title: eAML-NGS-S46


title: eAML-NGS-S66

status: Public on Jan 01 2018

type: genomic

city: Berlin

first: Patricia

last: Silva

address: Hindenburgdamm 30

department: Campus Benjamin Franklin, Hematology

country: Germany

institute: Charité Berlin

hyb_protocol: 500 ng bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. Sample preparation and readout was done by High Throughput sequencing unit at German Cancer Research Center (Heidelberg, Germany).

scan_protocol: Arrays were imaged using iScan SQ instrument (Illumina)  using standard recommended Illumina scanner setting

data_processing:
Data was treated in R, homogenized using the dasen function (minfi package). dbSNP related CpGs with MAF>0.01 were filtered out. Beta values of methylation in sex related positions CpGs were removed.
The non-normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow

label_protocol: Standard Illumina Protocol

growth_protocol: Bone marrow aspirates were obtained from eldely AML patients, mononuclear cells were isolated using density centrifugation

extract_protocol: genomic DNA was extracted from the blasts derived from AML patients using AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Standard Illumina Protocol

tag: subject status

value: acute myeloid leukemia (AML) patient

tag: tumor stage

value: First diagnosis

tag: tissue

value: F

tag: Sex

value: bone marrow


title: eAML-NGS-S43


title: eAML-NGS-S38


title: microRNA profile of case T148

type: RNA

city: Guangzhou

first: jingye

last: hu

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs from breast cancer and noncancerous breast were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

molecule: total RNA

source_name: breast cancer

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted from the paraffin-embedded breast cancer and noncancerous breast samples, using a modification of the phenol/chloroform extraction method after processing by dimethylbenzene.

tag: survival

value: breast cancer


title: eAML-NGS-S45


title: eAML-NGS-S42

value: M


title: eAML-NGS-S51


title: eAML-NGS-S65


title: microRNA profile of case T146


title: eAML-NGS-S52


title: microRNA profile of case T147


title: microRNA profile of case T145


title: microRNA profile of case T144


title: eAML-NGS-S37


title: microRNA profile of case T143


title: eAML-NGS-S14


title: microRNA profile of case T142


title: microRNA profile of case T141


title: eAML-NGS-S53


title: eAML-NGS-S63


title: microRNA profile of case T140


title: eAML-NGS-S64


title: microRNA profile of case T14


title: microRNA profile of case T139


title: eAML-NGS-S12


title: eAML-NGS-S02


title: microRNA profile of case T151


title: microRNA profile of case T138


title: microRNA profile of case T137


title: microRNA profile of case T135


title: eAML-NGS-S62


title: microRNA profile of case T134


title: microRNA profile of case T133


title: eAML-NGS-S06


title: microRNA profile of case T131


title: eAML-NGS-S15


title: microRNA profile of case T13


title: eAML-NGS-S16


title: eAML-NGS-S10


title: microRNA profile of case T128


title: eAML-NGS-S03


title: microRNA profile of case T132


title: microRNA profile of case T127


title: microRNA profile of case T126


title: microRNA profile of case T125


title: eAML-NGS-23


title: eAML-NGS-S05


title: eAML-NGS-S40


title: microRNA profile of case T124


title: eAML-NGS-S33


title: eAML-NGS-25


title: eAML-NGS-30


title: eAML-NGS-19


title: eAML-NGS-26


title: microRNA profile of case T123


title: microRNA profile of case T122


title: microRNA profile of case T121


title: eAML-NGS-63


title: microRNA profile of case T118


title: eAML-NGS-20


title: eAML-NGS-31


title: microRNA profile of case T116


title: microRNA profile of case T117


title: microRNA profile of case T115


title: microRNA profile of case T12


title: eAML-NGS-7


title: eAML-NGS-24


title: eAML-NGS-6


title: microRNA profile of case T120


title: microRNA profile of case T112


title: eAML-NGS-8


title: eAML-NGS-S21


title: microRNA profile of case T113


title: microRNA profile of case T111


title: microRNA profile of case T109


title: eAML-NGS-21


title: eAML-NGS-10


title: eAML-NGS-12


title: eAML-NGS-28


title: eAML-NGS-22


title: microRNA profile of case T107


title: eAML-NGS-62


title: microRNA profile of case T105


title: eAML-NGS-64


title: eAML-NGS-1


title: microRNA profile of case T110


title: microRNA profile of case T104


title: eAML-NGS-59

source_name: Periferal Blood

value: Periferal Blood


title: eAML-NGS-37


title: microRNA profile of case T102


title: microRNA profile of case T101


title: microRNA profile of case T100


title: microRNA profile of case T103


title: eAML-NGS-36


title: microRNA profile of case N9

source_name: noncancerous breast tissue

value: non-cancerous breast tissue


title: eAML-NGS-55


title: eAML-NGS-11


title: eAML-NGS-S29


title: microRNA profile of case T1


title: eAML-NGS-38


title: microRNA profile of case T10


title: eAML-NGS-35


title: microRNA profile of case N33


title: microRNA profile of case N4


title: microRNA profile of case N8


title: microRNA profile of case N32


title: eAML-NGS-40


title: eAML-NGS-44


title: microRNA profile of case N7


title: microRNA profile of case N3


title: eAML-NGS-S27


title: microRNA profile of case N6


title: microRNA profile of case N31


title: eAML-NGS-46


title: microRNA profile of case N29


title: eAML-NGS-43


title: eAML-NGS-42


title: eAML-NGS-S25


title: microRNA profile of case N27


title: microRNA profile of case T106


title: microRNA profile of case N28


title: microRNA profile of case N23


title: microRNA profile of case N30


title: eAML-NGS-33


title: microRNA profile of case N22


title: microRNA profile of case N25


title: eAML-NGS-S17


title: microRNA profile of case N2


title: microRNA profile of case N26


title: microRNA profile of case T108


title: microRNA profile of case N16


title: microRNA profile of case N13


title: microRNA profile of case N14


title: microRNA profile of case N15


title: microRNA profile of case N21


title: microRNA profile of case N17


title: zebrafish, anterior intestine, fed

type: SAGE

anchor: NlaIII

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

country: France

institute: Université Bordeaux

description: 30 micrograms of total RNAs of the pool of 6 animals were used to generate the long-SAGE library using the I-SAGE Long kit (Invitrogen, Cergy Pointoise, France).

data_processing: SAGE-tag extraction, counting and quality control were undertaken by Skuld-Tech (Montpellier, France, http://www.skuldtech.com)

organism: Danio rerio

source_name: anterior intestine, fed

extract_protocol: The anterior intestine was isolated from 6 animals. Total RNA were extracted from the intestines with the Nucleospin RNAII kit (Machery-Nagel, Hoerdt, France).

treatment_protocol: Adult zebrafish were deprived of food during 22 hours, and subsequently fed during 2 hours.

tag: genotype

value: wild type

tag: developmental stage

value: adult

value: anterior intestine

tag: treatment

value: fed


title: microRNA profile of case N18


title: microRNA profile of case N19


title: microRNA profile of case N5


title: microRNA profile of case N10


title: microRNA profile of case N1


title: microRNA profile of case TR9


title: microRNA profile of case N12


title: microRNA profile of case N11


title: microRNA profile of case TR8


title: microRNA profile of case TR7


title: microRNA profile of case TR5


title: microRNA profile of case TR3


title: microRNA profile of case TR4


title: GC-2_rep3

city: Gwangju

first: Seonghyeon

last: Hong

address: 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Korea

department: School of Life Science

country: South Korea

institute: GIST

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Agilent E-array (Teleaulax) (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Mus musculus

source_name: GC-2, replicate 3

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: F9, GC-1 and GC-2 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM) (Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT, USA). The culture dishes for the F9 cells were pre-coated with 0.1 % gelatin.

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

tag: cell line

tag: gender

value: Male


title: GC-1_rep2

source_name: GC-1, replicate 2


title: microRNA profile of case TR6


title: GC-1_rep3

source_name: GC-1, replicate 3


title: MDA-replicate1

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: 200 ng of labeled RNA were hybridized on Agilent SurePrint G3 Human Gene Expression 8x60K glass arrays;

scan_protocol: The glass slide was scanned using an Agilent scanner and images were analyzed using Agilent Feature Extraction Software (version 10.7.3.1);

data_processing: raw data were then processed using the Bioconductor package Limma (Linear models for microarray analysis);

label_protocol: 1 microgram of total RNA was amplified with ammino-allyl message amp II kit (Ambion) and labeled with Cy3 (GE-Heathcare), using the indirect labelling protocol;

growth_protocol: Cells were maintaned in DMEM medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS (Euroclone, Milano, Italy) and 1% penicillin streptomycin (Thermo Fisher Scientific, Waltham, MA, USA)

extract_protocol: Total RNA was extracted using Trizol AND Absolute RNA miRNA kit (Agilent) following manufacturer's instructions;

treatment_protocol: Cells were previously infected with a lentiviral PGIPZ vector containing shRNA targeting Morgana (MDA-sh) or an empty vector as control (MDA)

tag: genotype/variation

value: control


title: GC-2_rep1

source_name: GC-2, replicate 1


title: GC-2_rep2

source_name: GC-2, replicate 2


title: GC-1_rep1

source_name: GC-1, replicate 1


title: MDA-shRNA-morgana-replicate1

value: sh-morgana infected


title: MDA-replicate2


title: F9_rep2

source_name: F9, replicate 2


title: Testis_rep3

source_name: Testis, 8weeks, replicate 3

value: Testis

tag: age

value: 8 weeks


title: F9_rep1

source_name: F9, replicate 1


title: F9_rep3

source_name: F9, replicate 3


title: Testis_rep2

source_name: Testis, 8weeks, replicate 2


title: MDA-shRNA-morgana-replicate2


title: Testis_rep1

source_name: Testis, 8weeks, replicate 1


title: Liver_rep3

source_name: Liver, 8weeks, replicate 3

value: Liver


title: Liver_rep2

source_name: Liver, 8weeks, replicate 2


title: Kidney_rep3

source_name: Kidney, 8weeks, replicate 3

value: Kidney


title: BBC2_DMSO-2

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

country: USA

institute: Augusta University

description: DMSO treatment

hyb_protocol: Following labeling, RNAs were hybridized for 18 hr at 48C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).

