaf sheath at daytime 27 days after transplanting

source_name: Leaf sheath, 27 days after transplanting, 12:00, replicate 2

value: Oryza sativa L. ssp. japonica


title: LeafSheath_76DAT_12:00_rep2

source_name: Leaf sheath, 76 days after transplanting, 12:00, replicate 2

value: Nipponbare


title: Septic Shock_biological rep28 01-0036A


title: Septic Shock_biological rep34 01-0061A


title: LeafSheath_27DAT_12:00_rep3

source_name: Leaf sheath, 27 days after transplanting, 12:00, replicate 3


title: LeafSheath_76DAT_24:00_rep2

source_name: Leaf sheath, 76 days after transplanting, 24:00, replicate 2


title: LeafSheath_76DAT_12:00_rep1

source_name: Leaf sheath, 76 days after transplanting, 12:00, replicate 1


title: LeafSheath_27DAT_24:00_rep1

description: Gene expression of leaf sheath at nighttime 27 days after transplanting

source_name: Leaf sheath, 27 days after transplanting, 24:00, replicate 1


title: LeafSheath_27DAT_24:00_rep3

source_name: Leaf sheath, 27 days after transplanting, 24:00, replicate 3


title: LeafSheath_27DAT_24:00_rep2

source_name: Leaf sheath, 27 days after transplanting, 24:00, replicate 2


title: LeafSheath_27DAT_12:00_rep1

source_name: Leaf sheath, 27 days after transplanting, 12:00, replicate 1


title: LeafBlade_125DAT_24:00_rep3

description: Gene expression of leaf blade at nighttime 125 days after transplanting

source_name: Leaf blade, 125 days after transplanting, 24:00, replicate 3

value: Leaf blade

value: 125 days after transplanting


title: Septic Shock_biological rep9 01-0033A

source_name: Children ≤ 10 years old


title: Septic Shock_biological rep33 01-0060A


title: Septic Shock_biological rep8 01-0030


title: LeafBlade_125DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 125 days after transplanting

source_name: Leaf blade, 125 days after transplanting, 12:00, replicate 3


title: Septic Shock_biological rep10 01-0045A


title: Septic Shock_biological rep12 01-0051A


title: Septic Shock_biological rep13 01-0052A


title: LeafBlade_125DAT_24:00_rep2

source_name: Leaf blade, 125 days after transplanting, 24:00, replicate 2

value: Nighttime 24:00


title: LeafBlade_76DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 76 days after transplanting

source_name: Leaf blade, 76 days after transplanting, 24:00, replicate 2

value: 76 days after transplanting


title: Septic Shock_biological rep14 01-0053A


title: LeafBlade_76DAT_12:00_rep1

description: Gene expression of leaf blade at daytime 76 days after transplanting

source_name: Leaf blade, 76 days after transplanting, 12:00, replicate 1

value: Daytime 12:00


title: LeafBlade_76DAT_24:00_rep3

source_name: Leaf blade, 76 days after transplanting, 24:00, replicate 3


title: LeafBlade_76DAT_12:00_rep3

source_name: Leaf blade, 76 days after transplanting, 12:00, replicate 3


title: Septic Shock_biological rep11 01-0049A


title: Septic Shock_biological rep5 01-0024


title: LeafBlade_27DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 27 days after transplanting

source_name: Leaf blade, 27 days after transplanting, 12:00, replicate 3


title: LeafBlade_125DAT_12:00_rep2

source_name: Leaf blade, 125 days after transplanting, 12:00, replicate 2


title: LeafBlade_76DAT_24:00_rep1

source_name: Leaf blade, 76 days after transplanting, 24:00, replicate 1


title: Septic Shock_biological rep7 01-0026


title: Root_76DAT_24:00_rep2

source_name: Root, 76 days after transplanting, 24:00, replicate 2

value: Root


title: Septic Shock_biological rep2 01-0014

value: whole blood


title: Septic Shock_biological rep3 01-0019

value: septic shock patient


title: LeafBlade_76DAT_12:00_rep2

source_name: Leaf blade, 76 days after transplanting, 12:00, replicate 2


title: LeafBlade_125DAT_12:00_rep1

source_name: Leaf blade, 125 days after transplanting, 12:00, replicate 1


title: LeafBlade_125DAT_24:00_rep1

source_name: Leaf blade, 125 days after transplanting, 24:00, replicate 1


title: Septic Shock_biological rep4 01-0021

value: Survivor


title: Septic Shock_biological rep6 01-0025


title: LeafBlade_27DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 27 days after transplanting

source_name: Leaf blade, 27 days after transplanting, 24:00, replicate 2


title: LeafBlade_27DAT_12:00_rep1

source_name: Leaf blade, 27 days after transplanting, 12:00, replicate 1


title: LeafBlade_27DAT_24:00_rep3

source_name: Leaf blade, 27 days after transplanting, 24:00, replicate 3


title: LeafBlade_27DAT_24:00_rep1

source_name: Leaf blade, 27 days after transplanting, 24:00, replicate 1


title: Murine knee joint_Operated (DMM)_7days_rep2

city: London

first: Annika

last: Burleigh

address: 65 Aspenlea Road

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: Imperial College London

hyb_protocol: The resulting biotin-labeled cDNA was hybridised to the GeneChip Mouse Gene 1.0 ST Array (MoGene_1-0_st-v1) (Affymetrix). Hybridisation was carried out using a GeneChip 450 fluidics station and GeneChip Hybridization Oven 640 at UCL Genomics Department (University College London, London, UK) using a standard protocol.

scan_protocol: Genechips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) at UCL Genomics Department (University College London, London, UK).

data_processing: Data were processed using aligent Genespring GX software and Robust multiarray average (RMA-16) normalisation algorithim. Default settings for Affymetrix single probe genechips were used. Each sample was assigned the parameter 'time' (time post surgery) and 'treatment' (type of surgery). Signal intensity values for all experimental replicates were average and used for analysis.

organism: Mus musculus

source_name: Whole murine knee joint, destabilised medial meniscus (DMM), 7days post surgery

label_protocol: 100ng of total RNA from each sample underwent the first cycle of 1st and 2nd strand cDNA synthesis and subsequent in vitro transcription of antisense RNA (cRNA) using the GeneChip WT cDNA Synthesis and Amplification Kit (900673) (Affymetrix, Santa Clara, CA, USA) following manufacturer’s instructions. cRNA was cleaned up using the GeneChip Sample Clean-up Module, Affymetrix (900371). 10ug of cRNA was put into the second cycle of 1st strand cDNA synthesis using random primers and cRNA hydrolised using the GeneChip WT cDNA Synthesis and Amplification Kit, Affymetrix (900673). cDNA was cleaned up using the GeneChip Sample Clean-up Module, Affymetrix (900371) and 5.5ug single stranded cDNA fragmented and labeled using the GeneChip WT Terminal Labeling Kit, Affymetrix (900671).

growth_protocol: Upon receipt from Harlen the mice were kept in an approved animal-care facility, with strict compliance to care and usage protocols. All mice were housed 3-6 per cage in 63x54x30 cm3 standard IV cages and maintained with a 12 h/12h light/dark cycle at an ambient temperature of 21°C. Animals were fed a certified mouse diet (RM3 from Special Dietary Systems, Essex, UK) and water ad libitum.

extract_protocol:
Ipsilateral (right) legs were removed and ‘debulked’ by removing skin and surrounding muscle. The joint was isolated by sharp severance at the upper and lower edges of the para-pateller tendon ensuring the joint capsule was left intact. These were regarded as reliable, fixed anatomical landmarks.
Harvested knees were snap frozen immediately in liquid nitrogen and kept on dry ice or at -70degC until homogenisation. Frozen tissue was freeze fractured using a pre chilled bio-pulveriser (Stratech Ltd, Suffolk, UK). The resulting fine powder was added to 1ml of TRI® reagent (Trizol) (Helena Biosciences Europe, Sunderland, UK). Trizol extraction protocol was then performed using 1-Bromo-3-Chloropropane (BCP) as a phase separation agent. The upper RNA containing aqueous layer was carefully aspirated and RNA precipitated in an equal volume of 70% ethanol prior to binding on a QIAmp spin column and washed using QIAamp RNA Blood Mini Kit (Qiagen, Hilden, DE) according to the manufacturer’s protocol. RNAase-free DNAase (Qiagen) was used at an intermediate step during the procedure to reduce DNA contamination of the extracted RNA. RNA was eluted in 40ul of Nuclease free water (Promega) and was stored at -80degC until further use.

