title: BoNT/A1 exposed cells, sample 1, 2 weeks


title: Liver_HCV_0701-0057

status: Public on Sep 15 2014

type: RNA

city: Izunokuni

first: Shunsuke

last: Sato

state: Shizuoka

address: 1129 Nagaoka

department: Department of Internal Medicine

country: Japan

institute: Juntendo University Shizuoka Hospital

description: chronic hepatitis C

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.1

molecule: total RNA

organism: Homo sapiens

source_name: Liver tissue

label_protocol: Agilent one-color Quick Amp Labeling Kit labeling protocol

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and evaluated by the Agilent 2100 Bioanalyzer (Agilent Technologies). Only high quality RNA with RNA integrity numbers greater than 7.0 was used for experiments

treatment_protocol: We performed percutaneous liver biopsy for diagnosis and they were not conducted by anti-viral treatment until biopsy.

tag: disease state

value: chronic hepatitis C

tag: tissue

value: Liver biopsy specimens

tag: gender

value: female

tag: afp(ng/ml)


title: Liver_HCV_0701-0022

description: chronic hepatitis C

value: male


title: Nagina22 in 6-BA solution Replicate 2

city: Hyderabad

first: Rajeshwari

last: Ramanan

state: Andhra Pradesh

address: Uppal Road

department: Plant Science

country: India

institute: Centre for Cellular and molecular biology

description: PLIER.Variance Stabilization.N226BA-2

hyb_protocol: biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 58rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450.

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected for further analysis using AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India). The PLIER and RMA algorithms were used for data normalization

label: biotin

organism: Oryza sativa

source_name: Nagina22 in 6-BA solution

label_protocol: 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

growth_protocol: Nagina 22 rice seeds were germinated and grown for 7 days on petriplates containing moist filter paper. 7-days old seedlings were transferred to pots containing soil and grown in green house for 21 days. 3rd leaf of the plants were excised cleaned with water. Fresh weight of 5 grams leaf sample was used for each replicate.

extract_protocol: 5 gram leaf samples treated for 72 hours in darkness in 35 ml of 6-BA or control solution. After treatment the leaf samples were wiped with water and used for total RNA extraction using Trizol reagent (Invitrogen)

treatment_protocol: 6-Benzyl adenine - 2 mg/ml made soluble in 0.1N NaOH and then made upto 35 ml in 0.02% tween20. The control sample were dipped in 0.1N NaOH in 0.02% tween20.

tag: genotype/cultivar

value: Nagina 22 cv.

tag: age

value: 30-day-old plant

value: 3rd leaf

tag: treated for

value: 2 hrs in darkness in 6-BA solution


title: Liver_HCV_0703-0039

description: chronic hepatitis C


title: Liver_HCV_0703-0003

description: chronic hepatitis C


title: Nagina22 control Replicate 3

description: PLIER.Variance Stabilization.N22C-3

source_name: Nagina22 control

value: 2 hrs in darkness in control solution


title: Liver_HCV_0702-0047

description: chronic hepatitis C


title: Nagina22 in 6-BA solution Replicate 1

description: PLIER.Variance Stabilization.N226BA-1


title: Liver_HCV_0702-0024

description: chronic hepatitis C


title: Nagina22 in 6-BA solution Replicate 3

description: PLIER.Variance Stabilization.N226BA-3


title: Liver_HCV_0701-0009

description: chronic hepatitis C


title: Liver_HCV_0612-0087

description: chronic hepatitis C


title: BW25113-pCA24N_dosP

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description: Gene expression data for IPTG induction of cells containing pCA24N_dosP.

hyb_protocol: Following affymetrix protocol.  Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA.  After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol.  After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS).

organism: Escherichia coli K-12

source_name: overexpression of dosP (pCA24N_dosP)

label_protocol: Following affymetrix protocol.  cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: Strains were grown in LBCm30 at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted at 1:1000 into fresh LBCm30, grown to OD600 ~ 1.0, and induced with 1 mM IPTG for 90 min.

extract_protocol: Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104).

treatment_protocol: Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice.

tag: strain

tag: genotype/variation

value: overexpression of dosP (pCA24N_dosP)


title: Nagina22 control Replicate 1

description: PLIER.Variance Stabilization.N22C-1


title: Liver_HCV_0611-0071

description: chronic hepatitis C


title: Liver_HCV_0610-0018

description: chronic hepatitis C


title: BW25113-pCA24N

description: Gene expression data for IPTG induction of cells containing pCA24N (empty).

source_name: overexpression of empty vector (pCA24N)

value: empty vector (pCA24N)


title: Liver_HCV_0611-0025

description: chronic hepatitis C


title: Nagina22 control Replicate 2

description: PLIER.Variance Stabilization.N22C-2


title: Liver_HCV_0609-0023

description: chronic hepatitis C


title: genomic DNA_control 7

type: genomic

city: Sao Paulo

first: Érica Sara

middle: Souza de

last: Araújo

state: Sao Paulo

address: Taguá st, 440

department: CIPE - Internacional Center for Research and Training

country: Brazil

institute: A. C. Camargo Cancer Center

description: leukocyte's DNA from health individual 7

hyb_protocol: Bisulphite converted DNA  (EZ DNA methylation kit; Zymo Research) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan according  standard recommended Illumina scanner setting

data_processing: Data normalization was performed using the pipeline described in Touleimat and Tost, 2012 (Epigenomics, 4(3):325-41)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: control 7

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from leukocytes using Gentra Puregene Blood Core Kit (Qiagen) or QIAmp DNA Blood Mini QIACUBE kit (Quiagen)

tag: cdkn2a status

value: wild type


title: Rv RAW macrophages 2012-06-13

city: Notredame

first: prachi

last: singh

state: indiana

address: 130 Galvin

department: biological sciences

institute: university of notredame

description: Cells

hyb_protocol: Hybridization was performed according to Nimblegen protocols

scan_protocol: Scanning was performed according to Nimblegen protocol

data_processing: The raw data was subject to RMA using Nimblescan, quantile normalization

organism: Mus musculus

source_name: M.tb (H37Rv) infected macrophages

label_protocol: Labeling was performed using standard labeling procedures from Nimblegen and following manufacture's instructions

growth_protocol: Murine RAW264.7 macrophages were cultured in complete DMEM media at 37 degrees in a CO2 incubator; Mycobacteria was cultured in 7H9 broth with OADC at 37 degrees incubator shaker

extract_protocol: Total RNA was isolated using MirVana kit (Ambion) and treated with DNAse1 (Invitrogen)

treatment_protocol: Macrophages were infected with opsonized bacteria so as to achieve 80% infectivity of cells as determined by an uptake assay

tag: sample type

value: macrophages

tag: infection

value: M.tb (H37Rv)