label: biotin

source_name: BBC2 cell line

label_protocol: Biotinylated RNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA (The FlashTag Biotin HSR RNA Labeling Kit, Affymetrix).

growth_protocol: BBC2 cell was cultered in RPMI-1640  medium supplemented with 10% FBS, 100U/ml Penicillin G, 100µg/ml Streptomycin sulfate.

extract_protocol: miRNA was prepared using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA) following the user manual.

treatment_protocol: The BBC2 cells were treated with 50 nM BGJ398 (Selleckchem, Houston, TX) or DMSO control for 24h, then cells were harvested for miRNA isolation.


title: Heart_rep2

source_name: Heart, 8weeks, replicate 2

value: Heart


title: Kidney_rep2

source_name: Kidney, 8weeks, replicate 2


title: Liver_rep1

source_name: Liver, 8weeks, replicate 1


title: Kidney_rep1

source_name: Kidney, 8weeks, replicate 1


title: Heart_rep3

source_name: Heart, 8weeks, replicate 3


title: BBC2_DMSO-1

description: DMSO treatment


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_16hr_rep 1

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

description: Gene expression in flower AZ after flower removal at 16hr

hyb_protocol: The labeled cRNA samples were hybridized on to an Solanum lycopersicum Custom 4x180K Array designed by Genotypic Technology Private Limited. (AMADID: 043310).1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: slides were then scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Agilent Feature Extraction software.Feature extracted data was analyzed using GeneSpring GX Version 12 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization

organism: Solanum lycopersicum

source_name: Flower AZ after flower removal_16hr_rep 1

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields using Nanodrop-1000 (JH Bio) and specific activity determined based on the concentration of cRNA and dye incorporation.

growth_protocol: Flower bunches of transgenic line of  TAPG:: antisense TPRP gene was harvested between 9 and 11 AM from transgenic greenhouse in Israel.

extract_protocol: RNA isolation was done using Qiagen method [Qiagen RNeay Plant minikit (Cat. No.74904)] as per the manufacturer protocol with DNAse treatment

treatment_protocol: The TAPG:: antisense TPRP transgenic plant flower bunches containing at least two to four fresh open flowers were brought to the laboratory under high-humidity conditions. Senesced flowers and young (unopened) buds were removed, and the stem ends were trimmed. The flowers were immediately sorted by removing all but two or three fresh flowers from each stem. Bunches of five flower stalks were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. Tissue samples were taken from the AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. The  tissues were sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal.

value: Whole flower AZ

tag: nature of the az

value: partially separated

tag: time point


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_4hr_rep 2

description: Gene expression in flower AZ after flower removal at 4hr

source_name: Flower AZ after flower removal_4hr_rep 2

value: attached


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_8hr_rep 2

description: Gene expression in flower AZ after flower removal at 8hr

source_name: Flower AZ after flower removal_8hr_rep 2


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_12hr_rep 1

description: Gene expression in flower AZ after flower removal at 12hr

source_name: Flower AZ after flower removal_12hr_rep 1


title: Heart_rep1

source_name: Heart, 8weeks, replicate 1


title: BBC2_BGJ50-1

description: BGJ398 50 nM treatment


title: Brain_rep3

source_name: Brain, 8weeks, replicate 3

value: Brain


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_20hr_rep 2

description: Gene expression in flower AZ after flower removal at 20hr

source_name: Flower AZ after flower removal_20hr_rep 2


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_20hr_rep 1

source_name: Flower AZ after flower removal_20hr_rep 1


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_16hr_rep 2

source_name: Flower AZ after flower removal_16hr_rep 2


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_0hr_rep 1

description: Gene expression in flower AZ without flower removal at 0hr

source_name: Flower AZ without flower removal_0hr_rep 1


title: BBC2_BGJ50-2

description: BGJ398 50 nM treatment


title: ExVivo_BMDM_M2_rep3

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

description: Gene expression in IL-4 stimulated BMDM

hyb_protocol: Each SBC mouse(8*60K) array slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: The slides were scanned using an Agilent Microarray Scanner G2565C (Agilent Technologies) with default settings with the following settings: Dye channel: Green, Scan resolution = 3 μm, PMT: 100%, and 20-bit.

data_processing: The Agilent Feature Extraction software (version 10.7) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring software 11.0 (Agilent Technologies).

source_name: Bone marrow-derived macrophages, M2, IL-4 stimulated BMDM

label_protocol: Total RNA from each sample was amplified and labeled by using a Low Input Quick Amp WT Labeling Kit (Agilent Technologies), following the manufacturer’s instructions. Labeled cRNA were purified using an RNeasy mini kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-2000.

growth_protocol: Bone marrow-derived macrophages (BMDMs) were isolated from BALB/c mice by flushing the femurs with Dulbecco’s modified Eagle’s medium (DMEM) medium. Macrophages plated on 6-well plates (1 × 106 cells/well) were maintained in DMEM supplemented with 20% fetal bovine serum and 20% L929 supernatant at 37°C and 5% CO2 for 7 days.

extract_protocol: Total RNA was extracted using TRIzol (Life Technologies), following the manufacturer’s instructions. RNA quantity and quality were measured by using a NanoDrop ND-2000, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies) and denaturing agarose gel electrophoresis. Total RNA was further purified using an RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen).

treatment_protocol: After 7 d of culture, the medium was removed, and the cells were cultured in RPMI 1640 supplemented with 10% FBS for an additional 24 h. Macrophages were further stimulated for 48 h either with 100 ng/mL LPS and 20 ng/mL IFN-γ (for M1 polarization) or 20 ng/mL IL-4 (for M2 polarization) in DMEM containing 10% FBS.

value: Bone marrow-derived macrophages

tag: strain

value: BALB/c


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_12hr_rep 2

source_name: Flower AZ after flower removal_12hr_rep 2


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_0hr_rep 2

source_name: Flower AZ without flower removal_0hr_rep 2


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_8hr_rep 1

source_name: Flower AZ after flower removal_8hr_rep 1


title: TAPG:: antisense TPRP_Flower pedicel_ AZ_4hr_rep 1

source_name: Flower AZ after flower removal_4hr_rep 1


title: TAPG:: antisense KD_Flower pedicel_ AZ_20hr_rep 2

growth_protocol: Flower bunches of transgenic line of  TAPG:: antisense KD gene was harvested between 9 and 11 AM from transgenic greenhouse in Israel.

treatment_protocol: The TAPG:: antisense KD transgenic plant flower bunches containing at least two to four fresh open flowers were brought to the laboratory under high-humidity conditions. Senesced flowers and young (unopened) buds were removed, and the stem ends were trimmed. The flowers were immediately sorted by removing all but two or three fresh flowers from each stem. Bunches of five flower stalks were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. Tissue samples were taken from the AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. The  tissues were sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal.


title: ExVivo_BMDM_M2_rep2

description: Gene expression in IL-4 stimulated BMDM


title: Kiwifruit_614-E21-II_good_1

type: SRA

city: Hefei

first: Junyang

last: Yue

state: Anhui

address: Tunxi Road

institute: Hefei University of Technology

library_source: transcriptomic

data_processing:
remove the 5' and 3' adaptor sequences
align to the Actinidia chinensis genome
Measurement of the FPKM value for each gene
Identification of differentially expressed genes by using the DESeq package
Genome_build: Actinidia chinensis genome (http://bdg.hfut.edu.cn/kir/index)

organism: Actinidia chinensis

source_name: kiwifruit

growth_protocol: grown under natural conditions

extract_protocol:
use the BIOFIT Reagent Kit
Illumina HiSeq 2000 sequencing platform following manufacture’s protocols

value: outer pericarp

value: 90 days after anthesis

tag: cultivar

value: Hongyang


title: Kiwifruit_614-E22-II_good_1


title: ExVivo_BMDM_M2_rep1

description: Gene expression in IL-4 stimulated BMDM


title: Kiwifruit_614-E20-II_good_1

value: inner pericarp


title: Brain_rep2

source_name: Brain, 8weeks, replicate 2

value: Male


title: TAPG:: antisense KD_Flower pedicel_ AZ_16hr_rep 2


title: TAPG:: antisense KD_Flower pedicel_ AZ_20hr_rep 1


title: ExVivo_BMDM_M1_rep3

description: Gene expression in LPS+IFN-r stimulated BMDM

source_name: Bone marrow-derived macrophages, M1, LPS+IFN-r stimulated BMDM


title: Distal_K27ac_rep2

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: ChIP genomic DNA

hyb_protocol: For the custom  tilling arrays ChIP DNA and input DNA ChIP DNA and input DNA were amplified (WGA2 kit, Sigma),  and hybridized according to the manufacturer’s protocol

scan_protocol: NimbleGen MS 200 [Tiff converted by Agilent Tiff4FE tool] NimbleGen MS 200

data_processing: Raw data was imported from microrray image analysis output files and median raw signal extracted using the bioconductor package limma.