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field. The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach, thus avoiding damage to the medial collateral ligament and minimizing trauma to the quadriceps. The medial menicus was identified and the attachments of its anterior horn to the tibial plateau cut using a 3mm 15deg ophthalmic scalpel. Care was taken to avoid injury to the anterior cruciate ligament and the cartilage surfaces. The anterior third of the meniscus moved freely between the medial femoral condyle and tibial plateau.
The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage. The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 7 days post surgery.

tag: strain

value: C57B/6; Gender:Male; Age:10wks; Treatment:operated, destabilisation of medial meniscus (DMM) surgery; Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: Murine knee joint_Operated (Sham)_7days_rep2

source_name: Whole murine knee joint_Capsulotomy (Sham)_7days post surgery

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field. The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach. The medial menicus was identified as if for Destabilisation of medial meniscus (DMM) surgery but was not cut. The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage. The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 7 days post surgery.

value: C57B/6; Gender:Male; Age:10wks; Treatment:operated, Capsulotomy (Sham surgery for DMM model); Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: Murine knee joint_Operated (DMM)_6hr_rep3

hyb_protocol: The resulting biotin-labeled cDNA was hybridised to the GeneChip Mouse Gene 1.0 ST Array (MoGene_1-0_st-v1) (Affymetrix).  Hybridisation was carried out using a GeneChip 450 fluidics station and GeneChip Hybridization Oven 640 at UCL Genomics Department (University College London, London, UK) using a standard protocol.

source_name: Whole murine knee joint, destabilised medial meniscus (DMM), 6hrs post surgery

growth_protocol: Upon receipt from Harlen the mice were kept in an approved animal-care facility, with strict compliance to care and usage protocols.  All mice were housed 3-6 per cage in 63x54x30 cm3 standard IV cages and maintained with a 12 h/12h light/dark cycle at an ambient temperature of 21°C.  Animals were fed a certified mouse diet (RM3 from Special Dietary Systems, Essex, UK) and water ad libitum.

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field. The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach, thus avoiding damage to the medial collateral ligament and minimizing trauma to the quadriceps. The medial menicus was identified and the attachments of its anterior horn to the tibial plateau cut using a 3mm 15deg ophthalmic scalpel. Care was taken to avoid injury to the anterior cruciate ligament and the cartilage surfaces. The anterior third of the meniscus moved freely between the medial femoral condyle and tibial plateau.
The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage. The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 6hrs post surgery.


title: Murine knee joint_Operated (Sham)_6hr_rep1

source_name: Whole murine knee joint_Capsulotomy (Sham)_6hrs post surgery

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field. The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach. The medial menicus was identified as if for Destabilisation of medial meniscus (DMM) surgery but was not cut. The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage. The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 6hrs post surgery.


title: Control_biological rep17

description: Gene expression data from normal control

source_name: Children ≤ 10 years old

value: Whole Blood

value: normal control


title: Murine knee joint_Operated (Sham)_6hr_rep2


title: ASD3866

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

description: Total RNA of peripheral blood from subjects recruited from our research volunteer pool by the National Center of Neurology and Psychiatry (NCNP), Japan and by the Faculty of Medicine, the University of Tokushima.

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).

data_processing: Raw data output was imported into Genespring GX10 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization), and normalized each probe to the median expression of matched control intensity for that gene across all samples (per gene normalization). Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present.

source_name: human, venous blood leukocytes

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. The microarrays used were Agilent’s Whole Human Genome Oligo Microarrays (P/N G4112A). Probe sequence information is publicly available at Agilent's website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: Venous blood (5 ml) was taken from each subject and immediately poured into PAXgeneTM blood RNA tubes (Qiagen, Hilden, Germany). Total RNA was purified using a PAXgene Blood RNA kit (Qiagen) according to the manufacture’s protocol. Contaminated DNA was removed using a DNase kit (Qiagen). The quality of the purified RNA and its applicability for microarray analysis were assessed by the Agilent 2100 Bioanalyzer using a RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: disease

value: Autism spectrum disorder

tag: cell type

value: human blood leukocytes

tag: sample type

value: ASD

tag: sample id


title: Murine knee joint_Operated (Sham)_7days_rep1


title: Murine knee joint_Operated (DMM)_3day_rep2

scan_protocol: Genechips were scanned using the GeneChip® Scanner 3000 7G  (Affymetrix) at UCL Genomics Department (University College London, London, UK).

data_processing: Data were processed using aligent Genespring GX software and Robust multiarray average (RMA-16) normalisation algorithim.  Default settings for Affymetrix single probe genechips were used.  Each sample was assigned the parameter 'time' (time post surgery) and 'treatment' (type of surgery).  Signal intensity values for all experimental replicates were average and used for analysis.

source_name: Whole murine knee joint_destabilised medial meniscus (DMM)_3days

label_protocol: 100ng of total RNA from each sample underwent the first cycle of 1st and 2nd strand cDNA synthesis and subsequent in vitro transcription of antisense RNA (cRNA) using the GeneChip WT cDNA Synthesis and Amplification Kit (900673) (Affymetrix, Santa Clara, CA, USA) following manufacturer’s instructions.  cRNA was cleaned up using the GeneChip Sample Clean-up Module, Affymetrix (900371).  10ug of cRNA was put into the second cycle of 1st strand cDNA synthesis using random primers and cRNA hydrolised using the GeneChip WT cDNA Synthesis and Amplification Kit, Affymetrix (900673).   cDNA was cleaned up using the GeneChip Sample Clean-up Module, Affymetrix (900371) and 5.5ug single stranded cDNA fragmented and labeled using the GeneChip WT Terminal Labeling Kit, Affymetrix (900671).

extract_protocol:
Ipsilateral (right) legs were removed and ‘debulked’ by removing skin and surrounding muscle.  The joint was isolated by sharp severance at the upper and lower edges of the para-pateller tendon ensuring the joint capsule was left intact.  These were regarded as reliable, fixed anatomical landmarks.
Harvested knees were snap frozen immediately in liquid nitrogen and kept on dry ice or at -70degC until homogenisation. Frozen tissue was freeze fractured using a pre chilled bio-pulveriser (Stratech Ltd, Suffolk, UK).  The resulting fine powder was added to 1ml of TRI® reagent (Trizol) (Helena Biosciences Europe, Sunderland, UK).  Trizol extraction protocol was then performed using 1-Bromo-3-Chloropropane (BCP) as a phase separation agent.    The upper RNA containing aqueous layer was carefully aspirated and RNA precipitated in an equal volume of 70% ethanol prior to binding on a QIAmp spin column and washed using QIAamp RNA Blood Mini Kit (Qiagen, Hilden, DE) according to the manufacturer’s protocol.  RNAase-free DNAase (Qiagen) was used at an intermediate step during the procedure to reduce DNA contamination of the extracted RNA.  RNA was eluted in 40ul of Nuclease free water (Promega) and was stored at -80degC until further use.

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field.  The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach, thus avoiding damage to the medial collateral ligament and minimizing trauma to the quadriceps. The medial menicus was identified and the attachments of its anterior horn to the tibial plateau cut using a 3mm 15deg ophthalmic scalpel.  Care was taken to avoid injury to the anterior cruciate ligament and the cartilage surfaces. The anterior third of the meniscus moved freely between the medial femoral condyle and tibial plateau.
The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage.  The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 3 days post surgery.

value: C57B/6; Gender:Male; Age:10wks; Treatment:operated, destabilisation of mediasl meniscus (DMM) surgery; Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: Murine knee joint_Operated (DMM)_7days_rep3


title: Murine knee joint_Operated (DMM)_7days_rep1


title: ASD3875

value: nonaustistic control

value: control


title: Murine knee joint_Operated (Sham)_6hr_rep3


title: Murine knee joint_Operated (Sham)_7days_rep3


title: Murine knee joint_Operated (DMM)_6hr_rep1


title: ASD3878


title: Murine knee joint_Operated (Sham)_3day_rep2

source_name: Whole murine knee joint_Capsulotomy (Sham)_3days

treatment_protocol:
10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.
The ventral portion of the right (Ipsilateral) knee was shaved and swabbed with iodine to prepare a sterile surgical field. The surgical procedure was carried out with the aid of a dissecting microscope.
A midline incision over the ventral aspect of the knee was made with a no.15 scalpel and the medial compartment entered via a medial para-patellar approach. The medial menicus was identified as if for Destabilisation of medial meniscus (DMM) surgery but was not cut. The para-pateller window was closed using an absorbable 6/0 Vicryl suture (W9575) and a round-bodied needle to avoid tissue damage. The skin was closed using a 5/0 Ethilon suture (W1601T) with reverse cut needle (Ethilon, USA).
Mice were culled and knees harvested 3 days post surgery.


title: Murine knee joint_Naive_0hr_rep3

source_name: Whole murine knee joint_non-operated_0hr

treatment_protocol: 10 week old male mice were anaesthetized by intra-peritoneal injection of a 1:1:2 mixture of Hypnorm (0.315mg/ml fentanyl citrate and 10mg/ml fluanisone; VetaPharma Ltd, Leeds, UK), Hypnovel (5mg/ml midazolam; Roche), and sterile water for injection, at a dose of 10ml/kg body weight.  Mice were left under anaesthetic for 15min, the time it would normally take to perform surgery to destabilise the Medial Meniscus (DMM surgery), prior to culling.