title: Liver_HCV_0609-0010

description: chronic hepatitis C


title: Rv RAW macrophages 2012-10-31

description: Cells


title: genomic DNA_control 8

description: leukocyte's DNA from health individual 8

source_name: control 8


title: Liver_HCV_0608-0071

description: chronic hepatitis C


title: Liver_HCV_0609-0017

description: chronic hepatitis C


title: Un RAW macrophages 2012-10-31

description: Cells

source_name: Uninfected macrophages


title: Un RAW macrophages 2012-06-13

description: Cells


title: M.tb

description: Total RNA from logarithmically grown MTB culture

organism: Mycobacterium tuberculosis H37Rv

source_name: M.tuberculosis RNA

value: M.tb culture

tag: treatment


title: Un RAW macrophages 2011-12-15

description: Cells


title: Liver_HCV_0608-0059

description: chronic hepatitis C


title: Liver_HCV_0608-0051

description: chronic hepatitis C


title: Liver_HCV_0610-0030

description: chronic hepatitis C


title: Un exosomes 2012-06-13

description: vesicles from cells

source_name: Exosomes from uninfected macrophages

value: exosomes


title: Un exosomes 2012-10-31

description: vesicles from cells


title: genomic DNA_control 6

description: leukocyte's DNA from health individual 6

source_name: control 6


title: Un exosomes 2011-12-15

description: vesicles from cells


title: Rv RAW macrophages 2011-12-15

description: Cells


title: genomic DNA_sporadic melanoma 6

description: leukocyte's DNA from sporadic melanoma patient 6

source_name: sporadic melanoma 6


title: genomic DNA_sporadic melanoma 8

description: leukocyte's DNA from sporadic melanoma patient 8

source_name: sporadic melanoma 8


title: genomic DNA_control 5

description: leukocyte's DNA from health individual 5

source_name: control 5


title: genomic DNA_control 4

description: leukocyte's DNA from health individual 4

source_name: control 4


title: Liver_HCV_0604-0067

description: chronic hepatitis C


title: Liver_HCV_0606-0050

description: chronic hepatitis C


title: genomic DNA_sporadic melanoma 7

description: leukocyte's DNA from sporadic melanoma patient 7

source_name: sporadic melanoma 7


title: Rv exosomes 2012-10-31

description: vesicles from cells

source_name: Exosomes from M.tb (H37Rv) infected macrophages


title: Rv exosomes 2012-06-13

description: vesicles from cells


title: Liver_HCV_0608-0006

description: chronic hepatitis C

source_name: Liver tissue


title: genomic DNA_control 3

description: leukocyte's DNA from health individual 3

source_name: control 3


title: genomic DNA_control 2

description: leukocyte's DNA from health individual 2

source_name: control 2


title: Rv exosomes 2011-12-15

description: vesicles from cells


title: genomic DNA_sporadic melanoma 5

description: leukocyte's DNA from sporadic melanoma patient 5

source_name: sporadic melanoma 5


title: genomic DNA_control 1

description: leukocyte's DNA from health individual 1

source_name: control 1


title: Liver_HCV_0602-0064

description: chronic hepatitis C


title: Liver_HCV_0605-0086

description: chronic hepatitis C


title: Liver_HCV_0603-0052

description: chronic hepatitis C


title: Liver_HCV_0602-0049

description: chronic hepatitis C


title: genomic DNA_sporadic melanoma 2

description: leukocyte's DNA from sporadic melanoma patient 2

source_name: sporadic melanoma 2


title: genomic DNA_sporadic melanoma 1

description: leukocyte's DNA from sporadic melanoma patient 1

source_name: sporadic melanoma 1


title: genomic DNA_sporadic melanoma 3

description: leukocyte's DNA from sporadic melanoma patient 3

source_name: sporadic melanoma 3


title: genomic DNA_CDKN2A-mutation carrier 8

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 8

source_name: CDKN2A-mutation carrier 8

value: mutated


title: Ct_1

status: Public on Sep 14 2014

city: Vancouver

first: Philip

last: Beer

address: 675 West 31st Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

description: Gene expression CD34+38- transduced with IK6 lentivirus

hyb_protocol: An input of 30ng of total RNA was used to generate Cyanine-3 labeled cRNA. 600ng of Cy3-labeled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1ul Agilent fragmentation buffer and 5ul of 10X Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human GE 8x60K arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried for 1min in acetonitrile.

scan_protocol: Data were acquired by Agilent DNA Microarray Scanner at a 3 mm scan resolution, and processed with Agilent Feature Extraction 11.0.1.1.

data_processing: Probes were retained if detectable in all control or all IK6 samples and had an EntrezGene identifier. Following trimming, data were analysed using R software. Raw signals were quantile normalized.

source_name: Control replicate 1

label_protocol: Samples were prepared following the Agilent One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling v1.0.  Total RNA is initially converted into cDNA using a mixture of T7 polymerase dT and T7 polymerase random primed reverse transcriptase reaction to synthesize first and second strand of cDNA. This cDNA then served as a template for cRNA synthesis by T7 RNA polymerase in the presence of Cyanine 3-labeled CTP (Cy3).

growth_protocol: Human CD34+ cord blood cells transduced with control or IK6 lentivirus were transplanted into NGS mice.

extract_protocol: RNA was extract using QIAGEN spin columns.

treatment_protocol: 10 weeks after transplantation control and IK6 transduced progeny CD34+38- cells were acquired by FACS.

tag: cell type

value: CD34+38- Blood HSC


title: Liver_HCV_0512-0029

description: chronic hepatitis C

value: chronic hepatitis C

value: Liver biopsy specimens


title: IK6_3

description: Gene expression CD34+38- transduced with control lentivirus

source_name: IK6 replicate 3


title: P3-022A

status: Public on Sep 13 2014

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Agilent SureScan scanner

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suite.

source_name: Anterior cruciate ligament

label_protocol: The labeled DNA was hybridized using Agilent Human 8x60K microarray chips (Agilent Technologies) at 65oC for 20 h followed by routine washing. The microarrays were scanned on an Agilent SureScan scanner to detect Cy5 fluorescence. Gridding and analysis of images were performed using Agilent Feature Extraction software v10.7.3.1.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Anterior cruciate ligament

tag: age (years)

tag: time from injury (months)

tag: Sex

value: Female

tag: body mass index (kg/m2)

tag: rna

value: degraded


title: P3-020A

tag: tissue


title: P3-025A

value: Male

value: partially degraded


title: P3-023A


title: genomic DNA_CDKN2A-mutation carrier 7

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 7

source_name: CDKN2A-mutation carrier 7

tag: gender

value: female


title: P3-026A


title: P3-19A


title: P3-027A


title: P3-18A


title: Ct_3

source_name: Control replicate 3


title: IK6_1

source_name: IK6 replicate 1


title: IK6_2

source_name: IK6 replicate 2


title: genomic DNA_sporadic melanoma 4

description: leukocyte's DNA from sporadic melanoma patient 4

source_name: sporadic melanoma 4


title: P3-021A


title: genomic DNA_CDKN2A-mutation carrier 6

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 6

source_name: CDKN2A-mutation carrier 6


title: P3-017A


title: genomic DNA_CDKN2A-mutation carrier 5

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 5

source_name: CDKN2A-mutation carrier 5


title: genomic DNA_CDKN2A-mutation carrier 4

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 4

source_name: CDKN2A-mutation carrier 4


title: P3-016A


title: P3-008A

value: borderline


title: P3-013A


title: P3-005A


title: Ct_2

source_name: Control replicate 2


title: Escherichia coli 60 min vs 30 min Rep2

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 2 of 2

hyb_protocol: Standard Agilent procedures

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1 was used for background subtraction and LOWESS normalization.

source_name: 60 min

label_protocol: Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets

growth_protocol: Overnight culture of E. coli BW25113 in LB was diluted in M9 minimal medium with supplements to OD600=0.02 and was incubated at 37 Ceilsus degree with shaking at 250rpm until its OD600 reached 0.1.

extract_protocol: Total RNA was extracted from 5ml cell culture at 0, 10, 30 and 60 min incubation after addition of 5% isooctane using RNeasy mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: One conditions: 5% (v/v) isooctane, 37 Ceilsus degree, 250rpm

tag: time

value: 60 min

value: 5 percent isooctane

source_name: 30 min

value: 30 min


title: P3-010A


title: P3-006A


title: P3-011A


title: P3-007A


title: P3-009A


title: P3-012A


title: Escherichia coli 10 min vs 0 min Rep2

description: Biological replicate 2 of 2

source_name: 10 min

value: 10 min

source_name: 0 min

value: 0 min


title: P3-014A


title: Escherichia coli 30 min vs 60 min Rep1

description: Biological replicate 1 of 2


title: P3-015A


title: Escherichia coli 0 min vs 10 min Rep1

description: Biological replicate 1 of 2


title: P3-004A


title: genomic DNA_CDKN2A-mutation carrier 2

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 2

source_name: CDKN2A-mutation carrier 2

value: male


title: pbMEC_short_C_rep2

city: Dummerstorf

first: Juliane

last: Guenther

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz-Institute for Farm Animal Biology (FBN)

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4290

hyb_protocol: 10 µg of biotin labelled, purified and fragmented cRNA was then hybridized onto GeneChip® Bovine Genome Arrays (Affymetrix) during a 16-hour incubation at 45°C. Posthybridization staining and washing was performed using an automated protocol on the Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned with a GeneChip® scanner 3000 7G

data_processing: Background correction, normalization and summation was performed using GCRMA. Transcripts were defined as significant differentially expressed among Control (C.) and Priming (P.) as well as among Induction (I.) and Induction post Priming (I.p.P.) groups if their fold change exceeded >1.5 and the p-value of the univariate t-test between values paired according the pbMEC preparation was <0.005.

organism: Bos taurus

source_name: pbMEC unstimulated control_short waiting experiment

label_protocol: cDNA was linearly amplified with T7-RNA polymerase in an in vitro transcription (IVT) reaction, and labeled with biotinylated ribonucleotides (GeneChip® IVT Labeling Kit, Affymetrix)

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

value: pbMEC

tag: challenge

tag: protocol

value: Control (C.)

value: short waiting period


title: genomic DNA_CDKN2A-mutation carrier 1

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 1

source_name: CDKN2A-mutation carrier 1

value: mutated


title: pbMEC_short_I_rep3

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4288

source_name: pbMEC challenged with E. coli_short waiting experiment

value: Induction (I.)


title: pbMEC_short_C_rep1

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4289


title: pbMEC_short_P_rep1

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4283

source_name: pbMEC primed with LPS_short waiting experiment

value: Priming (P.)


title: P3-003A

source_name: Anterior cruciate ligament

value: Anterior cruciate ligament

value: Female

value: degraded


title: pbMEC_short_P_rep3

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4285


title: pbMEC_short_I_rep2

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4287


title: pbMEC_short_P_rep2

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4284


title: pbMEC_short_C_rep3

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4291


title: genomic DNA_CDKN2A-mutation carrier 3

description: leukocyte's DNA from CDKN2A-mutation carrier melanoma patient 3

source_name: CDKN2A-mutation carrier 3


title: pbMEC_short_IpP_rep2

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4281

source_name: pbMEC primed and challenged with E. coli_short waiting experiment

value: Induction post priming (I.p.P.)


title: pbMEC_short_I_rep1

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4286


title: pbMEC_long_C_rep2

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4278

source_name: pbMEC unstimulated control_long waiting experiment

value: long waiting period


title: pbMEC_short_IpP_rep1

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4280


title: pbMEC_short_IpP_rep3

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_short waiting experiment
Sample name: J_4282


title: frontal cortex_subject_33

city: Exeter

first: Jonathan

last: Mill

address: RD&E NHS Foundation, Trust Campus, Barrack Rd

department: Medical School, RILD Building

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al, 2013 (n=34,548) (PMID 233115698) were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.  Unmethylated and methylated signal intensities for each sample can be found on the series record in the file preprocessed_Montreal_data.txt.

label: Cy3 and Cy5

source_name: frontal cortex (BA9)