source_name: Mouse E115 distal limb bud tissue

label_protocol: For the custom  tilling arrays ChIP DNA and input DNA ChIP DNA and input DNA were amplified (WGA2 kit, Sigma), and labelled according to the manufacturer’s protocol

extract_protocol: Cells from dissected E11.5 limbs and 14fp were fixed with 1% formaldehyde (25°C, 10 min) and stopped with 0.125 M glycine. Crosslinked ChIP was performed as described (Stock et al., 2007). In brief, the nuclei were sonicated using a Diagenode Bioruptor (Leige, full power 30s on, 30s off, in an ice bath for 50 min) to produce fragments of <300 bp. Chromatin (350 mg) was incubated with 5 mg prebound (to Protein A or G magnetic beads, Invitrogen) IgG (Santa Cruz, sc-2025) or the previously mentioned antibodies, raised to in the presence of 50 mg of BSA, washed, and eluted. Reverse crosslinked DNA was purified with Proteinase K (Glenaxxon) and QIAGEN PCR purification kit.  All antibodies used in this study have been previously reported as suitable for ChIP and/or ChIP-seq, H3K4me1 (ab8895, Abcam), H3K27ac (s39133, Active motif).

value: distal limb bud

tag: ChIP

value: H3K27ac (s39133, Active motif)


title: TAPG:: antisense KD_Flower pedicel_ AZ_16hr_rep 1

source_name: Flower AZ after flower removal_16hr_rep 1


title: ExVivo_BMDM_M1_rep1


title: TAPG:: antisense KD_Flower pedicel_ AZ_12hr_rep 1

source_name: Flower AZ after flower removal_12hr_rep 1


title: Distal_K4me1_input_rep2

description: ChIP genomic DNA

value: Input


title: ExVivo_BMDM_M1_rep2


title: TAPG:: antisense KD_Flower pedicel_ AZ_8hr_rep 2

source_name: Flower AZ after flower removal_8hr_rep 2

value: Attached


title: Distal_K27ac_input_rep2

description: ChIP genomic DNA


title: TAPG:: antisense KD_Flower pedicel_ AZ_8hr_rep 1


title: TAPG:: antisense KD_Flower pedicel_ AZ_12hr_rep 2


title: Distal_K4me1_input_rep1

description: ChIP genomic DNA


title: Distal_K4me1_rep1

description: ChIP genomic DNA

value: H3K4me1 (ab8895, Abcam)


title: Distal_K27ac_rep1

description: ChIP genomic DNA


title: Brain_rep1

source_name: Brain, 8weeks, replicate 1

value: 8 weeks


title: Distal_K4me1_rep2

description: ChIP genomic DNA


title: Subject 14 with normal HbF,HbF_14

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Following fragmentation, cRNA were hybridized for 17 hr at 65℃ on Human LncRNA Microarray V4.0 (Arraystar) . GeneChips were washed several times using Wash buffer kit (Agilent).

scan_protocol: GeneChips were scanned using the Agilent microarray scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 7 out of 14 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: peripheral blood

label_protocol: Cy3-labeled cRNA were prepared according to the standard Exiqon's manual from 1 ug total RNA (Agilent p/n 5190-0442).

growth_protocol: 2 mL peripheral blood anticoagulated by ethylene diamine tetraacetic acid EDTA was collected from every subject and stored at 4 ℃.

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

treatment_protocol: Each sample was depleted of CD45+ cells to remove leukocytes and then enriched for CD71+ erythroid cells by Miltenyi magnetic microbeads (Miltenyi Biotec), and placed on ice in the Trizol solution(invitrogen).

tag: cell

value: circulating CD71+ erythroid progenitors

value: 39 years

value: Female

tag: sample type

value: control


title: TAPG:: antisense KD_Flower pedicel_ AZ_4hr_rep 1

tag: tissue

value: Whole flower AZ


title: TAPG:: antisense KD_Flower pedicel_ AZ_4hr_rep 2

source_name: Flower AZ after flower removal_4hr_rep 2


title: Distal_K27ac_input_rep1

description: ChIP genomic DNA


title: Kiwifruit_614-E19-II_good_1


title: Subject 13 with normal HbF,HbF_13

description: Each sample was depleted of CD45+ cells to remove leukocytes and then enriched for CD71+ erythroid cells

value: 30 years

tag: Sex


title: TAPG:: antisense KD_Flower pedicel_ AZ_0hr_rep 1


title: TAPG:: antisense KD_Flower pedicel_ AZ_0hr_rep 2


title: Subject 11 with normal HbF,HbF_11

value: 31 years


title: Subject 9 with normal HbF,HbF_09

value: 41 years


title: Subject 8 with normal HbF,HbF_08

value: 32 years


title: Subject 6 with high HbF,HbF_06

value: b-thalssemia minor with high HbF


title: Subject 5 with high HbF,HbF_05


title: Subject 4 with high HbF,HbF_04

value: 33 years


title: Subject 1 with high HbF,HbF_01

value: 34 years


title: Subject 2 with high HbF,HbF_02

value: 27 years


title: CD8+T cells_N04_post-ATI

city: Bethesda

first: Jana

last: Blazkova

address: 9000 Rockville Pike

institute: NIH

hyb_protocol: 6µg of labeled cRNA was hybridized for 16h in 45°C to Affymetrix Human Genome U219 Array Strip. The arrays were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays.

scan_protocol: Human Genome U219 array strips were processed in GeneAtlas according to manufacturer's instructions.

data_processing: The data were analyzed with RMA using Partek Genomics Suit 6.6.

source_name: CD8+T cells_post-ATI

label_protocol: 100 ng of total RNA was amplified and labeled using GeneChip 3’IVT PLUS Reagent Kit (Affymetrix), according to manufacturer’s instructions.

extract_protocol: RNA from CD4+ and CD8+ T cells was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s specifications with on-column DNase I digestion to remove genomic DNA.

tag: subject status

value: HIV-infected individual

tag: subject id

value: Male

tag: race

value: White

tag: study time point

value: 1 year after interruption of antiretroviral therapy; post-ATI

value: periphral blood

tag: cell type

value: CD8+ T lymphocytes


title: CD8+T cells_N04_pre-ATI

source_name: CD8+T cells_pre-ATI

tag: gender

value: before interruption of antiretroviral therapy; pre-ATI


title: CD4+T cells_N10_pre-ATI

source_name: CD4+T cells_pre-ATI

value: CD4+ T lymphocytes


title: Subject 10 with normal HbF,HbF_10

value: circulating CD71+ erythroid progenitors

value: Female

value: control


title: CD8+T cells_N06_post-ATI


title: CD4+T cells_N09_post-ATI

source_name: CD4+T cells_post-ATI


title: CD8+T cells_N08_post-ATI


title: CD8+T cells_N01_post-ATI

value: Black


title: CD8+T cells_N08_pre-ATI


title: CD8+T cells_N01_pre-ATI


title: CD8+T cells_N09_post-ATI


title: CD8+T cells_N09_pre-ATI


title: CD8+T cells_N02_pre-ATI


title: Subject 7 with high HbF,HbF_07

value: 38 years


title: CD8+T cells_N06_pre-ATI


title: CD8+T cells_N10_post-ATI


title: Subject 12 with normal HbF,HbF_12

value: 28 years


title: CD4+T cells_N08_pre-ATI


title: CD8+T cells_N10_pre-ATI


title: CD4+T cells_N08_post-ATI


title: Subject 3 with high HbF,HbF_03

value: 41 years

value: b-thalssemia minor with high HbF


title: CD4+T cells_N06_post-ATI


title: CD8+T cells_N02_post-ATI


title: CD4+T cells_N04_pre-ATI


title: CD4+T cells_N10_post-ATI


title: H3K27ac Rep 2

description: ChIP genomic DNA

hyb_protocol: For the custom tilling arrays ChIP DNA and input DNA ChIP DNA and input DNA were amplified (WGA2 kit, Sigma), and hybridized according to the manufacturer’s protocol

scan_protocol: NimbleScan version 2.5.26, scanner NimbleGen MS 200

data_processing: The perfect match signal (PM) was extracted from the Nimblegen Pair Report file (range from 0 to 65536). Microarray data were analysed in R/Bioconductor with the Epigenome (PROT43) protocol (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid= 43) with the following parameters. The mean signal intensity of the two replicate probes on each array was taken. Loess normalization was used within replicates group to control inter-array variability using the R package limma. The log2 enrichment for each ChIP group was calculated by subtracting the mean of log2 input intensities from the mean of enriched intensities and averaging over the two biological replicates.  BED  files on the series record include the log2 ChIP/input for the average of the two replicates.