value: C57B/6; Gender:Male; Age:10wks; Treatment:non-operated; Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: ASD3867


title: ASD3870


title: Murine knee joint_Operated (DMM)_3day_rep3


title: Murine knee joint_Operated (DMM)_3day_rep1

source_name: Whole murine knee joint, destabilised medial meniscus (DMM), 3days post surgery


title: ASD3880


title: Murine knee joint_Naive_0hr_rep2


title: Murine knee joint_Operated (Sham)_3day_rep3


title: Murine knee joint_Naive_0hr_rep1

source_name: Whole murine knee joint, non-operated, 0hr


title: ASD3877


title: ASD3864


title: ASD3863


title: LeafBlade_27DAT_12:00_rep2

source_name: Leaf blade, 27 days after transplanting, 12:00, replicate 2

value: Oryza sativa L. ssp. japonica

value: Nipponbare

value: Leaf blade

value: 27 days after transplanting


title: ASD3757


title: ASD3865


title: ASD3844


title: ASD2799


title: ASD3759


title: ASD2801


title: ASD3843


title: ASD3842


title: ASD3749


title: ASD1491

value: control (ctrlMO)


title: ASD3869


title: ASD3841

value: nonaustistic

value: healthy women who had children with ASD (asdMO)


title: ASD3839


title: ASD1416


title: ASD3334


title: Murine knee joint_Operated (DMM)_6hr_rep2

value: C57B/6; Gender:Male; Age:10wks; Treatment:operated, destabilisation of medial meniscus (DMM) surgery; Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: ASD2689


title: ASD3838


title: ASD3840


title: ASD1574


title: ASD3873


title: ASD3836


title: ASD3833


title: Septic Shock_biological rep37

value: Whole Blood

value: septic shock patient

value: Survivor


title: ASD3835

value: human blood leukocytes


title: ASD2871


title: ASD3837


title: ASD3830


title: Septic Shock_biological rep41

value: Nonsurvivor


title: ASD1415


title: ASD2836


title: ASD3335


title: ASD3829

value: Autism spectrum disorder

value: ASD


title: ASD3834


title: ASD3832


title: ASD1405

value: nonaustistic control


title: ASD3626


title: ASD3831


title: ASD1467


title: ASD3624


title: ASD3723

value: control


title: ASD2800


title: ASD2834


title: ASD3619


title: ASD3623


title: ASD3621


title: ASD1387


title: ASD3874


title: ASD3868


title: ASD3622


title: ASD3625


title: Murine knee joint_Operated (Sham)_3day_rep1

value: C57B/6; Gender:Male; Age:10wks; Treatment:operated, Capsulotomy (Sham surgery for DMM model); Tissue:whole knee joint, skin and muscle bulk removed, sample taken using ends of patella and quadriceps tendon as anatomical dissection markers.


title: ASD1934


title: ASD3620


title: inVitro6-Normox_NAg13P

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 3620 Hamilton Walk

department: Radiation Oncology

institute: University of Pennsylvania

hyb_protocol: Microarrays were stained with streptavadin-phycoerythrin and incubated with biotinylated anti-streptavadin to enhance fluorescence signal detection. Comparison of signal intensity yielded relative gene expression under hypoxia/normoxia.

scan_protocol: standard Affymetrix scan protocol

data_processing: Affymetrix .cel files were imported into Partek Genomics Suite (v6.5b, Partek Inc., St. Louis, MO). Robust Multichip Average (RMA) normalization was applied.

label: Biotin

organism: Rattus norvegicus

source_name: 9L glioma cells

label_protocol: The resulting amplified cDNA was fragmented, biotinylated and hybridized to Rat Gene 1.0ST Arrays (Affymetrix).

growth_protocol: Six week old male Fischer 344 rats (F344/Ncr, NCI-Frederick, MD) were inoculated via subcutaneous injection on the hind flank with 9L cells (106) to generate passage ‘zero’ tumors (p0). The tumor was excised, cut into 1-2mm3 pieces and used to generate subsequent passages. The epigastric tumors were initiated by tying p5 or p6 tumor pieces onto the epigastric artery-vein pair. 9L gliosarcoma cells were grown in MEM media with 12% newborn calf serum with twice-weekly transfer.

extract_protocol: The RNAqueous-micro kit from Ambion which includes an application for LCM-generated tissue was used to isolate total RNA. A DNase I treatment was performed according to the manufacturer’s protocol. An additional centrifugation step (14,000rpm for 1.5 min) and subsequent supernatant removal were performed to ascertain that all resin had been eliminated. Total RNA was linearly amplified using the NuGEN Ovation WT-Pico kit. Briefly, total RNA (2ng/sample) was reverse transcribed to generate cDNA that incorporated an RNA primer binding sequence. After second-strand synthesis, cDNA templates were amplified by ribo-SPIA. T

treatment_protocol: For in vivo samples: LCM was applied to EF5-positive and negative areas. For in vitro samples: To initiate the experiment, cells were either incubated at ~20% O2 (“Normoxia”) or 0.2% O2 (“Hypoxia”) for 6h or 16h. Cells were subsequently washed with HBSS (Invitrogen), detached with 0.25% trypsin-EDTA and resuspended in RNA lysis solution (Ambion) at a concentration of 50,000cells/100μl lysis solution.

value: Fisher

value: 9L glioma cells

tag: condition

value: Cells exposed to normoxia


title: ASD3613


title: ASD3618


title: inVitro6-Hypox_HAg13P

value: Cells exposed to hypoxia


title: inVitro6-Hypox_HAg26P


title: Septic Shock_biological rep29


title: ASD2859

value: control (ctrlMO)


title: inVitro6-Hypox_HAg6P


title: inVitro6-Normox_NAg26P


title: Septic Shock_biological rep14


title: ASD3876


title: ASD3616


title: ASD3612

value: nonaustistic

value: healthy women who had children with ASD (asdMO)


title: ASD2833


title: inVitro16-Hypox_HY29


title: inVitro16-Hypox_HY28


title: ASD3825


title: ASD1922


title: inVitro6-Normox_NAg6P


title: inVitro16-Normox_NO29


title: ASD3331


title: ASD3333


title: inVitro16-Normox_NO22


title: ASD2872


title: Patient 110

city: Dundee

first: Gino

last: Miele

address: James Arrot Drive, Ninewells Hospital

institute: Translational Medicine Research Collaboration

description: Gene expression data from endothelial cells

hyb_protocol: Following fragmentation, cDNA probes were hybridised for 18 hrs at 45oC to Genechip Human U133 Plus 2.0 arrays. Arrays were stained and washed in Affymetrix fluidics station 450 using fluidics script FS450-0004

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000 and software GCOS for image processing

data_processing: Report files summarising the arrays were generated using GCOS and the MAS5.0 algorithm. Quality control metrics were generated using Expression console (Affymetrix) and data visualisation using Partek software.

source_name: Endothelial cells, condition B

label_protocol: Biotinylated cDNA probes were synthesised according to the WT-Ovation FFPE RNA Amplificiation system V2 protocol followed by fragmentation and labelling using the FL-ovation cDNA Biotin module V2 (NuGEN Technologies Inc).

extract_protocol: RNA extracted from CD146-enriched endothelial cells using a Rneasy micro kit modified method optimal for high yield from minimal input material

value: B

tag: cdna quality

tag: patient gender

value: Male

tag: age

tag: rna isoaltion batch

tag: rna yield (ug)

tag: cdna batch

tag: cdna yield (ng)

tag: fragmentation batch

tag: hybridisation batch


title: ASD3332


title: Patient 114


title: inVitro16-Normox_NO28


title: ASD3617


title: Patient 116


title: Patient 113


title: Patient 115


title: Patient 120


title: Tumor 3-inVIVO-Normox_Sp8N

source_name: 9L glioma tumor

value: 9L glioma tumor

value: Normoxic region


title: Tumor 2-inVIVO-Normox_Ag26PN


title: Patient 108


title: ASD3795

value: human blood leukocytes


title: Patient 102


title: Patient 119


title: Patient 106


title: inVitro16-Hypox_HY22


title: ASD3327


title: Tumor 2-inVIVO-Hypox_Ag26PH

value: Hypoxic region


title: Patient 98


title: Tumor 3-inVIVO-Hypox_Sp8H


title: Patient 99


title: Patient 100


title: ASD3872


title: muscle MeDIP replicate 1 (slide 1 of 2)

type: genomic

city: Salt Lake City

first: Shan-Fu

last: Wu

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description:
Biological replicate 1 of 2, MeDIP-chip in zebrafish adult muscle
MeDIP muscle-rep1

hyb_protocol: Fluorescently labeled DNA samples were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution. Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization Oven and were incubated at 65ºC for 40 hours with a rotational speed of 20 rpm. Following incubation, the microarray slide was washed for 5 minute in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC). Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution. TIF files generated from the scanned microarray image were loaded into Agilent Feature Extraction Software version 10.1.1.1 for processing.

data_processing:
TIMAT2, the open source application, was used in this analysis and obtained from the project website, http://sourceforge.net/projects/timat2. Zebrafish annotation and genomic sequence (Zv7 assembly, April 2007) were retrieved from the Ensembl website. Microarray data from two biological replicas or inputs were first quantile normalized and median scaled to 100. Oligos with calculated enrichment ratio (mean ChIP / mean Input in the log2 ratio) were then mapped to Zv7 assembly.
Our analysis program is able to extract data from either ch1 or ch2, so we put different ChIP eluates on the same microarray. Some samples come from the same input when performing ChIP experiments, so we don't need Input on each microarray. This way we can save slides during hybridization.