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from ~50 mg of each dissected brain region using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

value: brain frontal cortex

tag: diagnosis

value: control

tag: age

value: M


title: pbMEC_long_C_rep3

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4279


title: pbMEC_long_C_rep1

description:
Gene expression data from unchallenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4277


title: pbMEC_long_I_rep2

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4275

source_name: pbMEC challenged with E. coli_long waiting experiment


title: pbMEC_long_I_rep3

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4276


title: pbMEC_long_I_rep1

description:
Gene expression data from E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4274


title: frontal cortex_subject_32

value: schizophrenia


title: pbMEC_long_P_rep3

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4273

source_name: pbMEC primed with LPS_long waiting experiment


title: pbMEC_long_P_rep2

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4272


title: WT_MICROOXIC-vs-OXIC_DS_rep3

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

description: Biological replicate 3 of 3

hyb_protocol: The combined Cy3/Cy5-labelled targets were dried in a speed vac and further dissolved in 60 µl DIG Easy hybridization solution (Roche, Mannheim, Germany). 1 µl of sonicated salmon sperm (5 µg/µl) was further added. The transcriptome microarray spotted on epoxysilane-coated Nexterion Slide E (Schott) (CeBiTec, University Bielefeld)  contained 70mer oligonucleotide probes for the 3,989 predicted protein-coding genes from Azoarcus sp. strain BH72 in four replicates (Hauberg 2012). Before hybridization, the targets were denatured at 65°C for 10 min. The hybridization of fluorescently labelled cDNA targets to oligonucleotide microarrays was performed at 42°C in a hybridization chamber (ArrayIt, Sunnyvale, CA, USA) in a water bath for 14 to 18 hours. followed by appropriate  washing steps as recommended.

scan_protocol: The Cy3- and Cy5-fluorescence was scanned at 532 nm and 635 nm with the GenePix Scanner 4000A (Molecular Devices, Sunnyvale, CA, USA) with a pixel size of 10 µm.The image analysis was performed with the GenePix 4.1 program and the subsequent analyses were carried out with the open-source software Microarray Data Analysis System (MIDAS v2.19) of TM4 (Saeed et al. 2003, http://www.tm4.org/). After scanning, raw data images of the slides that contain information about gene expression levels were obtained by the GenePix software. These images were analyzed by identifying each spot on the array (with the help of an array layout template) with measurements of its fluorescence intensity and the corresponding background intensity.

data_processing: With the file transformation tool Express Converter v.2.1 (http://www.tm4.org/utilities.html), data files generated from GenePix (.gpr) were converted to TM4 files (.mev) that could be uploaded to the MIDAS platform. Normalization with MIDAS (TM4 suite) was done in order to reduce variability by appropriately adjusting the data. In this study, the LOWESS (locally weighted scattered plot smoothing) normalization was performed using the block mode as set-up parameter as this mode allowed correction of systematic spatial variation between the grids of the array. The normalized data for each spot were exported to Excel and aligned to the corresponding Azoarcus sp. BH72 gene name. Overall, three independent experiments were performed. Average expression fold were determined from normalized values of the three sets. Statistical analysis was performed using the intensity values in a one tail paired t-test. Overall, three independent experiments (biological experiments) were performed. Average expression fold were determined from normalized values of the three sets. Genes with an expression factor  1.8 and P value  0.05 were considered as differentially expressed.

organism: Azoarcus olearius

source_name: pure culture of bacteria

label_protocol: For transcriptome microarray analysis, 20 µg of total RNA from each condition, was reverse transcribed with BioScript RT in respective reaction buffer (Bioline) with random hexamers and 4:1 aminomodified-dUTP/dTTP nucleotide mix for 90 min at 42°C. For coupling of fluorescent dyes to the aminoallyl-labelled first strand cDNA, aliquots of Cy3-NHS or Cy5-NHS esters (GE Healthcare) were dissolved in 60 µl of first strand cDNA, mixed and incubated for 90 min at room temperature in the dark. Blocking of all remaining dyes (quenching) was necessary after labelling. This quenching was achieved by adding 4.5 µl hydroxylamine (4 M) to the sample solution, followed by an incubation for 15 min at room temperature. Subsequent cleaning up of labelled cDNA from remaining dyes was performed with the CyScribe GFX Purification Kit (GE Healthcare) according to manufacturer’s instructions. The Cy5- and Cy3-labelled cDNA that was used in one hybridization experiment were cleaned up together. The labelled cDNA (60 µl) was stored at -20°C until microarray hybridization (Hauberg et al. 2012).

growth_protocol: Azoarcus sp. BH72 was grown in an oxygen-controlled bioreactor (Biostat B; B. Braun Melsungen AG, Melsungen, Germany) at 37°C with constant stirring at 6000 r.p.m, either under microaerobic condition (0.3% oxygen concentration) or under aerobic condition (21% oxygen concentration) respectively, in synthetic medium (SM), supplemented with 10 mM ammonium chloride as nitrogen source and malate as carbon source

extract_protocol: The cell pellets were re-suspended in a 1:1 mixture of pre-warmed phenol-chloroform-isoamylalcohol (25:24:1, pH 4.7) and NAES solution (50 mM sodium acetate, 10 mM EDTA, 1 % SDS, pH 5.1). This suspension was incubated for 5 min at 65°C in a water bath, followed by 10 min incubation on ice. For phase separation, the mixture was centrifuged for 10 min at 12°C and 8000 x g. The upper phase was transferred and mixed with the same volume of phenol-chloroform-isoamylalcohol. This phenol extraction was repeated three times, followed by an extraction with equal volume of chloroform isoamylalcohol (24:1). RNA precipitation was performed with the same volume of isopropanol for 45 min on ice. The RNA was pelleted by centrifugation (12900 x g, 10 min at 4°C) and salts were removed with 1 ml of Ethanol (70 %). The dried RNA was dissolved in 100 µl 1 x RNAsecure, frozen in liquid nitrogen and kept at -80°C until further processing. Contaminating DNA was removed from RNA preparations by DNase I using Qiagen columns (RNeasy Mini Kit, Qiagen, Hilden, Germany) according to manufacturer’s instructions. The DNase I treated RNA was eluted twice in 30 µL of elution buffer, pooled and finally stored in 1x RNA secure in -80°C.

treatment_protocol: The cells were pelleted by centrifugation (6000 rpm, 28°C, 10 min), pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

tag: strain

value: BH72, wild type

value: cells grown under aerobic condition (21% oxygen) on combined nitrogen

value: cells grown under microaerobic condition (0.3% oxygen) on combined nitrogen


title: pbMEC_long_IpP_rep3

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4270

source_name: pbMEC primed and challenged with E. coli_long waiting experiment

value: pbMEC


title: pbMEC_long_P_rep1

description:
Gene expression data from LPS primed primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4271


title: pbMEC_long_IpP_rep2

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4269


title: frontal cortex_subject_27

value: F


title: frontal cortex_subject_31


title: pbMEC_long_IpP_rep1

description:
Gene expression data from LPS primed and E. coli challenged primary bovine mammary epithelial cells_long waiting experiment
Sample name: J_4268


title: frontal cortex_subject_28


title: WT_MICROOXIC-vs-OXIC_rep2

description: Biological replicate 2 of 3


title: frontal cortex_subject_24


title: frontal cortex_subject_22


title: frontal cortex_subject_29


title: frontal cortex_subject_23


title: frontal cortex_subject_25


title: DRG_KO_1.9_2

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

institute: Oxford University

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

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

data_processing: Data analysed using the Affymetrix Expression Console, rma-bg normalization and summarization, default analysis methods

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

extract_protocol: Dorsal  root ganglia from all spinal levels of littermate control and Nav1.7, Nav1.8 and Nav1.9 null mutants (n = 3) were  extracted with RNAeasy kits

tag: genotype

value: Nav1.9 KO

value: dorsal root ganglia


title: frontal cortex_subject_26


title: frontal cortex_subject_20


title: frontal cortex_subject_30


title: DRG_KO_1.9_1

source_name: Dorsal  root ganglia from all spinal levels of littermate control


title: WT_MICROOXIC-vs-OXIC_rep1

description: Biological replicate 1 of 3


title: frontal cortex_subject_17


title: DRG_KO_1.9_3


title: frontal cortex_subject_21


title: frontal cortex_subject_19


title: frontal cortex_subject_16


title: frontal cortex_subject_18


title: frontal cortex_subject_15


title: 4765861067_H

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: Gene expression in the liver of humans with a history or active for schistosomiasis and viral heapatitis

hyb_protocol: cRNA was hybridised to Illumina HumanHT-12_V3 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing:
Data was analysed using GenomeStudio version 1.1.1 and Genespring GX 11
Values reported were derived using Illumina GenomeStudio version 1.1.1. Raw data represent relative signal intensity; normalised data were normalised to the median of all samples and are presented in log2 scale.

source_name: Liver tissue

label_protocol: cRNA was synthesised from total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

growth_protocol: A subset of thirteen liver biopsies from long-term residents of the schistosomiasis endemic region of Dongting Lake area, Hunan Province China, was selected based on a clinical diagnosis of advanced schistosomiasis. A further four liver biopsies from control patients ([C]) were collected from those from non-endemic areas for schistosomiasis.

extract_protocol: Total RNA was extracted from liver tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Surgical intervention included splenectomy, left gastric vein ligature, and devascularization of the great curvature of the stomach for treatment of portal hypertension.