source_name: E11.5 limb derived cell line (14Fp cell line)

label_protocol: For the custom tilling arrays ChIP DNA and input DNA ChIP DNA and input DNA were amplified (WGA2 kit, Sigma), and labelled according to the manufacturer’s protocol

extract_protocol: Crosslinked ChIP was performed as described ( Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, Brockdorff N, Fisher AG, Pombo A. (2007) Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol. 9:1428-35.). from approximately 10^7 cells per experiment. All antibodies used in this study have been previously reported as suitable for ChIP and/or ChIP-seq, p300 (sc-585, Santa Cruz Biotechnology), H3K4me1 (ab8895, Abcam), H3K27ac (s39133, Active motif), GABPα (sc-22810, Santa Cruz), with the exception at ETV4 (ABE635, Millipore).

tag: chip target

tag: developmental stage

tag: cell line

value: limb bud mesenchymal cell line

tag: antibody

value: s39133, Active motif


title: H3K4me1 input Rep2

description: Input genomic DNA

value: Input

tag: strain


title: H3K27ac Rep 1

description: ChIP genomic DNA


title: CD4+T cells_N06_pre-ATI

value: HIV-infected individual

value: Male

tag: age

value: White


title: H3K4me1 input Rep 1

description: Input genomic DNA


title: CD4+T cells_N04_post-ATI

value: 1 year after interruption of antiretroviral therapy; post-ATI

value: periphral blood


title: Ep300 Rep 2

description: ChIP genomic DNA

value: sc-585, Santa Cruz Biotechnology


title: Ep300 input Rep2

description: Input genomic DNA


title: H3K4me1 Rep 1

description: ChIP genomic DNA

value: ab8895, Abcam


title: H3K27ac input Rep 1

description: Input genomic DNA


title: Ep300 input Rep 1

description: Input genomic DNA


title: CD4+T cells_N02_post-ATI

value: CD4+ T lymphocytes


title: Gabpa Rep 2

description: ChIP genomic DNA

value: Gabpa

value: sc-22810, Santa Cruz


title: Ep300 Rep 1

description: ChIP genomic DNA


title: Gabpa input Rep 1

description: Input genomic DNA


title: Gabpa Rep 1

description: ChIP genomic DNA


title: Gabpa input Rep 2

description: Input genomic DNA


title: H3K4me1 Rep 2

description: ChIP genomic DNA


title: CD4+T cells_N01_post-ATI

value: Female

value: Black


title: CD4+T cells_N01_pre-ATI

value: before interruption of antiretroviral therapy; pre-ATI


title: Hdac2 input Rep 2

description: Input genomic DNA


title: Hdac2 Rep 2

description: ChIP genomic DNA

value: ab16032, Abcam


title: Hdac2 Rep1

description: ChIP genomic DNA

value: limb bud mesenchymal cell line


title: CD4+T cells_N02_pre-ATI


title: Hdac2 input Rep1

description: Input genomic DNA


title: Etv4  Rep2

description: ChIP genomic DNA

value: ABE635, Millipore


title: Etv4 input Rep1

description: Input genomic DNA

value: Input


title: Etv4 input Rep 2

description: Input genomic DNA


title: ATO treated polysomal RNA

city: Chicago

first: Matthew

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

hyb_protocol: GeneChip Hybridization, Wash & Stain Kit according to manufacturer’s instructions.  GeneChips were washed and stained by the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data files were produced using the Affymetrix Expression Console.  The values represent the average of three replicates per group.

source_name: LN229 ATO treated polysomal RNA fraction

label_protocol: The manufacturer's instructions were followed to synthesize and label ss-cDNA using the Affymetric GeneChip WT Reagent kit.

growth_protocol: LN229 cells were grown in DMEM with 10% FBS and gentamycin in the presence or absence of ATO

extract_protocol: Cells were lysed using hypotonic lysis buffer containing cyclohexamide.  Polysomal RNA was isolated by ultracentrifugation and fractionation using a sucrose gradient.  Total and polysomal RNA fractions were processed using the AllPrep kit (Qiagen).

treatment_protocol: untreated or ATO (5 micromolar) for 6 hours in DMEM


title: CD4+T cells_N09_pre-ATI

value: HIV-infected individual


title: untreated total RNA

source_name: LN229 untreated total RNA fraction


title: ATO treated total RNA


title: untreated polysomal RNA

source_name: LN229 untreated polysomal RNA fraction


title: Etv4  Rep1

description: ChIP genomic DNA


title: HB_ACKR2-/-_small intestine

status: Public on Dec 31 2017

city: Louisville

first: Venkatakrishna

middle: R

last: Jala

state: KY

address: 505 S Hancock Street # 323

department: Dept. Microbiology and Immunology

institute: University of Louisville

description: gene expression of ACKR2-/- small intestine 110 day old

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Mouse 430 2.0 arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and GCOS Software v1 (Affymetrix)

data_processing: The CEL data was normalized using MAS5 imported into Partek Genomic Suite (Partek Inc) to set up contrasts.

label: Biotin

source_name: ACKR2-/-small intestine tissue - 110 day old

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Reagent Kit

growth_protocol: Min in ApcMin/+ background develop spontaneous intestinal tumors. RNA from Tumors or non tumor tissues (non ApcMIn/+ mice) were isolated at the age of 110 days.

extract_protocol: RNA isolated using Trizol based lysis followed by QIAGEN RNAesy mini columns.

treatment_protocol: Spontaneous tumors

tag: genotype

value: small intestine tissue

value: 110 days


title: HB_ACKR2-/-ApcMin_Colon Tumors

description: gene expression of ACKR2-/-ApcMin colon tumors at 110 day old

source_name: ACKR2-/- ApcMin/+ colon tumors -110 day old

value: colon tumors


title: HB_ACKR2-/-_Colon

description: gene expression of ACKR2-/- colon tissue at 110 day old

source_name: ACKR2-/- colon tissue - 110 day old

value: colon tissue


title: WT1 vs. WT2 (array 4)

city: new orleans

first: IHOR

last: YOSYPIV

state: Louisiana

address: 1430 tulane ave.

department: PEDIATRICS

institute: Tulane University

description:
array 4 WT1 vs. WT2
wild type FACS Six2CrePRRflox cells pool1
wild type FACS Six2CrePRRflox cells pool2

hyb_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

scan_protocol: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

data_processing: LogRatio extracts from Agilent Feature Extraction exports.

organism: Mus

source_name: WT FACS cells

label_protocol: Manufacturer's protocol (Agilent)

growth_protocol: Total RNA was isolated from Six2 EGFP+ Cap Mesenchym FACS-sorted from Embyonic day 15.5  Six2 7CreEGFP+; PRR flox/flox  and Six2 CreEGFP+ PRR+/+ using Qiagen RNA purification kit. The quality was checked using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

extract_protocol: Manufacturer's protocol (Agilent)

treatment_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

value: kidney

value: Embryonic day15.5

tag: genotype/variation

value: WT


title: WT3 vs. KO3 (array 3)

description:
array 3 WT3 vs. KO3
wild type FACS Six2CrePRRflox cells pool3
KO FACS Six2CrePRRflox cells pool3

source_name: KO FACS CELLS

value: PRR KO


title: HB_C57BL/6 -WT-Small intestine

description: gene expression of C57BL/6 small intestine tissue at 110 day old

source_name: HB_C57BL/6 -WT-Small intestine tissue


title: WT1 vs. KO1 (array 1)

description:
array 1 WT1 vs. KO1
wild type FACS Six2CrePRRflox cells pool1
KO FACS Six2CrePRRflox cells pool 1


title: HB_ApcMin_SI Tumors

description: gene expression of ApcMin small intestine (ileum) tumors at 110 day old

source_name: ApcMin/+ mice  small intestine tumors-110 day old

value: ApcMin/+

value: small intestine (ileum) tumors


title: WT2 vs. KO2 (array 2)

description:
array 2 WT2 vs. KO2
wild type FACS Six2CrePRRflox cells pool2
KO FACS Six2CrePRRflox cells pool2


title: CAR4_No Activation_Biological Rep 2

first: Yinmeng

last: Yang

address: 10 Center Drive

institute: NCI

description: Unstimulated CAR4 cells

hyb_protocol: Three biological replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.  Significant genes were analyzed for enrichment for pathways using DAVID bioinformatics database (http://david.abcc.ncifcrf.gov/) and Ingenuity Pathway Analysis software.