molecule: genomic DNA

organism: Danio rerio

source_name: muscle

label_protocol: The pulled-down fragments and input from MeDIP and ChIP were amplified by whole genome amplification kit (Sigma WGA2). Amplified DNA samples were labeled using the Invitrogen BioPrime Array CGH Genomic Labeling Module. The labeling kit uses random primers and the exo-Klenow fragment to label DNA through incorporation of fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP). Following termination of the labeling reaction, fluorescently labeled DNA molecules were purified by isopropanol precipitation. Precipitated pellets were dried and then rehydrated in distilled water. The concentration of purified samples was determined using a NanoDrop ND-1000 spectrophotometer.  A fraction of the labeled DNA (100 ng) was run on an Agilent BioAnalyzer to validate the size distribution of the labeled DNA molecules.

extract_protocol:
For MeDIP, 4 μg of sheared genomic DNA (~400 bp) from mature sperm cells or dissected muscle tissues were incubated with Dynabeads (Invitrogen) conjugated with antibody against 5-methylcytidine (Eurogentec BI-MECY-1000).
For ChIP, 10e7 of sperm cells were treated with 0.05% lysophosphatidylcholine (Sigma L1381) in PBS on ice for 10 minutes. 15 units of micrococcal nuclease (MNase, USB 70196Y) was then applied to release oligonucleosomes at 37ºC for 5 minutes. 2 μg of specific antibody conjugated to Dynabeads were incubated with the oligonucleosomes. Bound complexes were washed sequentially with washing buffer (50 mM Hepes pH 7.5, 1 mM EDTA, 0.4% Triton X-100) with 140 mM NaCl, 250 mM NaCl, and buffer (10 mM Tris pH 8, 1 mM EDTA, 0.4% NP-40) with 200 mM LiCl. DNA fragments were eluted with TES (50 mM Tris, pH 8, 10 mM EDTA, 1% SDS) and decrosslinked at 65ºC for overnight. After RNase treatment, eluate and input DNA were purified by Qiagen PCR purification kit.

tag: tissue

value: muscle

tag: chromatin feature

value: Input

value: Tu

tag: chip antibody

value: none (input)

value: muscle MeDIP rep1


title: muscle MeDIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, MeDIP-chip in zebrafish adult muscle
MeDIP muscle-rep2

tag: strain

value: muscle MeDIP rep2


title: sperm MeDIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, MeDIP-chip in zebrafish sperm
MeDIP sperm-rep2

source_name: mature sperm

tag: cell type

value: mature sperm

value: sperm MeDIP rep2


title: Patient 93


title: Patient 97


title: Tumor 1-inVIVO-Hypox_Ag25PH

value: Fisher


title: ASD3879

tag: disease

value: nonaustistic control

tag: sample type

value: control


title: ASD3326

value: Autism spectrum disorder

value: ASD

tag: sample id


title: Patient 90

tag: condition

value: B

tag: cdna quality

value: Male


title: Patient 92

tag: patient gender

tag: age


title: Tumor 1-inVIVO-Normox_Ag25PN

value: 6 weeks old

tag: Sex

value: male

value: 9L glioma tumor

value: Normoxic region


title: Patient 91

tag: rna isoaltion batch

tag: rna yield (ug)

tag: cdna batch


title: sperm expression replicate 2

description:
Biological replicate 2 of 2, total RNA from zebrafish sperm
sperm exp-rep2

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers. Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm. Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each. Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution. TIF files generated from the scanned microarray image were loaded into Agilent Feature Extraction Software version 9.5.1 for processing.

data_processing:
Data were extracted with Agilent Feature Extraction Software version 9.5.1 and LOWESS normalization.
The data table includes all oligos that have intensity detected above background. The reason for the small percentage of the array features is because transcription in sperm is almost inactive.

source_name: whole fish

label_protocol: The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.   Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

extract_protocol: Mature sperm cells were screened under microscope. RNA from 6 x 10e7 of mature sperm cells was extracted with Qiagen RNA isolation kit.

value: whole fish

value: Tu


title: sperm expression replicate 1

description:
Biological replicate 1 of 2, total RNA from zebrafish sperm
sperm exp-rep1


title: Patient 81

tag: cdna yield (ng)

tag: fragmentation batch

tag: hybridisation batch


title: Patient 89


title: Patient 87


title: ASD3329

value: nonaustistic

value: human blood leukocytes

value: healthy women who had children with ASD (asdMO)


title: ASD3330


title: Patient 77


title: sperm MeDIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, MeDIP-chip in zebrafish sperm
MeDIP sperm-rep1

value: mature sperm

tag: chromatin feature

value: Input

tag: chip antibody

value: none (input)

value: sperm MeDIP rep1


title: ASD1816

value: nonaustistic control

tag: cell type

value: control (ctrlMO)


title: Patient 78

value: B


title: ASD3328

tag: disease

value: Autism spectrum disorder

value: ASD


title: Patient 80

value: Male


title: Patient 83


title: Patient 75


title: TW03-LMP2A-2 CM200_006

type: other

city: Stockholm

first: ZiMing

last: Du

address: Nobels vagen

country: Sweden

institute: Karolinska Institutet

description: Sample was used for hybridization on each miRNA microarray chip containing 509 probes in triplicate, corresponding to 435 human (including 122 predicted miRNAs), 261 mouse, and 196 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk/sequences/; accessed October 2005).

hyb_protocol: Standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Image intensities were measured as a function of the median of foreground minus the background

data_processing: Raw data were normalized and analyzed in GenePix Pro 4.0 software (Axon Instruments)

source_name: Naspharyngeal Carcinoma cell line

label_protocol: MiRNAs was labeled with Flurescein, as described as (Thomson JM, 2004).About 2μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

growth_protocol: All the cell line were cultured in IMEM (Gibco USA) containing 10% fetal calf serum.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, USA), then miRNA was separated from 30-50 mg total RNA using the Ambion miRNA Isolation Kit.

treatment_protocol: TW03 cells was transfected with LMP1 expressing vector (pJ124-A8-CAO-LMP1), then selected by mycophenolic acid, Xanthine and Hypoxanthine . TW03 cells expressing LMP2A were generated by retrovirus infection and G418 selection.

tag: cell line

value: TWO3-EBV transfected with LMP2A


title: TW03LMP1-2 CM200_004

value: TWO3-EBV transfected with LMP1


title: sperm H3K36me3 ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H3K36me3 ChIP-chip in zebrafish sperm
H3K36me3-rep2

tag: strain

value: H3K36me3 ChIP rep2


title: sperm H3K36me3 ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K36me3 ChIP-chip in zebrafish sperm
H3K36me3-rep1

value: H3K36me3 ChIP rep1

value: Tu

value: H3K9me3 ChIP rep1


title: Patient 73

tag: condition


title: Patient 71

tag: cdna quality


title: TW03LMP1-1 CM200_003


title: sperm H3K9me3 ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K9me3 ChIP-chip in zebrafish sperm
H3K9me3-rep1


title: TW03LMP2A-1 CM200_005


title: TW03-2 CM200_002


title: Patient 67

tag: patient gender


title: sperm H2AFV ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H2AFV ChIP-chip in zebrafish sperm
H2AFV-rep2

value: H2AFV ChIP rep2

value: N/A (experiments that either failed or serve as a pilot study)


title: sperm H2AFV ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H2AFV ChIP-chip in zebrafish sperm
H2AFV-rep1

value: mature sperm

value: H2AFV ChIP rep1


title: TW03-1 CM200_001


title: Patient 65

tag: age


title: Patient 60


title: ASD1490

value: human blood leukocytes

tag: sample type

tag: sample id


title: Patient 70

tag: rna isoaltion batch

tag: rna yield (ug)


title: sperm H3K27me3 ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H3K27me3 ChIP-chip in zebrafish sperm
H3K27me3-rep2

value: H3K27me3 ChIP rep1

value: H3K14ac ChIP rep2


title: Patient 48

value: B

value: Female

tag: cdna batch

tag: cdna yield (ng)


title: Patient 52

tag: fragmentation batch

tag: hybridisation batch


title: Patient 56


title: sperm H3K27me3 ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K27me3 ChIP-chip in zebrafish sperm
H3K27me3-rep1

tag: chromatin feature

value: H3K14ac ChIP rep1

tag: chip antibody


title: ASD3871

tag: disease

value: nonaustistic control

tag: cell type

value: control (ctrlMO)


title: Patient 45

value: Male


title: sperm H3K14ac ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K14ac ChIP-chip in zebrafish sperm
H3K14ac-rep1

tag: strain


title: Turkey Muscle Array ALD_19_17

city: Raleigh

first: Lidia

middle: Sylwia

last: Nierobisz

state: NC

address: 2711 Founders Dr.

institute: North Carolina State University

description: 19 wks,bird 6

hyb_protocol: The microarray slides were pre-hybridized and hybridized using Pronto Plus Microarray Hybridization Kit (Corning Inc., Corning, NY).  The Cy3- and Cy5-labeled cDNA samples were applied to pre-hybridized array slides and covered with a pre-cleaned glass cover slip (Lifterslip, Portsmouth, NH).  The slides were hybridized for 18 hours at 42°C, washed, and air-dried by centrifugation in a slide centrifuge for 2 minutes.

scan_protocol: The hybridized microarray slides were scanned using a ScanArray Gx PLUS Microarray Scanner (PerkinElmer Life and Analytical Sciences, Shelton, CT) with laser intensity adjusted to 65%.  The ScanAlyze Software (Stanford University, Stanford, CA) was utilized to extract the intensity of the scanned array spots for each dye combination on each array slide.  The intensity of the data points was then analyzed with JMP Genomics software (SAS Institute Inc., Cary, NC).