value: Liver tissue

tag: patient id

tag: infection

value: Schistosomiasis and Heaptitis B

tag: sample code

value: SH

tag: fibrosis grade

tag: enlarged liver


title: frontal cortex_subject_12


title: DRG_WT_1.9_2

value: Wild Type


title: DRG_WT_1.9_1


title: frontal cortex_subject_11


title: 4765861067_G

tag: Sex


title: 4765861067_I


title: 4765861067_K


title: frontal cortex_subject_9


title: CH34_H2O2_5mM_rep2

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

hyb_protocol: The Cy3-labeled cDNA from the control samples and the Cy5-labeled cDNA from exposed samples were suspended in the Universal Hybridization Buffer (Pronto Plus Kit; Promega), mixed together, and applied to the spotted glass slide microarrays for hybridization overnight at 42°C. The slides were washed using the Pronto Plus Hybridization protocol and dried by centrifugation at 1,600 x g for 2 min.

scan_protocol: The slides were scanned with a laser scanner at 532 and 635 nm to obtain independent excitations of the fluorescent dyes Cy3 and Cy5 (Genepix4100A; Axon Instruments). Spots were analyzed using GenePix Pro v.6.0.1 software and flagged according to their quality.

data_processing: Raw median intensity data were imported into R version 2.10.1 for statistical analysis using the LIMMA package version 3.2.3 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: non-induced culture

label_protocol: From 10 µg high-quality total RNA, cDNA was synthesized by reverse transcription with the Pronto kit (Corning-Promega) using random priming in the presence of Cy3- or Cy5-dCTP nucleotides (Amersham Biosciences), according to the manufacturer's instructions.

growth_protocol: C. metallidurans CH34 was cultured in aerobic conditions at 28 °C in liquid Tris-buffered mineral salts medium (TMSM) supplemented with 0.2 % (w/v) Na-gluconate as carbon source.

extract_protocol: RNA was extracted from three independent cultures. RNA isolation was performed using the SV total RNA isolation kit (Promega) according to the manufacturers instructions. Purified RNA was quantified by NanoDrop ND-1000 (Nanodrop) and its integrity was assessed using a Bioanalyzer 2100 instrument (Agilent Technologies). Only samples having the RNA integrity number above 8.0 were considered suitable for further transcriptomic analysis.

treatment_protocol: Actively dividing cells (i.e., at a log phase with an OD600 of around 0.500 and a cell density of approximately 4.0 x 108 CFU ml-1) were harvested for exposure and for RNA preparation. Exposure of cells to H2O2 was conducted in saline instead of growth medium, to limit partial neutralization of H2O2 molecules by media ingredients. Thus, actively dividing cells in saline solution were exposed to 5 mM H2O2 for 30 min to induce the oxidative stress response for transcriptomic analyses.

tag: agent

source_name: induction with 5mM H2O2

value: induction with 5mM H2O2


title: frontal cortex_subject_8


title: frontal cortex_subject_14


title: frontal cortex_subject_13


title: frontal cortex_subject_10


title: frontal cortex_subject_6


title: hPDLCs_Transfected with FDC-SP _ rep3

city: chengdu

first: Lin

last: Xiang

address: No. 14, Third Section Renmin Nan Road.

country: China

institute: SCU

description: Gene expression after transfection with FDC-SP in hPDLCs

hyb_protocol: Each 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: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

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

source_name: human periodontal ligament cells (hPDLCs), transfected with FDC-SP, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Premolars extracted from healthy voluntary donors with matching ages (12-14 yrs old) were used. Periodontal ligament were separated from only the middle third of the roots and were cut into small pieces. After a 30-min enzymatic digestion and centrifugation, single cells in suspension were obtained and then cultured in Dulbecco’s modiﬁed Eagle’s medium, containing 20% fetal bovine serum, 200 mM L-glutamine (Invitrogen, Life Technologies Co.), 100 U/ml penicillin, and 100 mg/ml streptomycin sulfate, at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: hPDLCs were incubated in the mixture containing growth medium and viral supernatant (1:1) with 5 ug/ml polybrene (Sigma) for 10 h. Two different groups were designed for further research experiments, including the control group (transfection with empty lentiviral vector), and the experimental group (transfection with lentiviral vector containing FDC-SP).

value: periodontal ligament

value: male


title: CH34_H2O2_5mM_rep1


title: CH34_H2O2_5mM_rep3


title: DRG_KO_1.8_2

value: Nav1.8 KO


title: 4765861067_F


title: DRG_WT_1.9_3


title: DRG_KO_1.8_1


title: 4765861067_J

description: Gene expression in the liver of humans with a history or active for schistosomiasis but no indicators of viral heapatitis

value: Schistosomiasis only

value: S


title: 4765861067_D


title: frontal cortex_subject_3

value: brain frontal cortex

value: control

value: M


title: hPDLCs_Transfected with FDC-SP _ rep2

source_name: human periodontal ligament cells (hPDLCs), transfected with FDC-SP, replicate 2


title: DRG_KO_1.8_3


title: frontal cortex_subject_2


title: double transgenic mice non-tumorous liver section rep.3

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

department: Department of Medical Laboratory Science and Biotechnology

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 1 of 3. HBx and pre-S2 mutant LHBS double transgenic mice non-tumorous liver section

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, V6.2

scan_protocol: Scanned on an Agilent Microarray Scanner Images were quantified using Agilent Feature Extraction 10.5.1.1 software

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization

label_protocol: Agilent Genomic DNA Enzymatic Labeling Kit

growth_protocol: Male C57Bl/6 mice were housed 4 per cage in a light-and-temperature controlled facility (lights on 6:00 to 19:00, 25°C).

extract_protocol: QIAamp DNA Mini Kit

treatment_protocol: no treatment

value: Liver

value: 12 month

source_name: normal B6 12m


title: frontal cortex_subject_7

value: schizophrenia


title: DRG_WT_1.8_3

value: dorsal root ganglia


title: frontal cortex_subject_1


title: hPDLCs_Transfected with FDC-SP _ rep1

source_name: human periodontal ligament cells (hPDLCs), transfected with FDC-SP, replicate 1


title: hPDLCs_Transfected with empty vector _ rep1

description: Gene expression after transfection with empty vector in hPDLCs

source_name: human periodontal ligament cells (hPDLCs), transfected with empty vector, replicate 1


title: 4765861067_E

value: Liver tissue


title: frontal cortex_subject_5


title: DRG_WT_1.8_2


title: double transgenic mice non-tumorous liver section rep.1


title: U87MG - CASP2siRNA, biological rep2

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

description: Gene expression data from U87MG treated with Casp2-siRNA

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Human Gene 1.0 ST Array.

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

data_processing: Data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the t-test as implemented in the R statistical package. A minimum standard deviation was assumed corresponding to the median percentile of all standard deviations in order to avoid fortuitously large t statistics. Differentially expressed genes were selected based on >1.5 fold change and P<0.05.

source_name: Human glioblastoma cell line U87MG treated with a siRNA against CASP2

label_protocol: RNA sample was labeled according to the standard one cycle amplification and labeling protocol (Affymetrix).

growth_protocol: Human glioblastoma cell line U87MG were grown in DMEM supplemented with 10% FBS, penicillin (100 U/mL), glutamine (2 mmol/L), and streptomycin (100 μg/mL) at 37°C in 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen).

treatment_protocol: RNA oligos for interference (RNAi) were purchased from Dharmacon.

tag: cell line

tag: treatment

value: siRNA against CASP2


title: hPDLCs_Transfected with empty vector _ rep3

source_name: human periodontal ligament cells (hPDLCs), transfected with empty vector, replicate 3

tag: tissue

tag: gender


title: DRG_KO_1.7_3

value: Nav1.7 KO


title: 4765861067_C

value: Schistosomiasis and Heaptitis B

value: SH


title: DRG_WT_1.8_1

value: Wild Type


title: double transgenic mice non-tumorous liver section rep.2

description: Biological replicate 2 of 3. HBx and pre-S2 mutant LHBS double transgenic mice non-tumorous liver section

value: male


title: 4765861067_A


title: U87MG - CASP2siRNA, biological rep1


title: 4860956002_B


title: pre-S2 mutant LHBS transgenic mice non-tumorous liver section rep.4

description: Biological replicate 4 of 4. pre-S2 mutant LHBS transgenic mice non-tumorous liver section

value: 9 month

source_name: normal B6 9m


title: pre-S2 mutant LHBS transgenic mice non-tumorous liver section rep.3

description: Biological replicate 3 of 4. pre-S2 mutant LHBS transgenic mice non-tumorous liver section

value: 18 month

source_name: normal B6 18m


title: 4765861067_L

value: Schistosomiasis only

value: S


title: 4860956002_C


title: hPDLCs_Transfected with empty vector _ rep2

source_name: human periodontal ligament cells (hPDLCs), transfected with empty vector, replicate 2

value: periodontal ligament


title: DRG_KO_1.7_1


title: U87MG - control siRNA, biological rep1

description: Gene expression data from U87MG treated with control siRNA

source_name: Human glioblastoma cell line U87MG treated with a control siRNA

value: control siRNA


title: DRG_KO_1.7_2


title: 4860956002_J

description: Gene expression in the liver of humans without history or indicators of schistosomiasis or viral heapatitis

value: Control Uninfected

value: C


title: U87MG - control siRNA, biological rep2


title: pre-S2 mutant LHBS transgenic mice non-tumorous liver section rep.2

description: Biological replicate 2 of 4. pre-S2 mutant LHBS transgenic mice non-tumorous liver section

value: Liver


title: 4860956002_I


title: frontal cortex_subject_4

source_name: frontal cortex (BA9)

value: brain frontal cortex

value: control

value: M


title: DRG_WT_1.7_3

value: dorsal root ganglia


title: K96243vsCLi

status: Public on Sep 12 2014

type: mixed

city: Maung

first: THANATCHAPORN

last: BARTPHO

state: Khon Kaen

address: 123 Mitthaphap

department: Microbiology

country: Thailand

institute: Meliodosis Research Center, Faculty of Medicine, Khon Kaen University

description: B. pseudomallei 1909a in liver of infection C57BL/6 mice

hyb_protocol: Four micrograms of Cy5-labeled cDNA from each sample were mixed with 2 µg of Cy3 labeled gDNA of the K96243, dry in a SpeedVac concentrator for 30 min and re-suspended in 50 µl Corning hybridization solution (Corning, NY, USA). Post-processed slides were hybridized while the LifterSlip Microarray Coverslips (Erie Scientific, USA) was placed over the array slide and incubated at 42°C in a water bath for 16-20 h and post-hybridization washed according to the recommended protocol described by Corning before scanning

scan_protocol: The slides were scanned by a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA) and initially analyzed with GenePix Pro 6.1 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal and across arrays using the Aroma package, R software was used.