source_name: CAR4_No Activation

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: murine CAR T cells were generated by transduction with a gamma-retrovirus encoding a second generation CAR specific for the murine CD19 antigen (Kochenderfer et al, Blood, 2010, PMID:20631379) transduced into CD4 T cells from female Maryland mice or CD8 from female Matahari mice to generate CAR4 and CAR8 cells, respectively

extract_protocol: After co-culture, B cells were removed by magnetic bead extraction.  RNA was isolated from CAR T cells using QIAGEN RNEasy Micro Kit, following manufacturer's instructions

treatment_protocol: CAR4 or CAR8 cells were activated through the CAR and/or TCR by a 10 hour co-incubation with B cells expressing the following antigens:  B cells from WT (CD19+) female (HY-) mice were used to activate the CAR only.  B cells from CD19 knock out (CD19-) male mice (HY+) were used to activate the TCR only.  B cells from WT (CD19+) Male (HY+) mice were used to activate the CAR and TCR simulataneously.  B cells from CD19 knock out (CD19-) Female (HY-) mice were used as non-activating/negative controls

value: CD4-derived CAR T cell

tag: treatment

value: No activation


title: CAR4_CAR+TCR Activation_Biological Rep 2

description: CAR4 cells activated through both CAR and TCR

source_name: CAR4_CAR+TCR Activation

value: receptor activation through CAR and TCR


title: CAR8_CAR+TCR Activation_Biological Rep 2

description: CAR8 cells activated through both CAR and TCR

source_name: CAR8_CAR+TCR Activation

value: CD8-derived CAR T cell


title: CAR4_TCR Activation_Biological Rep 1

description: CAR4 cells activated through TCR

source_name: CAR4_TCR Activation

value: receptor activation through TCR


title: HB_ApcMin_Colon Tumors

description: gene expression of ApcMin colon tumors at 110 day old

source_name: ApcMin/+ mice Colon tumors-110 day old

tag: tissue


title: CAR8_TCR Activation_Biological Rep 3

description: CAR8 cells activated through TCR

source_name: CAR8_TCR Activation


title: CAR4_CAR Activation_Biological Rep 1

description: CAR4 cells activated through CAR

source_name: CAR4_CAR Activation

value: receptor activation through CAR


title: HB_C57BL/6 -WT_colon

description: gene expression of C57BL/6 colon tissue at 110 day old

source_name: HB_C57BL/6 -WT_colon tissue


title: CAR4_CAR Activation_Biological Rep 2

description: CAR4 cells activated through CAR


title: CAR8_CAR+TCR Activation_Biological Rep 1


title: HB_ACKR2-/-ApcMin_SI_Tumors

description: gene expression of ACKR2-/-ApcMin small intestine (ileum) tumors at 110 day old

source_name: ACKR2-/- ApcMin/+ small intestinal tumors -110 day old


title: CAR4_CAR+TCR Activation_Biological Rep 1


title: CAR4_No Activation_Biological Rep 3

description: Unstimulated CAR4 cells


title: CAR4_CAR+TCR Activation_Biological Rep 3


title: CAR4_TCR Activation_Biological Rep 3

description: CAR4 cells activated through TCR


title: CAR4_No Activation_Biological Rep 1

description: Unstimulated CAR4 cells


title: CAR8_CAR+TCR Activation_Biological Rep 3


title: CAR4_CAR Activation_Biological Rep 3

description: CAR4 cells activated through CAR


title: CAR8_TCR Activation_Biological Rep 2

description: CAR8 cells activated through TCR


title: CAR4_TCR Activation_Biological Rep 2

description: CAR4 cells activated through TCR


title: CAR8_No Activation_Biological Rep 3

description: Unstimulated CAR8 cells

source_name: CAR8_No Activation


title: CAR8_No Activation_Biological Rep 1

description: Unstimulated CAR8 cells


title: CAR8_CAR Activation_Biological Rep 3

description: CAR8 cells activated through CAR

source_name: CAR8_CAR Activation


title: CAR8_CAR Activation_Biological Rep 2

description: CAR8 cells activated through CAR


title: normal 1

city: Beijing

first: yijun

last: qi

address: You an men,Xi tou tiao

department: Biochemistry

institute: Capital Medical university

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: Adj normal 1

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: adjacent normal kidney

tag: Sex

value: Male

tag: Stage

value: stage 1


title: H3K27ac input Rep 2

description: Input genomic DNA

source_name: E11.5 limb derived cell line (14Fp cell line)

value: Input

value: limb bud mesenchymal cell line


title: normal 3

source_name: Adj normal 3

value: stage 3


title: stage 1

description: clear cell renal cell carcinoma

source_name: ccRCC 1

value: ccRCC tumor


title: CAR8_CAR Activation_Biological Rep 1

description: CAR8 cells activated through CAR


title: RD1

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

institute: Dongguk Uvi.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were preprocessed and normalized using the robust multi-array average (RMA) method in the oligo R package

source_name: regular diet

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Five-week-old C57BL/6 mice (Envigo, Indianapolis, IN, USA) were housed in a temperature- (22 ± 2°C) and humidity-controlled (50 ± 5%) room with a 12/12 h light/dark cycle and free access to food and water.

extract_protocol: Epididymal adipose tissue was dissected from the mice after an overnight fast, snap-frozen in liquid nitrogen, then stored at -75°C until analysis. Total RNA was extracted from epididymal adipose tissue of the RD, HFD, and MET groups using an RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Tissue samples used were from mice in three different treatment groups: a regular diet-fed (RD) group, a high fat diet-fed (HFD) group, and an HFD plus 300 mg/kg of metformin treatment (MET) group. The RD (10% kcal from fat; D12450B) and HFD (60% kcal from fat; D12492) were purchased from Research Diets (New Brunswick, NJ, USA). Mice were orally administered with either vehicle or metformin once a day for 12 weeks.

tag: diet

value: regular diet

value: epididymal adipose tissue


title: normal 2

source_name: Adj normal 2

value: stage 2


title: MET1

description: Mice were orally administered with either vehicle or metformin once a day for 12 weeks.

source_name: high fat diet-fed + metformin

value: high fat diet-fed + metformin


title: CAR8_TCR Activation_Biological Rep 1

description: CAR8 cells activated through TCR


title: CAR8_No Activation_Biological Rep 2

description: Unstimulated CAR8 cells


title: Muscle invasive Bladder_cancer_tissue 3

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

institute: Sun Yat-sen Memorial Hospital

description: Gene expression without treatment

hyb_protocol: Each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent) in Hybridization Oven (Agilent), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon) with Gene Expression Wash Buffer Kit (Agilent), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent) with default settings, Dye channel: Green, Scan resolution=3 μm, 20 bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

label_protocol: Total RNA was then amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN).

extract_protocol: Total RNA from cells was isolated using Trizol reagent (Life technologies). RNA purity and integrity was analyzed by Agilent Bioanalyzer 2100 (Agilent). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN) and RNase-free DNase set (QIAGEN).

treatment_protocol: Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were used directly for total RNA extraction.

value: bladder cancer

value: male


title: Normal_adjacent_tissue 3

description: Gene expression without treatment

value: normal blader


title: HFD1

source_name: high fat diet

value: high fat diet


title: Muscle invasive Bladder_cancer_tissue 2

description: Gene expression without treatment


title: root -N, biological rep 1

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data from rice roots without NH4NO3 treatment

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

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The Affymetrix CEL data were generated from GCOS and normalized using RMA algorithm in Genespring 11.5 software. Baselines were transformed to median of control samples. Expression value of probeset that >100 was defined as present. Unpaired t-test was performed to examine the reproducibility of the data sets. Probesets with P-value <0.05 and at least two-fold change between control and treatment groups were selected into the final list.

organism: Oryza sativa Japonica Group

source_name: rice roots without NH4NO3 treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) seeds were germinated in continuous dark at 30°C for 3 days and then transferred to hydroponic solution (Yoshida et al., 1976) without NH4NO3 (-N) and grown under controlled conditions (30°C, 12-h photoperiod, 200 µmol photons m-2 s-1, 70% relative humidity) for 2 weeks.

extract_protocol: Total RNA from –N and + NH4NO3-treated roots was extracted using a phenol extraction protocol.

treatment_protocol: 17-day-old rice seedlings grown in –N hydroponic solution were transferred to -N or +1.43 mM NH4NO3 solution for 30 min.

tag: variety

value: root

tag: growth stage

value: seedling


title: Normal_adjacent_tissue 2

city: Guangzhou

description: Gene expression without treatment


title: stage 3

description: clear cell renal cell carcinoma

source_name: ccRCC 3


title: root +NH4NO3, biological rep 2

description: Gene expression data from rice roots with NH4NO3 treatment for 0.5 hour


title: root +NH4NO3, biological rep 1

source_name: rice roots with NH4NO3 treatment for 0.5 hour


title: Group1 = Control Ad Libitum (no fasting) Liver 4 days 721

city: Thousand Oaks

first: Scott

last: Taylor

state: CA

address: One Amgen Center Drive

institute: Amgen Inc.