data_processing: Data was first Log2 transformed and then normalized by using locally weighed regression and smoothing within each array and across all arrays.  The normalized data was evaluated by distribution analysis of the transformed data.  Mixed model ANOVA [32] with Bonferroni correction of P=0.05 for multiple testing was performed to increase the sensitivity of detected differences in gene expression levels

organism: Meleagris gallopavo

label_protocol: Muscle RNA samples were reverse-transcribed to amino-allyl-cDNA using the ChipShot Indirect Labeling and Clean-up System kit per manufacturer protocol (Promega, Madison, WI).  Subsequently, the amino-allyl-cDNA was labeled either with Cy3 or Cy5 fluorescent dye (Amersham Biosciences Corp., Piscataway, NJ).

extract_protocol: A modified guanidinium thiocyanate-phenol-chlorophorm extraction method (Chomczynski and Sacchi, 1987) was utilized to isolate total RNA from each muscle sample.   In brief, 100mg of sample was placed in 1ml of Trizol reagent (Invitrogen, Carlsbad, CA) and homogenized using bead beater. Subsequently, 0.2 ml chloroform was added, followed by centrifugation at 12,000g, which yielded upper phase containing total RNA.  The RNA was precipitated by addition of 0.5 ml of isopropyl alcohol for 10 minutes followed by centrifugation at 12,000g.  The resulting RNA pellet was washed with 75% Ethyl alcohol, centrifuged at 7,500g, and resuspended in diethylpyrocarbonate-treated water.  The amount and quality of the isolated RNA was determined by measuring its absorbance at 260 nm with Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA integrity was further evaluated using agarose gel electrophoresis.  Samples with A260:280>1.8 were considered suitable for generating cDNA.

tag: muscle

value: ALD

value: 19 weeks

tag: bird number


title: sperm H3K14ac ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H3K14ac ChIP-chip in zebrafish sperm
H3K14ac-rep2

value: Tu


title: Turkey Muscle Array BF_19_17

description: 19 wks,bird 1

value: BF


title: Patient 43

description: Gene expression data from endothelial cells

tag: condition

tag: cdna quality

tag: patient gender


title: Turkey Muscle Array ALD_19_16

description: 19 wks,bird 5

tag: age


title: sperm H3K4me2 ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H3K4me2 ChIP-chip in zebrafish sperm
H3K4me2-rep2

value: H3K4me2 ChIP rep2


title: Patient 47

tag: rna isoaltion batch


title: Turkey Muscle Array PLD_19_15

description: 19 wks,bird 1

value: PLD


title: Turkey Muscle Array BF_19_16

description: 19 wks,bird 2


title: Patient 42

tag: rna yield (ug)


title: Patient 38

tag: cdna batch


title: Turkey Muscle Array PLD_1_15

description: 1 wk,bird 4(replicate)

value: 1 week


title: Patient 63

tag: cdna yield (ng)


title: sperm H3K4me2 ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K4me2 ChIP-chip in zebrafish sperm
H3K4me2-rep1

value: mature sperm

value: H3K4me2 ChIP rep1

value: Input

value: none (input)


title: Patient 31

value: B

tag: fragmentation batch


title: sperm H3K4me3 ChIP replicate 2 (slide 1 of 2)

description:
Biological replicate 2 of 2, H3K4me3 ChIP-chip in zebrafish sperm
H3K4me3-rep2

value: H3K4me3 ChIP rep2

value: N/A (experiments that either failed or serve as a pilot study)


title: Patient 25

tag: hybridisation batch


title: Patient 27


title: Patient 26


title: Patient 37


title: Patient 28


title: Turkey Muscle Array ALD_1_14

description: 1 wk,bird 6


title: Patient 57


title: Patient 22


title: Patient 19


title: sperm H3K4me3 ChIP replicate 1 (slide 1 of 2)

description:
Biological replicate 1 of 2, H3K4me3 ChIP-chip in zebrafish sperm
H3K4me3-rep1

tag: chromatin feature

value: H3K4me3 ChIP rep1


title: muscle MeDIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, MeDIP-chip in zebrafish adult muscle
MeDIP muscle-rep2

tag: tissue

value: muscle

tag: chip antibody

value: muscle MeDIP rep2


title: Turkey Muscle Array BF_1_14

description: 1 wk,bird 1


title: Patient 32

source_name: Endothelial cells, condition A

value: A

value: Male


title: Turkey Muscle Array BF_1_13

description: 1 wk,bird 2


title: muscle MeDIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, MeDIP-chip in zebrafish adult muscle
MeDIP muscle-rep1

value: Tu

value: muscle MeDIP rep1


title: Turkey Muscle Array ALD_1_13

description: 1 wk,bird 5

value: ALD


title: sperm MeDIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, MeDIP-chip in zebrafish sperm
MeDIP sperm-rep2

tag: cell type

value: sperm MeDIP rep2


title: sperm MeDIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, MeDIP-chip in zebrafish sperm
MeDIP sperm-rep1

tag: strain

value: sperm MeDIP rep1


title: Patient 17


title: Patient 21


title: Turkey Muscle Array BF_1_12

description: 1 wk,bird 3

tag: muscle

value: BF

value: 1 week


title: Patient 20


title: Turkey Muscle Array BF_1_11

description: 1 wk,bird 4

tag: bird number


title: Patient 15

tag: condition


title: Patient 3

tag: cdna quality


title: sperm H3K9me3 ChIP replicate 1 (slide 2 of 2)

value: mature sperm

value: H3K36me3 ChIP rep1

value: H3K9me3 ChIP rep1


title: Turkey Muscle Array PLD_1_12

description: 1 wk,bird 6

value: PLD


title: sperm H3K9me3 ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K9me3 ChIP-chip in zebrafish sperm
H3K9me3-rep2

value: H3K9me3 ChIP rep2

value: N/A (experiments that either failed or serve as a pilot study)


title: sperm H3K9me3 ChIP replicate 2 (slide 1 of 2)


title: Patient 5

tag: patient gender


title: sperm H3K36me3 ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K36me3 ChIP-chip in zebrafish sperm
H3K36me3-rep2

value: Input

value: none (input)

value: H3K36me3 ChIP rep2


title: Patient 9

value: A

value: Female

tag: age


title: Turkey Muscle Array BF_1_10

description: 1 wk,bird 5


title: Turkey Muscle Array PLD_1_11

description: 1 wk,bird 3


title: Patient 4

value: Male

tag: rna isoaltion batch


title: Patient 11

tag: rna yield (ug)


title: Patient 12

tag: cdna batch


title: Patient 14

tag: cdna yield (ng)


title: sperm H3K36me3 ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H3K36me3 ChIP-chip in zebrafish sperm
H3K36me3-rep1

value: Tu


title: Turkey Muscle Array BF_19_10

description: 19 wks,bird 3

value: 19 weeks


title: sperm H2AFV ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H2AFV ChIP-chip in zebrafish sperm
H2AFV-rep2

value: H2AFV ChIP rep2


title: sperm H2AFV ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H2AFV ChIP-chip in zebrafish sperm
H2AFV-rep1

value: H2AFV ChIP rep1


title: Patient 2

tag: fragmentation batch


title: Turkey Muscle Array BF_19_9

description: 19 wks,bird 4

value: BF


title: pituitary_fat_week7_rep4

city: College Park

first: Tom

middle: Eric

last: Porter

state: MD

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled test cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences). Slides were washed in increasing stringency using salt sodium citrate

scan_protocol: The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings: Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 22.5); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation. Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research). In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0. Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33 with Cy5 as the reference and then subjected to standard deviation regularization first by pin (block) then by slide with Cy5 as the reference. The data from each spot on each slide were then expressed as log2 ratio (normalized Cy3/raw Cy5), which is given in the data table below. Log2 ratios for the spots were statistically analyzed by two-way analysis of variance using Statistical Analysis Systems version 8.02 (SAS Institute, Cary, NC) to identify cDNAs that were differentially expressed between lines, among ages, and interactions between lines and ages (n = 4; p < 0.05), and a fold-change of > 1.6 was used as a filter for false positives.

organism: Gallus gallus

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), and either Cy3- (test) or Cy5- (reference) monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA. Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences).

growth_protocol: Standard broiler chicken growth protocol.

extract_protocol: Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a GneQuant II spectrophotometer (Pharmacia Biotech, Piscataway, NJ). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA). Total RNA was then amplified using a modification of the Eberwine Procedure (Phillips J, Eberwine JH 1996 METHODS: A Companion to Methods in Enzymology 10: 283-288). Briefly, 500 ng was reverse-transcribed using SuperScript II (Invitrogen, Carlsbad, CA) and an oligo (dT) primer containing a T7 promoter site (5'-GGCCAGTGAATTGTAATATCGACTCACTATAGGGAGGCGGT24-3'; Affymetrix, Santa Clara, CA). Following second strand synthesis and purification, double-stranded cDNA was used as a template for in vitro transcription using the T7 MEGAscript kit (Ambion, Austin, TX) and the resulting amplified antisense RNA was quantified with the Ribogreen RNA Quantitation Kit (Invitrogen, Carlsbad, CA).

treatment_protocol: Divergently selected on abdominal fat weight (FL genotype) for seven generations.