organism: Burkholderia pseudomallei K96243

source_name: Reference strain

label_protocol:
(Genomic DNA) 3. The 10-15 µg gDNA of B. pseudomallei K96243, used as reference strain, was labeled with Cy3-dCTP fluorescent dye using a standard nick-translation reaction to generate randomly labeled DNA fragments according to the manufacturer's protocol (Promega, Madison, WI, USA)
(cDNA) total RNA from each organ infected with B. pseudomallei or from in vitro were converted to cDNA in the presence of B. pseudomallei genome directed primers (bpGDPs). Briefly, The 15 µg of RNA samples were labeled using Pronto!TM Universal Hybridization kit (Corning, NY, USA) as described in the manufacturer’s manual, with the exception of using 10 µg of bpGDPs( B. pseudomallei genome-directed primers) to prime the transcription reactions instead of using random primers.

growth_protocol:
Bacterial growth protocol: (K96243) Bacteria were grown overnight in Luria Bertani broth (LB broth) and incubated at 37oC with shaking at 200 rpm.
Bacterial growth protocol: (1909a) B. pseudomallei 1909a were cultured in LB broth, at 37oC with shaking at 200 rpm until mid-log phase (0.4 - 0.5 OD600nm)

extract_protocol:
(Genomic DNA) gDNA extraction according to manufacturer's protocol (Generation capture column, QIAGEN Sciences, MD, USA)
(RNA from in vitro) Total RNA were extracted using Trizol® Reagent (Invitrogen, USA) as recommended by the manufactures.
(RNA from In vivo) The organs of infected BALB/c and C57BL/6 mice (spleen, lungs, and liver) (n = 15 from each mouse) were harvested (5 mice at a time) under a sterile condition at Day 4 post infection and immediately put in RNALater® (Ambion, USA) and chilled on ice. Each organ from each group of five mice were rapidly homogenized separately in Trizol® reagent by ground and sieved through a sterile stainless sieving device and then extracted using Trizol®’s protocol as recommended by the manufacturer.

treatment_protocol: BALB/c and C57BL/6 mice (male, 4-5 weeks old, n = 15 mice each) were intraperitoneally injected with 100µl 1X PBS containing 103 CFU of B. pseudomallei 1909a then 3 organs (spleen, lung, and liver) were harvested at day 4 post infection

tag: sample type

value: reference strain

organism: Burkholderia pseudomallei

source_name: C57BL/6 Liver

tag: isolate

tag: infected host

value: C57BL/6 mice

tag: infected host tissue

value: liver


title: DRG_WT_1.7_2

source_name: Dorsal  root ganglia from all spinal levels of littermate control

value: Wild Type


title: HBx transgenic mice non-tumorous liver section rep.4

description: Biological replicate 4 of 4. HBx transgenic mice non-tumorous liver section

tag: strain

value: male

tag: age


title: HBx transgenic mice non-tumorous liver section rep.3

description: Biological replicate 3 of 4. HBx transgenic mice non-tumorous liver section

value: 18 month


title: pre-S2 mutant LHBS transgenic mice non-tumorous liver section rep.1

description: Biological replicate 1 of 4. pre-S2 mutant LHBS transgenic mice non-tumorous liver section

value: 21.5 month

source_name: normal B6 21.5m


title: DRG_WT_1.7_1

tag: genotype


title: K96243vsBSp

description: B. pseudomallei 1909a in spleen of infection BALB/c mice

source_name: Balb/c Spleen

value: BALB/c mice

value: spleen


title: HBx transgenic mice non-tumorous liver section rep.2

description: Biological replicate 2 of 4. HBx transgenic mice non-tumorous liver section

value: 16 month

source_name: normal B6 16m


title: HBx transgenic mice non-tumorous liver section rep.1

description: Biological replicate 1 of 4. HBx transgenic mice non-tumorous liver section


title: K96243vsIn vitro

source_name: In vitro

value: control (B. pseudomallei in vitro sample)


title: K96243vsBLu

description: B. pseudomallei 1909a in lung of infection BALB/c mice

source_name: Balb/c Lung

value: lung


title: WT+CRC_NR_A

city: Charlottesville

first: Jeffrey

middle: S

last: Smith

email: jss5y@virginia.edu, sb3de@virginia.edu

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Gene expression data from WT cells grown to stationary phase in 9 mL SC media (2% glucose) + 1 mL CR media concentrate for total of 8 days in culture. CR media concentrate obtained by condensing 50 mL filtered WT CR media (harvested on day 5) to 1 mL.

hyb_protocol: Following fragmentation, 4 ug of labeled cRNA were hybridized for 16 hr at 45°C on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using R/Bioconductor using GCRMA with default settings which include quantile normalization and probe specific background correction. Related publication is based on identifying genes within the experimental conditions that were found to be differentially expressed compared to the control based on an FDR p<0.2. Log2 GCRMA values for the genes that were not deemed significant are not available. The matrrices provided include the normalized values that passed the 20% FDR cutoff (400-1500 values for each condition).

organism: Saccharomyces cerevisiae

source_name: WT cells, SC media+expired CR media concentrate, stationary phase (day 8)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one cycle eukaryotic target preparation protocol from 4 µg total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix). Approximately 100 µg of labeled cRNA was obtained from each sample.

growth_protocol: SC media with 2% glucose with 50x expired CR media concentrate (9:1)

extract_protocol: Cells were thawed and total RNA extracted using the hot acid phenol method (Ausuble et al. (editors), 2000 Current Protocols in Molecular Biology. John Wiley & Sons, New York). RNA pellets were resuspended in RNAase-free water.

treatment_protocol: Cells were collected by centrifugation in an Eppendorf 5810R centrifuge at 4°C. The cell pellets were washed with ice cold water, transferred to microfuge tubes and flash frozen in liquid nitrogen.

tag: genotype/variation

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

tag: growth phase

value: stationary (day 8)


title: ADE4_NR_B

description: Gene expression data from ade4∆ cells grown to stationary phase in 10 mL SC media (2% glucose) for total of 8 days in culture.

source_name: ade4∆ cells, SC media (2% glucose), stationary phase for 8 days

growth_protocol: SC media with 2% glucose

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 ade4∆::kanMX4


title: WT_CR_A

description: Gene expression data from WT cells grown to stationary phase in 10 mL SC media (0.5% glucose) for total of 8 days in culture.

source_name: WT cells, SC media (0.5% glucose), stationary phase (day 8)

growth_protocol: SC media with 0.5% glucose


title: ADE4_NR_A


title: WT_CR_B


title: WT_NR_B

description: Gene expression data from WT cells grown to stationary phase in 10 mL SC media (2% glucose) for total of 8 days in culture.

source_name: WT cells, SC media (2% glucose), stationary phase (day 8)


title: WT+CRC_NR_B


title: WT_NR_A


title: K96243vsCSp

description: B. pseudomallei 1909a in spleen of infection C57BL/6 mice

source_name: C57BL/6 Spleen


title: 4860956002_H

source_name: Liver tissue

value: Liver tissue

tag: patient id

tag: infection

value: Control Uninfected

tag: sample code

value: C

tag: fibrosis grade


title: WT+INAM_NR_B

description: Gene expression data from WT cells grown to stationary phase in 10 mL SC media (2% glucose, 25 mM isonicotinamide) for total of 8 days in culture.

source_name: WT cells, SC media+isonicotinamide, stationary phase (day 8)

growth_protocol: SC media with 2% glucose and 25 mM isonicotinamide


title: K96243vsCLu

description: B. pseudomallei 1909a in lung of infection C57BL/6 mice

value: reference strain

source_name: C57BL/6 Lung

value: C57BL/6 mice


title: WT+INAM_NR_A


title: 4860956002_A

description: Gene expression in the liver of humans without history or indicators of schistosomiasis or viral heapatitis

tag: enlarged liver

tag: Sex


title: human iPSC line 6

city: Cambridgeshire

first: Yichen

last: Shi

address: Suite 3, The Science Village Building, Chesterford Research Park, Little Chesterford

institute: Axol Bioscience Limited

description: gene expression data from human iPSC line 6

hyb_protocol: SourceBioscience provided the standard services for hybridization

scan_protocol: SourceBioscience provided the standard services for scanning

data_processing: The data were analyzed with Expression Console and Transcriptome Console using Affymetrix default analysis settings

label: Biotin

source_name: human iPSC line 6

label_protocol: SourceBioscience provided the standard services for labeling

growth_protocol: human iPSC cells were cultured on E8 medium; human NPCs were induced with NPC induce medium