hyb_protocol: Biotin-labeled aRNA products were hybridized to Affymetrix (Santa Clara, CA) GeneChip® Rat Genome 230 2.0 Arrays per manufacturer instructions provided on the product insert

scan_protocol: Scans were per manufacturer instructions provided on the product insert

data_processing: The scan files were processed using Expression Console (Affymetrix) for quality control and subsequent results were used in microarray data analysis. All statistical analyses were executed using the R statistical computing platform (version 3.0.1). Expression data were normalized using the Robust Multi-Array Average method implemented in the Bioconductor package affy (version 1.38.1)

organism: Rattus norvegicus

label_protocol:
Oligo dT primed RT using SSII, 2nd strand cDNA synthesis, cleanup via Qiagen MinElute
Synthesis of biotinylated cRNA using the Enzo (Farmingdale, NY) amp kit, cleanup of cRNA via Qiagen RNeasy Mini kit

extract_protocol: Qiagen (Valencia, CA) RNeasy Mini kit using qiazol to homogenize the tissues and chloroform for phase separation

treatment_protocol: Powdered feed was provided either ad libitum, reduced 15%, reduced 30% or reduced 60% according to study group

value: Sprague-Dawley

value: Liver

tag: subject id

value: GROUP 1 = CONTROL AD LIBITUM (NO FASTING)

tag: time point

value: 4 d


title: Muscle invasive Bladder_cancer_tissue 1

description: Gene expression without treatment

tag: gender


title: Group4 = 70% Food (fast overnight) Liver 4 days 739

value: Male

value: GROUP 4 = 70% FOOD (FAST OVERNIGHT)


title: root -N, biological rep 2


title: stage 2

description: clear cell renal cell carcinoma

source_name: ccRCC 2

value: ccRCC tumor


title: Group1 = Control Ad Libitum (no fasting) Liver 14 days 748


title: Group4 = 70% Food (fast overnight) Liver 14 days 761


title: Group4 = 70% Food (fast overnight) Liver 4 days 738


title: Normal_adjacent_tissue 1

description: Gene expression without treatment


title: Group2 = Control Ad Libitum (fast overnight) Liver 14 days 752

value: GROUP 2 = CONTROL AD LIBITUM (FAST OVERNIGHT)


title: Group3 = 85% Food (fast overnight) Liver 14 days 756

value: GROUP 3 = 85% FOOD (FAST OVERNIGHT)


title: Group4 = 70% Food (fast overnight) Liver 14 days 765


title: Group5 = 40% Food (fast overnight) Liver 14 days 770

value: GROUP 5 = 40% FOOD (FAST OVERNIGHT)


title: Group2 = Control Ad Libitum (fast overnight) Liver 14 days 751


title: Group4 = 70% Food (fast overnight) Liver 14 days 762


title: Group5 = 40% Food (fast overnight) Liver 4 days 744


title: Group1 = Control Ad Libitum (no fasting) Liver 4 days 724


title: Group2 = Control Ad Libitum (fast overnight) Liver 14 days 753


title: Group5 = 40% Food (fast overnight) Liver 4 days 745


title: Group4 = 70% Food (fast overnight) 14 days 764


title: Group2 = Control Ad Libitum (fast overnight) Liver 4 days 730


title: Group3 = 85% Food (fast overnight) Liver 14 days 760


title: Group5 = 40% Food (fast overnight) Liver 14 days 767


title: Group5 = 40% Food (fast overnight) Liver 14 days 769


title: Group3 = 85% Food (fast overnight) Liver 14 days 759


title: Group5 = 40% Food (fast overnight) Liver 4 days 742


title: Group5 = 40% Food (fast overnight) Liver 14 days 766


title: Group1 = Control Ad Libitum (no fasting) Liver 14 days 750


title: Group3 = 85% Food (fast overnight) Liver 4 days 733


title: Group3 = 85% Food (fast overnight) Liver 14 days 757


title: Group2 = Control Ad Libitum (fast overnight) Liver 14 days 755


title: Group4 = 70% Food (fast overnight) Liver 4 days 737


title: Group3 = 85% Food (fast overnight) Liver 4 days 732


title: Group2 = Control Ad Libitum (fast overnight) Liver 4 days 729


title: Group4 = 70% Food (fast overnight) Liver 14 days 763


title: Group1 = Control Ad Libitum (no fasting) Liver 14 days 746


title: Group5 = 40% Food (fast overnight) Liver 4 days 743


title: Group1 = Control Ad Libitum (no fasting) Liver 14 days 747


title: Group4 = 70% Food (fast overnight) Liver 4 days 740


title: Group4 = 70% Food (fast overnight) Liver 4 days 736


title: Group5 = 40% Food (fast overnight) Liver 14 days 768


title: Group3 = 85% Food (fast overnight) Liver 4 days 731


title: Group2 = Control Ad Libitum (fast overnight) Liver 4 days 728


title: Group3 = 85% Food (fast overnight) Liver 4 days 734


title: Group5 = 40% Food (fast overnight) Liver 4 days 741


title: Group1 = Control Ad Libitum (no fasting) Liver 4 days 725


title: Group2 = Control Ad Libitum (fast overnight) Liver 4 days 726


title: Group2 = Control Ad Libitum (fast overnight) Liver 14 days 754


title: Group1 = Control Ad Libitum (no fasting) Liver 4 days 722


title: Group2 = Control Ad Libitum (fast overnight) Liver 4 days 727


title: Group1 = Control Ad Libitum (no fasting) Liver 4 days 723


title: Group3 = 85% Food (fast overnight) Liver 14 days 758


title: Group3 = 85% Food (fast overnight) Liver 4 days 735


title: Sox11 knock-out caudal urogenital ridge at E10.75, biological rep4

city: Nice

first: Yasmine

last: Neirijnck

address: Parc Valrose

department: iBV

institute: University of Nice

description:
sox11-/-, caudal urogenital ridge
KO91

hyb_protocol: Fragmented cRNA was hybridized for using the GeneChip Hybridization Oven 645 and washed/stained using in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using the AFFYMETRIX GeneChip Scanner 3000 7G

data_processing:
Arrays have been quantile-normalize with respect to the probe GC content using the RMA algorithm. Not or low expressed transcripts have been removed by a maximum expression cutoff < 50. The data filtering resulted in 206768 of 234872 probe sets and 27478 meta-probe sets defined in the full dataset. The analysis on alternative splicing events has been performed using the two way ANOVA approach of the Partek Genomic Suite version 6.4. Resulting interaction p-values indicating the probability of splicing events. They have been multiple testing corrected using the Bejamini Hochberg procedure (Benjamini & Hochberg, 1995). Transcript clusters with an ANOVA FDR < 0.05 (n = 267) have been selected as a significant differential spliced subset. 103 and 34 of these Transcript clusters have one or more probe sets > two fold down regulated respectively up regulated in Sox11 knock out at p < 0.05. Differential expression of summarized gene level expression was calculated using the f-test statistic followed by a FDR multiple testing correction.
Genelevel_full_rmagc_max50 quantile-normalize with respect to the probe GC content using the RMA algorithm and Partek software (GenomicSuite 6.4)

source_name: sox11-/-, caudal urogenital ridge

label_protocol: Labeling was performed using the Affymetrix labeling kit according to manufacturers instructions

growth_protocol: Mice on a mixed genetic background were housed in a conventional animal facility with free access to food and water

extract_protocol: Total RNA was extracted, in 4 independent replicates for each genotype, from dissected caudal area of urogenital ridges of E10.75 embryos using the RNeasy MicroKit (Qiagen) followed by column DNase digestion to remove any contaminating genomic DNA. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen). cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: No treatment

value: caudal urogenital ridge

tag: developmental stage


title: Sox11 knock-out caudal urogenital ridge at E10.75, biological rep3

description:
sox11-/-, caudal urogenital ridge
KO76


title: wildtype caudal urogenital ridge at E10.75, biological rep4

description:
wild-type, caudal urogenital ridge
WT77

source_name: wild-type, caudal urogenital ridge

value: wildtype


title: Sox11 knock-out caudal urogenital ridge at E10.75, biological rep2

description:
sox11-/-, caudal urogenital ridge
KO45


title: wildtype caudal urogenital ridge at E10.75, biological rep1

description:
wild-type, caudal urogenital ridge
WT14


title: wildtype caudal urogenital ridge at E10.75, biological rep3

description:
wild-type, caudal urogenital ridge
WT60


title: JV_D6KO_10Wks_biological replicate 2

description: Exvivo cultured BMMCs for 10 weeks

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Mouse Gene 1.0 ST arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 3.1 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level, followed by a two-way ANOVA.

source_name: 10 weeks Cultured bone marrow derived mast cells from ACKR2-/- (D6-/-) mouse

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix WT Plus Reagent Kit from 250 ng total RNA

growth_protocol: Bone marrow derived mast cell (BMMC) cultures were generated from 4- to 6- week- old female mice. The bone marrow was flushed with RPMI from tibia and femur bones, gently mushed (pulped), filtered through 60 µm nylon mesh and centrifuged at 450 g for 5 min. The pellet was resuspended in BMMC culture medium (DMEM containing 10% FCS, 100 units/ml Penicillin, Streptomycin 100 µg/ml, 2 mM L-Glutamine, 50 µM β-mercaptoethanol) supplemented with 12.5 ng/ml recombinant Mouse SCF (R&D Systems # 455 MC), 10 ng /ml recombinant Mouse IL-3 (R&D Systems #403-ML) and plated at ~1 X 106 /ml density in T-75 cm2 flask containing 15 ml of medium. The non-adherent cells were transferred after 48 hours into fresh flasks without disturbing the adherent (fibroblast) cells. The flasks were changed weekly or as needed to separate the non-adherent mast cells from the contaminating adherent cells. The medium was changed once a week with medium containing SCF, IL-3. The homogenous population of mast cells were visible after 4 weeks of culture and  propagated further by dividing once or twice a week to 0.5 -1x10 6 cells/ml density. Cells were grown for 10 weeks and isolated total RNA. For some experiments mast cells were purified from non-homogenous cultures at the age of 2 weeks on MACS column (Miltenyi Biotec Inc.) using CD117 antibody. The purity of BMMCs confirmed by surface staining with mast cell specific markers c-Kit and FcR1 (eBioscience) by FACS analysis.