value: pituitary

tag: phenotype

value: fat

value: week 7

source_name: Reference pool of pituitary total RNA from fat and lean lines, weeks 1, 3, 5, and 7

tag: sample type


title: pituitary_fat_week7_rep3

tag: tissue

value: Reference pool of pituitary total RNA from fat and lean lines, weeks 1, 3, 5, and 7


title: pituitary_lean_week7_rep4

value: lean


title: Turkey Muscle Array BF_1_9

description: 1 wk,bird 6

value: 1 week


title: pituitary_lean_week7_rep2


title: pituitary_fat_week7_rep1


title: pituitary_fat_week7_rep2


title: pituitary_lean_week7_rep3


title: pituitary_fat_week5_rep4

value: week 5


title: sperm H3K27me3 ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K27me3 ChIP-chip in zebrafish sperm
H3K27me3-rep2

value: mature sperm

tag: chromatin feature

value: H3K27me3 ChIP rep1

tag: chip antibody

value: H3K14ac ChIP rep2


title: pituitary_fat_week5_rep3


title: sperm H3K27me3 ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H3K27me3 ChIP-chip in zebrafish sperm
H3K27me3-rep1

tag: cell type

value: H3K14ac ChIP rep1

tag: strain


title: Turkey Muscle Array ALD_1_8

description: 1 wk,bird 4

tag: muscle

value: ALD

tag: bird number


title: pituitary_lean_week7_rep1


title: sperm H3K14ac ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K14ac ChIP-chip in zebrafish sperm
H3K14ac-rep2

value: Tu


title: pituitary_fat_week5_rep2


title: pituitary_lean_week5_rep4


title: sperm H3K14ac ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H3K14ac ChIP-chip in zebrafish sperm
H3K14ac-rep1


title: sperm H3K4me2 ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K4me2 ChIP-chip in zebrafish sperm
H3K4me2-rep2

value: N/A (experiments that either failed or serve as a pilot study)

value: H3K4me2 ChIP rep2


title: Turkey Muscle Array PLD_1_7

description: 1 wk,bird 4

value: PLD


title: Turkey Muscle Array PLD_1_8

description: 1 wk,bird 5


title: sperm H3K4me2 ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H3K4me2 ChIP-chip in zebrafish sperm
H3K4me2-rep1

value: H3K4me2 ChIP rep1

value: Input

value: none (input)


title: pituitary_lean_week5_rep3

value: pituitary


title: Turkey Muscle Array ALD_1_7

description: 1 wk,bird 3


title: pituitary_fat_week5_rep1

value: fat

value: Reference pool of pituitary total RNA from fat and lean lines, weeks 1, 3, 5, and 7


title: Turkey Muscle Array ALD_1_6

description: 1 wk,bird 2

value: 1 week


title: sperm H3K4me3 ChIP replicate 2 (slide 2 of 2)

description:
Biological replicate 2 of 2, H3K4me3 ChIP-chip in zebrafish sperm
H3K4me3-rep2

value: H3K4me3 ChIP rep2


title: Turkey Muscle Array ALD_19_6

description: 19 wks,bird 4

value: 19 weeks


title: pituitary_fat_week3_rep3

value: week 3


title: Turkey Muscle Array ALD_1_5

description: 1 wk,bird 1


title: pituitary_lean_week5_rep2

value: lean

value: week 5


title: pituitary_fat_week3_rep2


title: pituitary_lean_week5_rep1


title: Turkey Muscle Array ALD_19_5

description: 19 wks,bird 3

value: ALD


title: pituitary_lean_week3_rep3


title: pituitary_fat_week3_rep1


title: pituitary_fat_week3_rep4


title: pituitary_lean_week3_rep1


title: Turkey Muscle Array PLD_19_4

description: 19 wks,bird 2


title: pituitary_fat_week1_rep3

value: week 1


title: pituitary_fat_week1_rep2


title: PBS-exposed mouse lung MSC in vitro mix (mouse array)

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 h at 45°C on MG-430 2.0 arrays in the Affymetrix Hybridization Oven 640. Arrays were washed and stained (GeneChip Hybridization, Wash and Stain Kit; Affymterix) using Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 7G Scanner (Affymetrix)

data_processing: Array CEL-files were transferred onto Partek Genomics Suite and normalized with RMA.

source_name: PBS-exposed mouse lung_MSC in vitro mix

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle cDNA Synthesis Protocol (Affymetrix)l from 3 ug of total RNA.

extract_protocol: Total RNA was obtained from lung tissue homogenized in TriPure Isolation Reagent (Roche) and was purified with RNeasy Mini Kit (Qiagen).

value: BALB/C

tag: gender

value: female

value: lung and MSC

tag: exposure

value: PBS


title: sperm H3K4me3 ChIP replicate 1 (slide 2 of 2)

description:
Biological replicate 1 of 2, H3K4me3 ChIP-chip in zebrafish sperm
H3K4me3-rep1

value: mature sperm

value: Input

value: Tu

value: H3K4me3 ChIP rep1


title: LPS-exposed mouse lung MSC in vitro mix (mouse array)

source_name: LPS-exposed mouse lung_MSC in vitro mix

value: LPS


title: PBS-exposed mouse lung MSC treated (mouse array)

source_name: PBS-exposed mouse lung_MSC treated

tag: treatment

value: MSC


title: Turkey Muscle Array PLD_1_3

description: 1 wk,bird 2

value: PLD

tag: age

value: 1 week


title: Patient 10

description: Gene expression data from endothelial cells

tag: condition

value: B

tag: cdna quality

tag: patient gender

value: Female

tag: rna isoaltion batch

tag: rna yield (ug)

tag: hybridisation batch


title: pituitary_fat_week1_rep1

tag: tissue

value: pituitary

tag: phenotype

value: fat

tag: sample type

value: Reference pool of pituitary total RNA from fat and lean lines, weeks 1, 3, 5, and 7


title: pituitary_fat_week1_rep4

value: week 1


title: Turkey Muscle Array PLD_19_3

description: 19 wks,bird 3

value: 19 weeks


title: CXCL12-treated Peripheral Blood Monocytes Replicate 3

city: Madrid

first: Lorena

last: Sánchez-Martín

address: C/ Dr Esquerdo 46

department: Inmunología

country: Spain

institute: Hospital General Gregorio Marañon

description: Codelink Human Whole Genome Bioarray

hyb_protocol: Standard Codelink protocols, as described in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

scan_protocol: Scanned on an GenePix 4000B scanner

data_processing: Scanned images using the Codelink Expression Software

source_name: CD14+ Peripheral Blood Monocytes

label_protocol: 2 ug of total RNA was used to obtain cRNA. 10 ug of cRNA was labeled with Cy5-Streptavidin. All experimental procedures were performed following manufacturer instructions. Now available in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

growth_protocol: Freshly isolated CD14+ monocytes were cultured in teflon dishes for 1h in RPMI 10% FCS

extract_protocol: Total RNA from each condition was extracted and purified using the RNasey kit (Qiagen).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Monocytes were treated with 100 ng/ml CXCL12 for 6h of left untreated as control

tag: disease state

value: Healthy donor

tag: cell type

value: CD14+ Peripheral Blood Monocytes


title: Turkey Muscle Array PLD_19_2

description: 19 wks,bird 4

tag: muscle


title: Turkey Muscle Array ALD_19_2

description: 19 wks,bird 2

value: ALD

tag: bird number


title: Turkey Muscle Array PLD_19_1

description: 19 wks,bird 5


title: LPS-exposed mouse lung MSC treated (mouse array)

source_name: LPS-exposed mouse lung_MSC treated

tag: strain

value: BALB/C

tag: gender

value: female

value: lung and MSC


title: pituitary_lean_week1_rep3

value: lean


title: pituitary_lean_week1_rep2


title: pituitary_lean_week3_rep4

value: week 3


title: LPS-exposed mouse lung PBS treated (mouse array)

source_name: LPS-exposed mouse lung_PBS treated

value: lung

tag: exposure

value: LPS

tag: treatment

value: PBS


title: Control Peripheral Blood Monocytes Replicate 3

description: Codelink Human Whole Genome Bioarray

value: control


title: CXCL12-treated Peripheral Blood Monocytes Replicate 2

description: Codelink Human Whole Genome Bioarray


title: Control Peripheral Blood Monocytes Replicate 2

description: Codelink Human Whole Genome Bioarray


title: Control Peripheral Blood Monocytes Replicate 1

description: Codelink Human Whole Genome Bioarray


title: pituitary_lean_week1_rep4

value: pituitary

tag: age


title: Turkey Muscle Array ALD_19_1

description: 19 wks,bird 1


title: pituitary_lean_week1_rep1


title: Turkey Muscle Array PLD_1_4

description: 1 wk,bird 1

value: PLD

value: 1 week


title: E9.5 embryo_Cop1KO_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: RNA from 6 different Cop-null embryos were mixed and subdivided into KO pool 1 and pool 2.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using RMA normalization. The package affy in Bioconductor was used for this.

source_name: Whole embryo, E9.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: The animals were maintained in accordance with the guidelines of the University of Gent Care and Use ethical Committee.

extract_protocol: RNeasy. RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technolgies) and RNA integrity was assessed using the Bioanalyser 2100 (Agilent).