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

tag: cell line

value: human iPSC line 6


title: human iPSC line 3

description: gene expression data from human iPSC line 3

source_name: human iPSC line 3

growth_protocol: human iPSC cells were cultured on E8 medium; human NPCs were induced with NPC induction medium

value: human iPSC line 3


title: human NPC ax0016, derived from line 6

description: gene expression data from human NPC ax0016

source_name: human NPC ax0016, derived from line 6

value: human NPC ax0016, derived from line 6


title: human NPC ax0013, derived from line 3

description: gene expression data from human NPC ax0013

source_name: human NPC ax0013, derived from line 3

value: human NPC ax0013, derived from line 3


title: MTF1782, biological rep 2

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

hyb_protocol: 350 ng of each labelled DNA were mixed to the hybridization buffer, and deposited on the array. The  hybridization was performed with continuous agitation for 17 hours at 51°C

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix pro7 software

data_processing:
Data importation and statistical analysis were performed using R 2.15.2 software and the limma package (provided in the sample data table)

Please note that data were further processed and transformed  to measure the allelic frequencies of each bulk at each SNP position. At each position, the differences  in hybrization signal (log ratio)  between the P3 specific probe and the RM11 specific probe were calculated (provided in the 'processed_data.txt', including data/column header description). Strain L2868 is related to P3, and the difference is +0.8 and MTF1782 is related to RM11, and the difference is -1.7  at locus:SACE-rm11-Chr01_13431_13416_13440_f.

label_protocol: After fragmentation with sonication, we labeled 1 µg of fragmented genomic DNA with Cy3 (for the two parental strains and the two bulks) or Cy5 (for the mixture 1/1 of each parental strain) using Agilent Genomic DNA Enzymatic labeling kit 5190-0449.

growth_protocol: For each strain a culture in 30 ml of YEPD at 28°C was prepared , and 7.5 x 10exp10 cells (5 x 10exp9 for each segregant) were kept for DNA extraction.

extract_protocol: Genomic DNA were extracted using  Qiagen Genomic-tip 100/G columns. After extraction, DNA, was prepared according to the protocole of Gresham2010(Methods Mol Biol. 2011;772:179-91).

source_name: Reference

value: reference (parental mix)


title: MTF1782, biological rep 1


title: Rhizosphere_rep3

city: Chengdu

first: Junpeng

last: Rui

state: Sichuan

address: No. 9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

description: GeoChip data of soil microbial community in maize rhizosphere, replicate 3

hyb_protocol: DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Microarray data were analyzed using the data analysis pipeline developed at the University of Oklahoma (http://ieg.ou.edu/microarray/). Normalized intensity of each gene was calculated by dividing the signal intensity by the mean intensity of the microarray.

organism: uncultured bacterium

label_protocol: DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) as previously described (Yang et al., 2013).

growth_protocol: Maize (Zea mays) was grown near the University of Illinois (Champaign, IL, USA, 40°03'N, 88°12W, 230 m elevation) in a soil classified as a fine-silty, mesic Typic Endoaquoll formed from loess and silt parent material. Samples were collected in August 4, 2009.

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as described previously (Zhou et al., 1996).

treatment_protocol: Fresh roots were collected into a 50 ml centrifuge tube, rinsed in phosphate buffer solution, shaken by hand and centrifuged at 8000 rpm for 10 min. Bulk soil cores of 0-30 cm depth were also collected between sampled plants for paired comparison to the rhizosphere samples.

tag: soil type

value: maize rhizosphere


title: L2868-C5, biological rep 2


title: Rhizosphere_rep2

description: GeoChip data of soil microbial community in maize rhizosphere, replicate 2


title: S249C mutant 2

city: Leeds

first: Erica

last: di Martino

address: Becket Street

department: Experimental Oncology

institute: University of Leeds

description: gene expression profile of normal urothelial cells with an S249C FGFR3 mutation

hyb_protocol: 20μg of fragmented cRNA was hybridized at 45°C for 16 hrs on Human U133 Plus 2.0 expression arrays. Washing and staining were carried out in the Affymetrix GeneChip Fluidics Station according to the manufacturer’s instructions.

scan_protocol: Scanning was carried out in the Affymetrix GeneChip Scanner 3000 system with Autoloader. Data collection and management was done in the Affymetrix GeneChip Operating Software (GCOS).

data_processing: The raw data were pre-processed and normalised using rma[1] from Bioconductor's [2] 'affy' package[3].

source_name: Normal urothelial cells expressing S249C FGFR3

label_protocol: 2 µg of total RNA was used to prepare biotinylated target cRNA, according to the Affymetrix One Cycle Target Preparation Protocol

growth_protocol: cell were grown in standard media at 37C and 5% CO2

extract_protocol: TriZol extraction followed by DNAse treatment and re-purification using Qiagen Rneasy mini kit

treatment_protocol: cells were harvested at confluence 10 days after seeding

tag: cell type

value: urothelial

tag: modifications

value: TERT-immortalized

tag: expression construct

value: FGFR3 mutation S249C


title: S249C mutant 1


title: Donor 5 LILRA3

city: Hannover

first: Hui Zhi

last: Low

address: Carl-Neuberg-Str. 1

department: Department of Clinical Immunology and Rheumatology

institute: Hannover Medical School

description:
M3537
Gene expression after 24 hr 1 µg/mL LILRA3 treated human PBMC

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent). Samples were hybridized on Human Gene Expression 4x44K v2 Microarrays (G4845A).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Using R/Bioconductor packages data preprocessing included background correction (normexp), quantile normalisation, probe summarisation, and log2 transformation.

source_name: PBMCs_1 µg/mL LILRA3

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0443, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: PBMCs were isolated from healthy donors by ficoll gradient density centrifugation

extract_protocol: total RNA was isolated from 10 million cells per sample using the Qiagen RNeasy Minikit, with in-column DNAse treatment to remove genomic DNA

treatment_protocol: Isolated PBMCs were cultured at 1 million cells/mL in RPMI 1640 supplemented with 10% AB serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2mM L-glutamine. No LILRA3 was added to the unstimulated controls and 1 µg/mL LILRA3 was used to stimulate cells

tag: donor id

value: donor 5

tag: gender

value: female

value: peripheral blood mononuclear cells (PBMCs)

tag: stimulated with

value: 1 µg/mL LILRA3


title: Donor 3 LILRA3

description:
M3533
Gene expression after 24 hr 1 µg/mL LILRA3 treated human PBMC

value: donor 3

tag: age


title: 18-sgs1 htb-K123R_Mexp4_IP_2

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

institute: Academia Sinica

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files] TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.
The discrimination of positive and negative signals for the binding were obtained by comparing IP fraction with Sup (supernatant) fraction. The reliability of strength of signal was judged by detection p-value of each locus (p-value 0.025) and presented as lowess normalized log2 ratio (IP/Sup) discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction.

source_name: IP fraction of BrdU of sgs1 htb-K123R-2 (YCL008)

label_protocol: Synthesis of cDNA, IVT amplification, and end-labeled with biotin-N11-ddATP following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD.

extract_protocol: For the analysis of BrdU incorporated regions, total DNA from 3X108 cells was purified by Quiagen Genomic-tip system (P/N10223, QIAGEN, Germany). DNA was sheared to 300bp by sonication, denatured, and mixed with 2μg of anti-mouse IgG1 dynabeads (P/N110.12, Dynal AS, Norway) bound anti-BrdU monoclonal antibody (MI-11-3, MBL). Immunoprecipitation and purification of antibody bound DNA fraction was carried out following the protocol of Cimbora et al. (Mol. Cel. Biol. 20, 5581-5591, 2000). Purified DNA was random primed and amplified by the WGA2 GenomePlex Complete Genome Amplification Kit. 2μg of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling.

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU for 90 min

tag: fraction

value: IP fraction

tag: chip antibody

value: anti-BrdU MI-11-3 (MBL)

tag: strain

tag: phase

value: S

tag: treatment

value: Glu


title: 18-sgs1 htb-K123R_Mexp4_Sup_2

source_name: SUP of BrdU of sgs1 htb-K123R-2 (YCL008)

value: supernatant


title: Bulk_soil_rep3

description: GeoChip data of soil microbial community in bulk soil, replicate 3

source_name: soil microbial community in bulk soil

value: bulk soil


title: Low Nitrogen Requirement bulk, biological rep 1

value: Low Nitrogen requirement strain group


title: Rhizosphere_rep1

description: GeoChip data of soil microbial community in maize rhizosphere, replicate 1


title: Empty vector control 3

description: gene expression profile of normal urothelial cells

source_name: Normal urothelial cells expressing empty vector

value: empty pFB vector


title: High Nitrogen Requirement bulk, biological rep 1

data_processing:
Data importation and statistical analysis were performed using R 2.15.2 software and the limma package (provided in the sample data table)

Please note that data were further processed and transformed  to measure the allelic frequencies of each bulk at each SNP position. At each position, the differences  in hybrization signal (log ratio)  between the P3 specific probe and the RM11 specific probe were calculated (provided in the 'processed_data.txt', including data/column header description). !Sample_data_processing = Strain L2868 is related to P3, and the difference is +0.8 and MTF1782 is related to RM11, and the difference is -1.7 at locus: SACE-rm11-Chr01_13431_13416_13440_f.