extract_protocol: For total RNA isolation, BMMCs were lysed using Trizol reagent followed by RNAse mini prep kit from Qiagen. Any residual DNA contamination was eliminated by DNAase treatment (Ambion Inc). The quality of RNA was examined using Bio-analyzer.

treatment_protocol: BMMCs were collected at 2 weeks and 10 weeks from C57BL/6 (wild type) and ACKR2-/- mice.

value: 10 weeks

tag: cell type

value: Cultured mast cells


title: RD2

value: regular diet

value: epididymal adipose tissue


title: JV_D6KO_10Wks_biological replicate 3

description: Exvivo cultured BMMCs for 10 weeks


title: wildtype caudal urogenital ridge at E10.75, biological rep2

description:
wild-type, caudal urogenital ridge
WT36


title: JV_WT_10Wks_biological replicate 1

description: Exvivo cultured BMMCs for 10 weeks

source_name: 10 weeks Cultured bone marrow derived mast cells from C57BL/6 mouse


title: Sox11 knock-out caudal urogenital ridge at E10.75, biological rep1

description:
sox11-/-, caudal urogenital ridge
KO18


title: JV_D6KO_10Wks_biological replicate 1

description: Exvivo cultured BMMCs for 10 weeks


title: JV_WT_10Wks_biological replicate 3

description: Exvivo cultured BMMCs for 10 weeks


title: JV_WT_10Wks_biological replicate 2

description: Exvivo cultured BMMCs for 10 weeks


title: JV_D6KO_2Wks_biological replicate 1

description: Exvivo cultured BMMCs for 2 weeks

source_name: 2 weeks Cultured bone marrow derived mast cells from ACKR2-/- (D6-/-) mouse

value: 2 weeks


title: JV_D6KO_2Wks_biological replicate 3

description: Exvivo cultured BMMCs for 2 weeks


title: JV_D6KO_2Wks_biological replicate 2

description: Exvivo cultured BMMCs for 2 weeks


title: JV_WT_2Wks_biological replicate 3

description: Exvivo cultured BMMCs for 2 weeks

source_name: 2 weeks Cultured bone marrow derived mast cells from C57BL/6 mouse


title: JV_WT_2Wks_biological replicate 2

description: Exvivo cultured BMMCs for 2 weeks


title: JV_WT_2Wks_biological replicate 1

description: Exvivo cultured BMMCs for 2 weeks


title: Aged adults keratinocytes- repl10

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

hyb_protocol: Following fragmentation, 1 ug of cRNA washybridized for 16 hr at 45C on GenChip miRNA 4.0

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

data_processing:
Scanned images of microarray chips were analyzed using Expression Console software (Affymetrix) with the default settings.
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Aged adults keratinocytes

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

growth_protocol: Human primary keratinocytes were cultured in KGM2 medium and RNA was extracted in ealy passage cells (P2) at confluency

extract_protocol: Extraction of total RNA including small RNA was performed using the miRvana isolation kit according to the manufacturer's instructions.

value: 60-70 years

value: Human primary keratinocytes

tag: passage

value: ealy passage cells (P2)


title: Aged adults keratinocytes- repl11


title: Young adult keratinocytes- repl7

source_name: Young adult keratinocytes

value: 20-40 years


title: Infant keratinocytes- repl4

source_name: Infant keratinocytes

value: 3-6 years


title: Aged adults keratinocytes- repl12


title: Aged adults keratinocytes- repl9


title: Young adult keratinocytes- repl8


title: Young adult keratinocytes- repl5


title: Young adult keratinocytes- repl6


title: Infant keratinocytes- repl3


title: Infant keratinocytes- repl1


title: Infant keratinocytes- repl2


title: HTNV1

city: Xi'an

first: Xuyang

last: Zheng

state: Shaanxi

address: No. 569 Xinsi Road, Baqiao District

department: Department of Infectious Diseases

institute: The Fourth Military Medical University

description: Gene expression in HUVEC cells infected with HTNV at a MOI of 1 for 48 hours

hyb_protocol: Hybridization was performed using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) in hybridization chamber (Agilent p/n G2534A) and hybridization oven (Agilent p/n G2545A). 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed using Gene Expression Wash Buffer produced by Agilent, fixed and scanned with using the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen p/n 74104). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HUVEC cells (ScienCell Research Laboratories, Carlsbad, CA, USA) were grown in ECM BulletKit (ScienCell Research Laboratories, Carlsbad, CA, USA) in a 5% CO2 incubator.

extract_protocol: 1. Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. 2. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. 3. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. 4. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. 5. At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. 6. Total RNA was cleaned-up using RNasey Mini Kit(Qiagen p/n 74104) and the quality of RNA was tested using NanoDrop ND-1000.

treatment_protocol: HUVECs were mock infected or infected by incubation with HTNV (moi=1) at 37 ℃ for 60 mins. Subsequently, the virus solution was removed and fresh medium added to the cell culture. 48 hours after infection, total RNA from cells were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and were sent for RNA microarray. Three independent experiments were conducted.

value: HUVEC


title: HTNV2

source_name: HUVEC cells infected with HTNV at a MOI of 1 for 48 hours


title: DEP 50 ug/ml treated PHNEC replicate 4

city: Goyang

first: Hyo-Jeong

last: Kim

address: 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea

institute: Dongguk University

hyb_protocol: Cy3 or Cy5 labeled cRNA was hybridize probe of Agilent-028004 chip for 17 hours.

scan_protocol: The array chip was scanned by SureScan MicroArray Scanner (Agilent Genomics, USA).

data_processing: Data normalization and visualization was conducted using GeneSpring GX (Agilent Genomics, USA).

source_name: Primary Human Nasal Epithelial Cell (PHNEC)

label_protocol: 200ng of total RNA was labeled with Cy3 or Cy5 using Low Input Amp Labeling Kit (Agilent).

extract_protocol: Total RNA were extracted using RNasy Mini Kit (Qiagen, Germany) following the manufactural protocols.

value: Nasal cavity

source_name: DEP 50 ug/ml treated PHNEC replicate 4


title: HTNV3


title: DEP 200 ug/ml treated PHNEC replicate 2

source_name: DEP 200 ug/ml treated PHNEC replicate 2


title: Control2

description: Gene expression in HUVEC cells mock infected for 48 hours

source_name: HUVEC cells mock infected for 48 hours


title: DEP 50 ug/ml treated PHNEC replicate 3

source_name: DEP 50 ug/ml treated PHNEC replicate 3


title: DEP 200 ug/ml treated PHNEC replicate 1

source_name: DEP 200 ug/ml treated PHNEC replicate 1


title: DEP 200 ug/ml treated PHNEC replicate 3

source_name: DEP 200 ug/ml treated PHNEC replicate 3


title: DEP 50 ug/ml treated PHNEC replicate 1

source_name: DEP 50 ug/ml treated PHNEC replicate 1


title: DEP 200 ug/ml treated PHNEC replicate 4


title: Control3


title: Control1


title: DEP 50 ug/ml treated PHNEC replicate 2

source_name: DEP 50 ug/ml treated PHNEC replicate 2


title: S0849R0028

city: Belfast

first: Wendy

last: Allen

address: 97 Lisburn Road

department: Centre For Cancer Research and Cell Biology

institute: Queen's University Belfast

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

hyb_protocol: Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

scan_protocol: Scanner GeneChip 3000 ; Wavelength : 570 nm, size pixel: 1.56 µm ; each chip is scanned once;

data_processing: RMA normalisation (Bioconductor R makecdfenv and affy package) + ComBat (R sva package )

source_name: Fresh frozen colorectal cancer biopsy

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

growth_protocol: Samples stored at -80 C

extract_protocol: total RNA was extracted using Manual-Rneasy Mini (Qiagen)

treatment_protocol: Total RNA was performed according to the manufacturer's instructions.