treatment_protocol: E9.5 Embryos were collected/dissected and immediately lyzed  in RNA extraction buffer.

value: Cop1-null embryos


title: E9.5 embryo_Cop1KO_rep1


title: E9.5 embryo_wild-type_rep2

description: RNA from 6 different control embryos (+/+ or +/-) were mixed and subdivided into control pool 1 and pool 2.

value: Cop1 control embryos


title: CXCL12-treated Peripheral Blood Monocytes Replicate 1

description: Codelink Human Whole Genome Bioarray

value: Healthy donor


title: E9.5 embryo_wild-type_rep1


title: HEK-TLR2 48h-LPS rep1

status: Public on Jan 12 2011

city: Dublin 8

first: Sinead

middle: Marian

last: Smith

address: St. James's Hospital

country: Ireland

institute: Trinity College Dublin

description: gene expression in untreated HEK-TLR2 cells at 48h

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 genechips. GeneChips were washed and stained in the Automated fluidics 450 station.

scan_protocol: Genechips were scanned using the GeneChip 3000 7G scanner

data_processing: Scanned images, obtained using Affymetrix Software (MAS5), were normalized using robust multichip average (RMA) analysis with RMAExpress version 0.4.1.

source_name: HEK-TLR2 cells untreated for 48h rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using the Affymetrix IVT labeling kit.

growth_protocol: HEK-TLR2 cells were routinely maintained in MEM alpha medium (Gibco) supplemented with 10% foetal calf serum (Gibco), 2 mM L-glutamine (Sigma), 100 U/ml penicillin (Sigma), 100 μg/ml streptomycin and 500 μg/ml G418 (Sigma). The day before treatment, cells were seeded in 6-well plates at 1x106 cells/well.

extract_protocol: At time points of 2, 4, 8, 24 and 48 h post-stimulation, cells were harvested and RNA isolated using the Nucleospin RNAII kit (Machery Nagel) according to the manufacturer's instructions.

treatment_protocol: The morning of treatment, the cell culture medium was replaced with either fresh medium (untreated) or medium containing 10 μg/ml H. pylori lipopolysaccharide

value: embryonic kidney

value: human embryonic kidney (HEK) cells stably transfected with Toll-like receptor 2 (TLR2)


title: HEK-TLR2 8h+LPS rep1

description: gene expression in treated HEK-TLR2 cells at 8h

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 8h rep 1


title: HEK-TLR2 48h+LPS rep1

description: gene expression in treated HEK-TLR2 cells at 48h

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 48h rep 1


title: HEK-TLR2 24h-LPS rep2

description: gene expression in untreated HEK-TLR2 cells at 24h

source_name: HEK-TLR2 cells untreated for 24h rep 2


title: HEK-TLR2 24h+LPS rep2

description: gene expression in treated HEK-TLR2 cells at 24h

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 24h rep 2


title: HEK-TLR2 48h+LPS rep2

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 48h rep 2


title: HEK-TLR2 48h-LPS rep2

source_name: HEK-TLR2 cells untreated for 48h rep 2


title: HEK-TLR2 8h+LPS rep2

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 8h rep 2


title: HEK-TLR2 8h-LPS rep1

description: gene expression in untreated HEK-TLR2 cells at 8h

source_name: HEK-TLR2 cells untreated for 8h rep 1


title: HEK-TLR2 24h+LPS rep1

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 24h rep 1


title: HEK-TLR2 24h-LPS rep1

source_name: HEK-TLR2 cells untreated for 24h rep 1


title: HEK-TLR2 2h+LPS rep1

description: gene expression in treated HEK-TLR2 cells at 2h

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 2h rep 1


title: HEK-TLR2 8h-LPS rep2

source_name: HEK-TLR2 cells untreated for 8h rep 2


title: HEK-TLR2 4h+LPS rep2

description: gene expression in treated HEK-TLR2 cells at 4h

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 4h rep 2


title: MKN45 untreated rep 2

description: gene expression in untreated MKN45 cells

source_name: MKN45 cells untreated for 8h rep 2

growth_protocol: MKN45 cells were routinely maintained in RPMI (Gibco) supplemented with 10% foetal calf serum (Gibco), 2 mM L-glutamine (Sigma), 100 U/ml penicillin (Sigma) and 100 μg/ml streptomycin. The day before treatment, cells were seeded in 6-well plates at 1x106 cells/well.

extract_protocol: 8h post-stimulation, cells were harvested and RNA isolated using the Nucleospin RNAII kit (Machery Nagel) according to the manufacturer's instructions.

value: gastric epithelial cells

tag: cell line


title: MKN45 treated rep 2

description: gene expression in H. pylori LPS-treated cells

source_name: MKN45 cells treated with 10 μg/ml H. pylori LPS for 8h rep 2


title: HEK-TLR2 4h+LPS rep1

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 4h rep 1


title: MKN45 treated rep 1

source_name: MKN45 cells treated with 10 μg/ml H. pylori LPS for 8h rep 1


title: HEK-TLR2 2h-LPS rep2

description: gene expression in untreated HEK-TLR2 cells at 2h

source_name: HEK-TLR2 cells untreated for 2h rep 2


title: MKN45 untreated rep 1

source_name: MKN45 cells untreated for 8h rep 1


title: AGS untreated rep 2

description: gene expression in untreated AGS cells

source_name: AGS cells untreated for 8h rep 2

growth_protocol: AGS cells were routinely maintained in nutrient mixture F-12 Ham (Sigma) supplemented with 10% foetal calf serum (Gibco), 2 mM L-glutamine (Sigma), 100 U/ml penicillin (Sigma) and 100 μg/ml streptomycin. The day before treatment, cells were seeded in 6-well plates at 1x106 cells/well.

value: AGS


title: HEK-TLR2 2h+LPS rep2

source_name: HEK-TLR2 cells treated with 10 μg/ml H. pylori LPS for 2h rep 2


title: HEK-TLR2 2h-LPS rep1

source_name: HEK-TLR2 cells untreated for 2h rep 1


title: AGS untreated rep 1

description: gene expression in untreated AGS cells

source_name: AGS cells untreated for 8h rep 1


title: HEK-TLR2 4h-LPS rep2

description: gene expression in untreated HEK-TLR2 cells at 4h

source_name: HEK-TLR2 cells untreated for 4h rep 2


title: AGS treated rep 2

source_name: AGS cells treated with 10 μg/ml H. pylori LPS for 8h rep 2


title: AGS treated rep 1

source_name: AGS cells treated with 10 μg/ml H. pylori LPS for 8h rep 1


title: CD200+CD49+Repeat2

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from FACS sorted human adult keratinocytes using cell surface markers

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to U133A Affymetrix microarray for human and 430 v2 for mouse. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing:
Affymetrix GeneChip Operating System (GCOS, v. 1.4, Affymetrix, Inc.) was used to quantitate expression signal levels for the arrays; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. These values were exported as .cel files. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. The flag values were additionally exported in .chp files.
Affymetrix probe intensities were imported into GeneSpring (v7.2, Agilent Technologies) where probeset signal values were calculated using the GC-RMA algorithm. Upon import of the Affymetrix flag values, the probesets were filtered to retain only those that were flagged P (present) in at least two of the repeat samples. This list was used for condition-based principle components analysis (PCA) to assess global trends in sample similarity. This analysis demonstrated groupings based on sample identity and prompted the use of mixed-model 2-way ANOVA as a means of finding differentially regulated genes between the sites of interest.
GC-RMA signal data was imported into Partek Genomics Solution (PGS, v6.2, Partek, Inc.), where the data were log2 transformed. Probesets not shared between mouse and human chips were removed.  Genes less than p<0.05 in p-values for the identity of sample term of the ANOVA, and less than 2 fold changes between positive and negative populations were also excluded. The resulting enriched gene lists for bulge, secondary hair germ, and CD200highITGA6high cells were then examined for intersection using Partek.

label_protocol: Briefly, 5ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Cells were not expanded but isolated enzymatically from biopsied human tissue

extract_protocol: RNAeasy Qiagen protocol

treatment_protocol: Cells were not treated

value: Haired Scalp

tag: sex

value: male


title: MO2-ers2a 48 hpf - MO-control 48 hpf

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

department: Biology

country: Italy

institute: University of Padua

description: Danio rerio embryos injected with a translation blocking morpholino for estrogen receptor beta2 (ers2a) compared to embryos injected with control morpholino. All the embryos are fixed at 48 hours post fertilization

hyb_protocol: The samples were mixed with 25X Fragmentation Buffer and 10X Blocking Agent (Agilent Gene Expression Hybridization Kit) and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on Agilent Technologies Scanner G2505B US22502723 - Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: MO2-ers2a embryos at 48 hours post fertilization

label_protocol: 200 ng of total RNA were primed and reversed transcribed using the Agilent Quick-Amp labeling Kit protocol following manufacturer's instructions

growth_protocol: Microinjected embryos were raised in fish water at 28.5 C degrees and were fixed at 8 hpf and 48 hpf

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

treatment_protocol: Danio rerio ovulated oocytes were microinjected with a translation blocking morpholino for estrogen receptor-beta2 (ers2a) (10.3 ng per embryo) or with control morpholino (10.3 ng per embryo).