value: High Nitrogen requirement strain group

value: reference (parental mix)


title: Donor 2 LILRA3

description:
M3531
Gene expression after 24 hr 1 µg/mL LILRA3 treated human PBMC

value: donor 2

value: male


title: Donor 5 Unstimulated

description:
M3536
Gene expression after 24 hr 0 µg/mL LILRA3 treated human PBMC

value: donor 5

value: none (unstimulated control)


title: Empty vector control 2

value: urothelial

value: TERT-immortalized


title: Low Nitrogen Requirement bulk, biological rep 2


title: Bulk_soil_rep2

description: GeoChip data of soil microbial community in bulk soil, replicate 2


title: L2868-C5, biological rep 1


title: High Nitrogen Requirement bulk, biological rep 2


title: Donor 4 1 LILRA3

description:
M3535
Gene expression after 24 hr 1 µg/mL LILRA3 treated human PBMC

value: donor 4

value: peripheral blood mononuclear cells (PBMCs)

value: 1 µg/mL LILRA3


title: 17-sgs1_Mexp4_IP_2

source_name: IP fraction of BrdU of sgs1-2 (YCL007)

value: IP fraction

value: anti-BrdU MI-11-3 (MBL)

value: S


title: 16-htb_K123R_Mexp4_Sup_S2

source_name: SUP of BrdU of htb-K123R-S2 (CFK1421)

value: supernatant

value: Glu


title: Donor 3 Unstimulated

description:
M3532
Gene expression after 24 hr 0 µg/mL LILRA3 treated human PBMC

value: donor 3

value: female


title: Donor 4 Unstimulated

description:
M3534
Gene expression after 24 hr 0 µg/mL LILRA3 treated human PBMC


title: Donor 2 Unstimulated

description:
M3530
Gene expression after 24 hr 0 µg/mL LILRA3 treated human PBMC


title: Empty vector control 1

value: empty pFB vector


title: S249C mutant 3

value: FGFR3 mutation S249C


title: 16-htb-K123R_Mexp4_IP_S2

source_name: IP fraction of BrdU of htb-K123R-S2 (CFK1421)


title: 15-WT_Mexp4_Sup_S2

source_name: SUP of BrdU of WT-S2 (CFK1204)


title: Bulk_soil_rep1

description: GeoChip data of soil microbial community in bulk soil, replicate 1

value: bulk soil


title: Donor 1 LILRA3

description:
M3529
Gene expression after 24 hr 1 µg/mL LILRA3 treated human PBMC

value: donor 1

value: male


title: 15-WT_Mexp4_IP_2

source_name: IP fraction of BrdU of WT of S2 (CFK1204)


title: 14-sgs1 htb-K123R_BrdU_Sup_1

source_name: SUP of BrdU of sgs1 htb-K123R-1 (YCL008)


title: 17-sgs1_Mexp4_Sup_2

source_name: SUP of BrdU of sgs1-2 (YCL007)


title: 14-sgs1 htb-K123R_BrdU_IP_1

source_name: IP fraction of BrdU of sgs1 htb-K123R-1 (YCL008)


title: Donor 1 Unstimulated

description:
M3528
Gene expression after 24 hr 0 µg/mL LILRA3 treated human PBMC

value: none (unstimulated control)


title: 13-sgs1_BrdU_Sup_1

source_name: SUP of BrdU of sgs1-1 (YCL007)


title: 13-sgs1_BrdU_IP_1

source_name: IP fraction of BrdU of sgs1-1 (YCL007)


title: 12-htb-K123R_BrdU_Sup_S1

source_name: SUP of BrdU of htb-K123R-S1 (CFK1421)


title: 12-htb-K123R_BrdU_IP_S1

source_name: IP fraction of BrdU of htb-K123R-S1 (CFK1421)


title: 11-WT_BrdU_Sup_S1

source_name: SUP of BrdU of WT-S1 (CFK1204)


title: 11-WT_BrdU_IP_1

source_name: IP fraction of BrdU of WT of S1 (CFK1204)


title: 10-dun1_htb-K123R_Sup_2

source_name: SUP of BrdU of dun1 htb-K123R-2 (YCL025)


title: Py8119T6

city: La Jolla

first: Lesley

middle: G

last: Ellies

state: California

address: 9500 Gilman Drive

department: Pathology

institute: University of California, San Diego

description:
LE23
This sample is of a Py8119 cell line-derived mammary tumor. It is the sixth tumor used in this experiment, each from independent animals.  This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.

hyb_protocol: Hybridization was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI, USA standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by  the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Py8119 cell line tumor

label_protocol: Labeling was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.

extract_protocol:
tumor collection protocol: Spontaneous C57Bl/6 PyVmT tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures.
tumor collection protocol: Tumor cells from various C57Bl/6 PyVmT-derived clonal cell lines were injected at 10^6 cells in 2 mg/ml matrigel into the abdominal mammary fat pads of female C57Bl/6 mice. At 6-8 weeks, tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures. In some cases tumors were enzymatically digested and cell suspensions reinjected into the mammary fat pads of new syngeneic recipients.
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the UCSD (University of California, San Diego, La Jolla, CA, USA).

tag: tumor type

value: C57BL/6 PyVmT cell line derived tumor

tag: tumor phenotype/subtype

value: Claudin low


title: Py8119T5

description:
LE22
This sample is of a Py8119 cell line-derived mammary tumor. It is the fifth tumor used in this experiment, each from independent animals.  This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: Py15-4T2

description:
LE41
This sample is of a Py15-4 cell line-derived mammary tumor. Py15-4 was derived from the Py230 cell line. It is the second tumor used in this experiment, each from independent animals.

source_name: Py15-4 cell line tumor


title: Py15-4T1

description:
LE40
This sample is of a Py15-4 cell line-derived mammary tumor. Py15-4 was derived from the Py230 cell line. It is the first tumor used in this experiment, each from independent animals.


title: BCVY_GR7

city: Valencia

first: Gloria

last: Ribas

state: Valencia

address: Blasco Ibañez, 17

department: Medical Oncology and Hematology Unit

country: Spain

institute: INCLIVA Biomedical Research Institute

hyb_protocol: RNA from each sample was hybridized over 18h at 56ºC onto a GeneChip miRNA 2.0 array

scan_protocol: Chips were scanned using an Agilent scanner, with the scan laser set to 635nm, scan resolution of 10μm, power 80 and PMT 70.

data_processing: The data were analyzed with Expression Console build 1.2.0.20, using Affymetrix default analysis settings and RMA+DABG (robust multichip average and detected above background) as normalization method.

source_name: Breast tumor tissue from BCVY

label_protocol: 300ng of total RNA was labeled with Hy3 fluorescent dye

growth_protocol: All samples were locked in parafine-formaline (FFPE) and stored at room temperature

extract_protocol: total RNA was extracted from four 20μm-thick sections of FFPE tissue samples using RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems, Life Technologies)

treatment_protocol: All samples did not receive neoadjuvant treatment

tag: subtype

value: Triple negative


title: Py8119T3

description:
LE20
This sample is of a Py8119 cell line-derived mammary tumor. It is the third tumor used in this experiment, each from independent animals.


title: Py8119T7

description:
LE24
This sample is of a Py8119 cell line-derived mammary tumor. It is the seventh tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: Py15-4T3

description:
LE42
This sample is of a Py15-4 cell line-derived mammary tumor. Py15-4 was derived from the Py230 cell line. It is the third tumor used in this experiment, each from independent animals.


title: BCVY_GR6

value: Luminal A


title: BCVY_GR8


title: 10-dun1_htb-K123R_2_IP

source_name: IP fraction of BrdU of dun1 htb-K123R-2 (YCL025)

value: IP fraction


title: Py8119T2

description:
LE19
This sample is of a Py8119 cell line-derived mammary tumor. It is the second tumor used in this experiment, each from independent animals.


title: Py8119T4

description:
LE21
This sample is of a Py8119 cell line-derived mammary tumor. It is the fourth tumor used in this experiment, each from independent animals.


title: Py8119T1

description:
LE11
This sample is of a Py8119 cell line-derived mammary tumor. It is the first tumor used in this experiment, each from independent animals.


title: Normal tissue_GR37

source_name: Breast normal tissue


title: BCVY_GR5

value: Luminal B


title: 9-htb-K123R_D2_Sup

source_name: SUP of BrdU of htb-K123R-D2 (CFK1421)

value: S


title: BCVY_GR3


title: Py117T6

description:
LE60
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the sixth tumor used in this experiment, each from independent animals.

source_name: Py117 cell line tumor

value: Basal


title: Normal tissue_GR36


title: Normal tissue_GR35


title: BCVY_GR9


title: Py5944CT1

description:
LE12
This sample is of a Py5944C cell line-derived mammary tumor. It is the only tumor from this cell line used in this experiment

source_name: Py5944C cell line tumor


title: Py117T4

description:
LE57
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the fourth tumor used in this experiment, each from independent animals.


title: 9-htb-K123R_D2_IP

source_name: IP fraction of BrdU of htb-K123R-D2 (CFK1421)

value: anti-BrdU MI-11-3 (MBL)

value: Glu


title: 8-dun1_Sup_2

source_name: SUP of BrdU of dun1-2 (YCL023)

value: supernatant


title: Py117T5

description:
LE59
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the fifth tumor used in this experiment, each from independent animals.