value: colorectal cancer biopsy

tag: site

value: Florence

tag: age diagnosis

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Left hemicolectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: S0849R0014

tag: tissue

tag: site

value: Aberdeen

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Caecum + Asc colon

tag: type of surgery

value: Right hemicolectomy

value: C

value: IIIB

value: pMx

value: CRISD


title: S0849R0016

value: colorectal cancer biopsy

value: Female

value: Sigmoid

value: Sigmoid colectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: UNK

value: CRISC


title: S0849R0012

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Poor

value: Yes

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

value: MT

tag: kras (codons 12, 13, 61)

value: WT


title: S0849R0022

value: Barcelona

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

value: Moderate


title: S0849-00184 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Yes - Extensive

value: Upper rectum

value: Open Anterior Resection

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: CRISD


title: S0849-00182 R1

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Yes

tag: lvi

value: Hepatic flexure

value: Laparoscopic assisted right hemicolectomy

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849R0023

tag: tissue

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

value: No

tag: tumour site

value: Rectum

tag: type of surgery

value: PROCECTOMY

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIB

tag: tstage

value: pMx

value: CRISB


title: S0849-00183 R1

value: colorectal cancer biopsy

value: SVH Dublin

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Ascending colon

value: Laparoscopic right hemicolectomy

value: C

value: IIIB

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: WT

value: MT


title: S0849-00181 R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Female

value: Caecum

value: Poor

value: Yes

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00179 R1

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Hepatic flexure

tag: type of surgery

value: Open right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage


title: S0849R0013

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: age diagnosis

tag: gender

value: Sigmoid

value: Sigmoid colectomy

tag: nstage

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: UNK

value: CRISC


title: S0849-00180 R1

value: SVH Dublin

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Laparoscopic assisted right hemicolectomy

value: B

value: IIA

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISB

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849R0024

tag: tissue

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

value: No

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIB

tag: tstage

value: Poor

value: Yes

value: Alive


title: S0849-00178 R1

value: colorectal cancer biopsy

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Ascending colon

value: Open right hemicolectomy

value: C

value: IIIB

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: CRISD

value: MT


title: S0849-00177 R1

tag: tissue

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Upper rectum

value: Laparoscopic Anterior Resection

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISB

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: PBMC Genomic DNA G00244

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: CFS Genomic DNA

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions

tag: Sex

value: female

tag: disease state

value: CFS


title: S0849-00176 R1

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Caecum

tag: type of surgery

value: Laparoscopic right hemicolectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

value: Poor

value: Alive

value: WT


title: S0849-00174 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Female

value: Yes

value: Sigmoid

value: Laparoscopic converted Anterior Resection

value: C

value: IIIC

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISD


title: S0849-00173 R1

value: SVH Dublin

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: Laparoscopic converted sigmoid colectomy

tag: curative resection

tag: dukes

value: IIB

value: Moderate

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: PBMC Genomic DNA G00256

description: CFS Genomic DNA

tag: Sex

value: female

tag: disease state

value: CFS


title: S0849-00171 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: No

value: Transverse colon

value: Laparoscopic extended right hemicolectomy

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: CRISB

value: WT


title: S0849-00172 R1

value: SVH Dublin

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Upper rectum

tag: type of surgery

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC


title: PBMC Genomic DNA G00159

description: CFS Genomic DNA

tag: Sex

tag: disease state


title: S0849-00169 R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Female

value: Caecum

value: Laparoscopic right hemicolectomy

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

value: Yes

value: Dead

value: UNK

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: PBMC Genomic DNA G00147

description: CFS Genomic DNA

value: female

value: CFS


title: PBMC Genomic DNA G00222

description: CFS Genomic DNA


title: PBMC Genomic DNA G00194

description: CFS Genomic DNA


title: PBMC Genomic DNA G00262

description: CFS Genomic DNA


title: PBMC Genomic DNA G00181

description: CFS Genomic DNA


title: PBMC Genomic DNA G00166

description: CFS Genomic DNA


title: PBMC Genomic DNA G00198

description: CFS Genomic DNA


title: PBMC Genomic DNA G00124

description: CFS Genomic DNA


title: S0849-00167 R1

value: colorectal cancer biopsy

value: SVH Dublin

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Descending colon

tag: type of surgery

value: Open subtotal colectomy

tag: curative resection

tag: dukes

value: B

value: IIA

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: CRISD

value: WT


title: S0849-00166 R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Sigmoid

value: Open Hartmann's Procedure

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: Moderate

tag: cms subgroup

tag: cris subgroup

value: CRISB


title: S0849-00170 R1

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Yes

tag: tumour site

value: Upper rectum

tag: type of surgery

value: Open High Anterior Resection

value: C

value: IIIB

tag: differentiation

value: Well

tag: adjuvanttreatment

value: Dead

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: S0849-00168 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Male

value: No

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

value: B

value: IIA

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: CRISC


title: PBMC Genomic DNA G00263

description: CFS Genomic DNA

tag: Sex

value: female

tag: disease state

value: CFS


title: PBMC Genomic DNA G00111

description: CFS Genomic DNA


title: PBMC Genomic DNA G00069

description: CFS Genomic DNA


title: S0849-00162 R1

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Yes

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Laparoscopic converted sigmoid colectomy

value: C

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: Moderate

tag: cms subgroup

tag: cris subgroup

value: CRISE

value: WT


title: PBMC Genomic DNA G00115

description: CFS Genomic DNA


title: PBMC Genomic DNA G00106

description: CFS Genomic DNA


title: PBMC Genomic DNA G00172

description: CFS Genomic DNA


title: S0849-00153 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Caecum

value: Laparoscopic right hemicolectomy

tag: curative resection

tag: dukes

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: S0849-00158 R1

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: Left hemicolectomy

value: B

tag: stage ii\iii

value: IIA

tag: tstage

value: Alive

tag: overall survival time

tag: progression-free survival time

value: CRISC


title: S0849-00161 R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Upper rectum

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

tag: nstage

tag: mstage

value: Dead

value: Yes

tag: cms subgroup

tag: cris subgroup


title: PBMC Genomic DNA G00074

description: CFS Genomic DNA

tag: Sex

value: female

tag: disease state

value: CFS


title: SAMPLE 88

city: Birmingham

first: John

middle: Kenneth

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

description:
SAMPLE 88
Hybridized with SAMPLE 80 on the array

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate was applied to each of 12 subarrays with the appropriate Sample Tracking Control (STC) following protocols described in Lopez, J.A. and J.K. Colbourne. 2011. Dual-Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations. CGB Technical Report 2011-02. doi:10.2506/cgbtr-201102.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Wyeomyia smithii

source_name: PBSD22 Replicate 1

label_protocol: DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: The mosquitoes were maintained as diapausing larvae on an 8:16 light:dark cycle at 21°C and reared on a typical 18:6 light:dark cycle with a sinewave thermoperiod with a maximum temperature of 32°C and minimum temperature of 15°C which lagged the light cycle by 3 hours. Larvae were fed ad lib. a 4:1 mixture by volume of ground freeze-dried brine shrimp (San Franciso Bay Brand, 8239 Enterprise Drive, Neward, CA 94560, USA) and guinea pig chow (Geisler Guine Pig Chow, Sergeant’s Pet Care Products, 10077 S 134th St, Omaha, NE 68138, USA) once a week.  Adults were offered a continuous supply of organic (pesticide free)  raisins as a carbohydrate source.

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Short Day (SD) Night Sampling (ZT22)

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00165 R1

value: colorectal cancer biopsy

value: SVH Dublin

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Rectosigmoid

tag: type of surgery

value: Open Anterior Resection

tag: stage ii\iii

tag: tstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: S0849-00151 R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

value: Male

value: Yes

value: Caecum

value: Open right hemicolectomy

tag: curative resection

tag: dukes

value: C

value: IIIB

tag: nstage

tag: mstage

value: Alive

tag: cms subgroup

tag: cris subgroup

value: CRISE


title: S0849-00150 D2 / R2

value: colorectal cancer biopsy

value: Barcelona

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy

tag: stage ii\iii

value: IIIC

tag: tstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

value: Dead

value: CRISB


title: PBMC Genomic DNA G00041

description: CFS Genomic DNA

tag: Sex

value: female

tag: disease state

value: CFS


title: S0849-00152 R1

tag: tissue

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Female

value: No

value: Yes

value: Upper rectum

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

value: Moderate

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: UNK

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: PBMC Genomic DNA G00077

description: CFS Genomic DNA


title: S0849-00146 D1 / R1

value: colorectal cancer biopsy

value: Barcelona

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

value: Alive

tag: cms subgroup

tag: cris subgroup

value: CRISE

value: WT

value: MT


title: SAMPLE 86

description:
SAMPLE 86
Hybridized with SAMPLE 66 & 43 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: PBMC Genomic DNA G00043

description: CFS Genomic DNA

tag: disease state

value: CFS


title: SAMPLE 87

description:
SAMPLE 87
Hybridized with SAMPLE 79 on the array

source_name: PBSD22 Replicate 2


title: SAMPLE 84

description:
SAMPLE 84
Hybridized with SAMPLE 42 & 67 on the array

source_name: PBSD22 Replicate 4


title: S0849-00145 D1 / R1

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

value: Yes

value: Left Colon

value: Sigmoidectomy

tag: curative resection

tag: dukes

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00148 D1 / R1

tag: tissue

value: Barcelona

tag: lvi

tag: tumour site

tag: type of surgery

value: B

tag: stage ii\iii

value: IIB

tag: tstage

tag: nstage

tag: mstage

value: Dead

tag: cms subgroup

tag: cris subgroup

value: WT

value: MT


title: SAMPLE 85

description:
SAMPLE 85
Hybridized with SAMPLE 76 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00142 D1 / R1

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

value: Right colon

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: IIA

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: CRISD

tag: braf (v600e)


title: SAMPLE 82

description:
SAMPLE 82
Hybridized with SAMPLE 62 & 41 on the array

source_name: PBSD22 Replicate 3

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod


title: PBMC Genomic DNA G00100

description: CFS Genomic DNA

tag: disease state

value: CFS


title: SAMPLE 83

description:
SAMPLE 83
Hybridized with SAMPLE 71 on the array

tag: sampling time


title: S0849-00144 D1 / R1

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Yes

tag: lvi

tag: tumour site

tag: type of surgery

value: B

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: Moderate

value: Dead

tag: cms subgroup

tag: cris subgroup

value: CRISA

value: WT

tag: kras (codons 12, 13, 61)