value: 48 hours post fertilization

source_name: MO-control embryos at 48 hours post fertilization


title: CD34-CD200-CD49+Replicate2

description: Gene expression data from FACS sorted mouse adult keratinocytes using cell surface markers

growth_protocol: Cells were not expanded but isolated enzymatically from mouse skin

value: Back Skin

value: female

value: 50 days

tag: hair stage

value: telogen


title: CD200+CD49+Repeat3


title: Endoderm_passage6_mes2_rep2

city: Cambridge

first: Julie

middle: Beth

last: Sneddon

state: MA

address: 7 Divinity Avenue

department: Department of Stem Cells and Regenerative Biology

institute: Harvard University

description: culture condition: co-culture with mesenchyme 2

hyb_protocol: Samples were hybridized onto Illumina Mouse Ref8 version 2 BeadChips as per the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Illumina machine according to the manufacturer's instructions.

data_processing: Data were analyzed with BeadStudio analysis software (Illumina).  Samples were normalized using Illumina's average normalization, with no background subtraction. The data were filtered for only genes for which the p value of detection was < 0.01.

source_name: mouse embryonic stem cell-derived endoderm, P6

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA amplification kit (Ambion).

growth_protocol: Mouse embryonic stem cells containing a Sox17-GFP construct were differentiated using growth factors (Activin A and Wnt3A) for six days to definitive endoderm.  Sox17-GFP(+) cells were sorted using fluorescence-activated cell sorting (FACS).

extract_protocol: Sox17-GFP(+) cells were isolated by FACS in buffer containing PBS/5% FBS.  Cells were spun for 5 minutes, 1000 rpm, and the supernatant was removed.  RNA was then harvested using the Rneasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The sorted Sox17-GFP(+) cells were split into 3 destinations:  1.  RNA was collected (for an unpassaged, freshly-differentiated sample of endoderm) OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 1 OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 2

value: embryonic stem cell


title: MO2-ers2a 8 hpf - MO-control 8 hpf

description: Danio rerio embryos injected with a translation blocking morpholino for estrogen receptor beta2 (ers2a) compared to embryos injected with control morpholino. All the embryos are fixed at 8 hours post fertilization

source_name: MO2-ers2a embryos at 8 hours post fertilization

value: 8 hours post fertilization

source_name: MO-control embryos at 8 hours post fertilization


title: CD200-CD49+Repeat2


title: CD200-CD49+Repeat3


title: CD200-CD49+Repeat1


title: CD200+CD49+Repeat1


title: pituitary_lean_week3_rep2

value: pituitary

value: lean

value: week 3

source_name: Reference pool of pituitary total RNA from fat and lean lines, weeks 1, 3, 5, and 7


title: CD34-CD200-CD49+Replicate4


title: liver-olive oil -8weeks-rep1

city: Tokyo

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Section for Studies on Metastasis

institute: National Cancer Center Research Institute

description: miRNA expression after 8 weeks in olive oil-administrated mouse liver

hyb_protocol: miRNA microarrays were manufactured by Agilent Technologies, and 100 ng of total RNA was labeled and hybridized using Mouse microRNA Microarray Kit according to manufacture’s protocol (Protocol for use with Agilent microRNA microarrays Version 1.0)

scan_protocol: Scanned on an Agilent G2505B scanner

data_processing: Data were analyzed using GeneSpring GX 7.3.1 software (Agilent Technologies) and normalized as follows: (i) Values below 0.01 were set to 0.01. (ii) Each measurement was divided by the 75th percentile of all measurements to compare one-color expression profiles.

source_name: Liver, 8 weeks, Olive oil, replicate 1

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

treatment_protocol: CCL4 or olive oil was administrated intraperitoneally in mouse twice a week for 4 weeks and then administrated once a week for four weeks. Mice were sacrificed on 4, 6, and 8 weeks.

value: Liver

tag: time

value: 8 weeks

tag: administrated reagent

value: Olive oil

value: control


title: liver-olive oil -6weeks-rep1

description: miRNA expression after 6 weeks in olive oil-administrated mouse liver

source_name: Liver, 6 weeks, Olive oil, replicate 1

label_protocol: miRNA microarrays were manufactured by Agilent Technologies, and 100 ng of total RNA was labeled and hybridized using Mouse microRNA Microarray Kit according to manufacture’s protocol (Protocol for use with Agilent microRNA microarrays Version 1.0)

tag: tissue

value: 6 weeks


title: liver-olive oil -4weeks-rep1

description: miRNA expression after 4 weeks in olive oil-administrated mouse liver

source_name: Liver, 4 weeks, Olive oil, replicate 1

value: 4 weeks


title: Endoderm_passage6_mes1_rep2

description: culture condition: co-culture with mesenchyme 1


title: liver-CCL4-8weeks-rep2

description: miRNA expression after 8 weeks in CCL4-administrated mouse liver

source_name: Liver, 8 weeks, CCL4, replicate 2

value: fibrosis


title: Endoderm_unpassaged_rep1

description: culture condition: gelatin

source_name: mouse embryonic stem cell-derived endoderm, P0


title: Endoderm_unpassaged_rep2

description: culture condition: gelatin


title: liver-CCL4-8weeks-rep1

source_name: Liver, 8 weeks, CCL4, replicate 1


title: Endoderm_passage6_mes1_rep1


title: Endoderm_passage6_mes2_rep1


title: HEK-TLR2 4h-LPS rep1

source_name: HEK-TLR2 cells untreated for 4h rep 1

value: embryonic kidney

value: human embryonic kidney (HEK) cells stably transfected with Toll-like receptor 2 (TLR2)


title: liver-CCL4-6weeks-rep2

description: miRNA expression after 6 weeks in CCL4-administrated mouse liver

source_name: Liver, 6 weeks, CCL4, replicate 2


title: CD34-CD200+CD49+Replicate3

value: Back Skin

value: female


title: CD34-CD200+CD49+Replicate4

value: 50 days

value: telogen


title: full ripe (S3) vs mature-firm ripe (S2) of apricot

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

institute: University of Padova

description: Analysis used to compare transcripts level in fully ripe fruit and firm-mature ripe fruit.

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm. Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 100-150 pmol of Cy3- and Cy5-labelled target cDNAs.  The glass slides were placed in a hybridisation chamber (Corning, USA) kept on a water bath at 48°C  at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing:
Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data.  Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones.  The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”, keeping as reference the Cy3 channel. The “IA” and “IB” values have been used to determine log2(IB/IA) reported in the “VALUE” column.  Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses. Since each comparison was repeated at least twice, and a “percentage cutoff filter”, set to 75%, was used to eliminate those gene with less than 3 data points, there were at least 3 values for each gene to be used in the SAM analysis. Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of about 5%.

Please see 'readme.txt' file on the Series record for the sample labeling scheme for each supplementary file.

organism: Prunus armeniaca

source_name: firm-mature ripe fruit (S2)

label_protocol: Total RNA (20 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dyes: the red-fluorescent cyanine5 (Cy5) and the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Fruit from apricot cv ‘Goldrich’ and peach cv 'Fantasia’ was used in the current study. By comparing the position of anchor markers in maps constructed with different Prunus species, it has been demonstrated that the genomes of the diploid Prunus species (including peach and apricot) are essentially collinear thus, at the genome level, the Prunus genus can be treated as a single genetic entity thus the platform developed for massive analysis of peach fruit transcriptome can be extended to apricot.

extract_protocol: Frozen fruit (3 g) was ground in liquid nitrogen to a fine powder and total RNA was extracted as described by Bonghi and co-workers (1998, Planta. 102:346-352). Fifty μg of total RNA were treated with 10 units of RQ1 RNase-Free DNAse (Promega) and 1 unit of RNAguard (RNase INHIBITOR) (Amersham) for 30 min, and then purified by phenol-chlorophorm according to the manufacturer’s instructions. The concentration of RNA was quantified by measuring the absorbance at 260 nm and its integrity was checked electrophoretically on agarose gels.

treatment_protocol: Apricot fruit were harvested 45, 80 and 87 days after full bloom. These harvest days corresponds to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage and onset of climacteric phase) and at fully-ripe stage (full climacteric phase) and designated as S1, S2 and S3 stages,respectively. Samples of 30 fruits were collected from each developmental stage and evaluated for color parameters (L, a*, b* values) using a Minolta colorimeter (model CM2500d), tissue firmness using an Effegi penetrometer, employed with an 8 mm probe and ethylene evolution as described by Tonutti et al., 1997 (J Am Soc Hort Sci 122:642–647). Fruit from each developmental stage were divided into three sub-lots (10 fruit for each) and mesocarp tissue from each sub-lot was removed, immediately frozen in liquid nitrogen and subsequently maintained at -80°C until needed.   Peach fruits (cv Fantasia) were harvested at distinct developmental stages, designated as S1, S2, S3, S4, as described by Trainotti  et al., 2007 (J Exp Bot 58:3299-3308) and stored at -80°C for subsequent molecular analysis.

tag: cultivar

value: Goldrich

tag: developmental stage

value: firm-mature ripe fruit (S2)

source_name: fully ripe fruit (S3)

value: fully ripe fruit (S3)


title: mature-firm ripe (S2) vs immature (S1) fruit of apricot

description: Analysis used to compare transcripts level in firm-mature  ripe fruit and immature-green fruit.

source_name: immature fruit (S1)

value: immature fruit (S1)