title: Py117T3

description:
LE56
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the third tumor used in this experiment, each from independent animals.


title: K96243vsBLi

description: B. pseudomallei 1909a in liver of infection BALB/c mice

source_name: Reference strain

tag: sample type

value: reference strain

source_name: Balb/c Liver

tag: isolate

tag: infected host

value: BALB/c mice

tag: infected host tissue

value: liver


title: BC_GR34

source_name: Breast tumor tissue


title: BC_GR33


title: 7-WT_IP_D2

source_name: IP fraction of BrdU of WT D2 (CFK1204)


title: 6-dun1_htb-K123R_1_Sup

source_name: SUP of BrdU of dun1 htb-K123R-1 (YCL025)


title: 8-dun1_IP_2

source_name: IP fraction of BrdU of dun1-2 (YCL023)


title: 6-dun1_htb-K123R_1_IP

source_name: IP fraction of BrdU of dun1 htb-123R (YCL025)


title: BC_GR32


title: 5-htb-K123R_D1_Sup

source_name: SUP of BrdU of htb-K123R-D1 (CFK1421)


title: 7-WT_Sup_D2

source_name: SUP of BrdU of WT-D2 (CFK1204)


title: Py117T1

description:
LE54
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the first tumor used in this experiment, each from independent animals.


title: 5-htb-K123R_D1_IP

source_name: IP fraction of BrdU of dun1 htb-K123R-D1 (YCL025)


title: BC_GR30


title: Py230T9

description:
LE34
This sample is of a Py230 cell line-derived mammary tumor. It is the ninth tumor used in this experiment, each from independent animals.

source_name: Py230 cell line tumor


title: BC_GR31


title: BCVY_GR2

source_name: Breast tumor tissue from BCVY


title: Py230T13

description:
LE50
This sample is of a Py230 cell line-derived mammary tumor. It is the thirtheenth tumor used in this experiment, each from independent animals.


title: Py230T14

description:
LE58
This sample is of a Py230 cell line-derived mammary tumor. It is the fourteenth tumor used in this experiment, each from independent animals.


title: Py117T2

description:
LE55
This sample is of a Py117 cell line-derived mammary tumor. Py117 was derived from a Py230 tumor. It is the second tumor used in this experiment, each from independent animals.


title: BC_GR28


title: BC_GR27


title: BC_GR26


title: Py230-18

description:
LE28
This sample is of a Py230 cell line-derived mammary tumor. It is the eighteenth tumor used in this experiment, each from independent animals.


title: Py230-16

description:
LE26
This sample is of a Py230 cell line-derived mammary tumor. It is the sixteenth tumor used in this experiment, each from independent animals.


title: 4-dun1_IP_1

source_name: IP fraction of BrdU of dun1-1 (YCL023)


title: Py230T3

description:
LE14
This sample is of a Py230 cell line-derived mammary tumor. It is the third tumor used in this experiment, each from independent animals.


title: Py230-15

description:
LE25
This sample is of a Py230 cell line-derived mammary tumor. It is the fifteenth tumor used in this experiment, each from independent animals.


title: Py230-17

description:
LE27
This sample is of a Py230 cell line-derived mammary tumor. It is the seventeenth tumor used in this experiment, each from independent animals.


title: 3-WT_IP_D1

source_name: IP fraction of BrdU of WT D1 (CFK1204)


title: Py230T2

description:
LE13
This sample is of a Py230 cell line-derived mammary tumor. It is the second tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: 3-WT_Sup_D1

source_name: SUP of BrdU of WT D1 (CFK1204)


title: 2_htb-K123R_BrdU_IP

source_name: IP fraction of BrdU of htb-K123R (CFK1421)


title: 1_WT_BrdU_Sup

source_name: SUP of BrdU of WT (CFK1204)


title: BC_GR24


title: BC_GR29


title: BCVY_GR22


title: BC_GR23


title: BC_GR25


title: Py5656T4

description:
LE52
This sample is of a Py5656 cell line-derived mammary tumor. It is the fourth tumor used in this experiment, each from independent animals.

source_name: Py5656 cell line tumor

value: Lum A


title: Py230T1

description:
LE9
This sample is of a Py230 cell line-derived mammary tumor. It is the first tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: 1_WT_BrdU_IP

source_name: IP fraction of BrdU of WT (CFK1204)


title: 2_htb-K123R_BrdU_Sup

source_name: SUP of BrdU of htb-K123R (CFK1421)


title: Py5656T5

description:
LE53
This sample is of a Py5656 cell line-derived mammary tumor. It is the fifth tumor used in this experiment, each from independent animals.


title: BCVY_GR1


title: BCVY_GR20


title: Py5656T3

description:
LE51
This sample is of a Py5656 cell line-derived mammary tumor. It is the third tumor used in this experiment, each from independent animals.


title: BCVY_GR21


title: Py5656T2

description:
LE38
This sample is of a Py5656 cell line-derived mammary tumor. It is the second tumor used in this experiment, each from independent animals.


title: BCVY_GR19


title: BCVY_GR18


title: Py5656T1

description:
LE10
This sample is of a Py5656 cell line-derived mammary tumor. It is the first tumor used in this experiment, each from independent animals.


title: Py230T12

description:
LE49
This sample is of a Py230 cell line-derived mammary tumor. It is the twelth tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: BCVY_GR15


title: BCVY_GR14


title: Py230T10

description:
LE35
This sample is of a Py230 cell line-derived mammary tumor. It is the tenth tumor used in this experiment, each from independent animals.


title: BCVY_GR16


title: MDA-MB-231/NC

city: Guangzhou

first: shaohua

last: Qu

address: 107 Yanjiang West Road

institute: Sun Yat-Sen university

description: human breast cancer cell line

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan v2.5 software, and low intensity genes were filtered (Genes that at least 3 out of 3 samples have intensities >= 50.0 were chosen for further analysis). The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: MDA-MB-231 transfected with negative control vector for 24 hours

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MDA-MB-231/NC cells were cultured in DMEM-L15 medium and then transfected with empty vector for 24 hours as negative control.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MDA-MB-231/BRMS1L cells were cultured in DMEM-L15 medium and then transfected with vector overexpressing BRMS1L for 24 hours.

tag: cell line

tag: cell type

value: breast cancer


title: Py230T8

description:
LE33
This sample is of a Py230 cell line-derived mammary tumor. It is the ninth tumor used in this experiment, each from independent animals.


title: BCVY_GR13


title: MDA-MB-231/BRMS1L

description: human breast cancer cell line

source_name: MDA-MB-231 transfected with vector over expressing BRMS1L for 24 hours


title: BCVY_GR12


title: Py230T5

description:
LE16
This sample is of a Py230 cell line-derived mammary tumor. It is the fifth tumor used in this experiment, each from independent animals.  This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: PyVmT-3

description:
LE37
This sample is of a spontaneous PyVmT mammary tumor. It is the third of three replicates used in this experiment, each from independent animals.

source_name: PyVmT spontaneous tumor

value: C57Bl/6 Spontaneous PyVmT Tumor


title: BCVY_GR17


title: PyVmT-1

description:
LE7
This sample is of a spontaneous PyVmT mammary tumor. It is the first of three replicates used in this experiment, each from independent animals.


title: Py230T7

description:
LE18
This sample is of a Py230 cell line-derived mammary tumor. It is the seventh tumor used in this experiment, each from independent animals.  This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.

value: C57BL/6 PyVmT cell line derived tumor


title: BCVY_GR10


title: BCVY_GR11


title: Py230T4

description:
LE15
This sample is of a Py230 cell line-derived mammary tumor. It is the forth tumor used in this experiment, each from independent animals.


title: MCF-7_CON_48h_rep1

status: Public on Sep 11 2014

first: Xiaochun

last: Bai

state: Guangdong

address: No.1838, North Guangzhou Avenue

department: Department of Cell Biology

institute: Southern Medical University

description: miRNAs expression in MCF-7 cells without treatment

hyb_protocol: labled RNA from above were hybridized for 20h at 55 ºC, 20 RPM according to the user manual of Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456)

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT XDR Hi is set to 100% while XDR Lo is set to 5%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using protocol miRNA-v1_95_May07 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MCF-7, control, 48h, rep1

label_protocol: total RNA (100ng) were treated with phosphatase for 30min at 37 ºC and were subsequently labled with Cy3 for 2h at 16 ºC.

growth_protocol: cells were maintained in high-glucose DMEM with 10% (v/v) FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA were extracted with TRIZOL Reagent

treatment_protocol: cells of about 70% confluence were serum-starved and exposed to rapamycin (100 nM) or PP242 (200 nM). At 24h post-treatment, serum was added back and treatment was maintained for additional 24h.


title: MCF-7_Rap_48h_rep1

description: miRNAs expression in MCF-7 cells with 48h of rapamycin treatment

source_name: MCF-7, rapamycin, 48h, rep1


title: MCF-7_pp242_48h_rep1

description: miRNAs expression in MCF-7 cells with 48h of pp242 treatment


title: PyVmT-2

description:
LE8
This sample is of a spontaneous PyVmT mammary tumor. It is the second of three replicates used in this experiment, each from independent animals.


title: Py230T6

description:
LE17
This sample is of a Py230 cell line-derived mammary tumor. It is the sixth tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.


title: Py230T11

description:
LE36
This sample is of a Py230 cell line-derived mammary tumor. It is the eleventh tumor used in this experiment, each from independent animals. This animal was treated with 4 mg/ml doxil IP once a week for 4 weeks prior to sacrifice.