title: spinach juice technical replicate 2

status: Public on Jul 20 2014

type: SRA

city: Freising

first: Richard

middle: B.

last: Landstorfer

address: Weihenstephaner Berg 3

department: Chair for Microbial Ecology

institute: Technische Universität München

description: rRNA depleted

library_source: transcriptomic

data_processing:
SOLiD output as QUAL and CSFASTA files was converted to FASTQ with Galaxy. We mapped SOLiD and Illumina FASTQ files to the reference genome using Bowtie (settings for SOLiD data: 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions; Illumina data: 20 nt seed length, 0 mismatches in the seed) implemented in Galaxy. Using Samtools output SAM files were filtered for mappable reads only. We further converted SAM files to BAM files and indexed them to create BAM.BAI files.
The number of reads were normalized to reads per kilobase per million mapped reads (RPKM). Using this method, the number of reads is normalized with respect to the sequencing depth and the length of a given gene. For determination of counts and RPKM values, BAM files were imported into R (R Development Core Team) using Rsamtools. For further processing, the Bioconductor packages GenomicRanges and IRanges were used. Gene locations were determined by RefSeq and GenBank PTT files. The locations of the 16S rRNA and 23S rRNA are given by the RNT file from RefSeq. The method countOverlaps of IRanges was used to determine the remaining reads overlapping a 16S or 23S rRNA gene. We discarded these reads from further analysis due to the artificial removal of these rRNAs using the Ribominus kit as described above. countOverlaps is also used to determine the number of reads overlapping a gene on the same strand (counts). With these counts, we generated the RPKM values. For the value “million mapped reads”, the number of reads mapped to the genome minus the reads overlapping a 16S or 23S rRNA gene were used (see above). The differential gene expression was analyzed with the Bioconductor package edgeR (version 3.2.3) using the counts.
Genome_build: Escherichia coli (str. O157H7 substr. EDL933: 259
Supplementary_files_format_and_content: The xlsx file contains information for each annotated gene in each condition. For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. The magnitude of the absolute value of logFC is indicated by shades of grey. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR).

organism: Escherichia coli O157:H7

source_name: whole organisms

extract_protocol:
RNA was extracted using Trizol, rRNA was removed with the Ribominus kit (life technologies).
The read fragments were phosphorylated and the library was constructed using the TruSeq smallRNA sample prep kit.

tag: growth phase

value: late logarthmic, early stationary phase

tag: growth condition and treatment

value: For spinach medium, whole spinach leaves were homogenized (Agienda Agricola Pistelle, Kaufland, Germany) on ice using an Ultraturrax D50. The mush was centrifuged (1 h, 30,000×g, 5°C), decanted, filtered (2.5 µm pore size), centrifuged (2 h, 30,000×g, 5°C), decanted and sterile filtered (0.2 µm). After 5 h of growth, we harvested the cells at 6.0 x 108 cfu/ml.


title: heads-light_dark-ZeitgeberTime8

status: Public on Aug 19 2014

type: RNA

city: Notre Dame

first: Matthew

last: Leming

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

country: USA

institute: University of Notre Dame

description: Wh_LD_8 hr light/dark

hyb_protocol: Hybridization was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, by using the Hybridization Kit, LS and Wash Buffer Kit (Roche NimbleGen, Madison, WI).

scan_protocol: Scanning was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, using a NimbleGen MS 200 Microarray Scanner at 2 μM resolution.

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

molecule: total RNA

organism: Aedes aegypti

source_name: Wh_LD_8 hr light/dark

label_protocol: Labeling was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, using the NimbleGen Single Color Labeling Kit (Roche NimbleGen, Madison, WI).

growth_protocol: ~30 mated non-blood fed female Ae. aegypti Higgs White eye (Wh) strain mosquitoes, aged 2-6 days, were placed in 24 cages, and sequestered in light controlled boxes.

extract_protocol: Heads were removed from bodies at 0C on a chilled metal plate and collected. The RNeasy RNA Isolation Kit (Qiagen, Valencia, CA) was used to isolate RNA from each sample, following manufacturer’s instructions. Genomic DNA was instead removed by using the DNA-free Kit (Applied Biosystems, Carlsbad, CA) per manufacturer instructions.

tag: strain

value: Higgs White Eye

tag: age

value: 2-6 days

tag: Sex

value: female

tag: treatment condition

value: light/dark conditions

tag: time point


title: LB-nitrite technical replicate 2

country: Germany

description: rRNA depleted

value: For nitrite, we added 200 mg/L sodium nitrite to 10-fold diluted LB and adjusted it to pH 6. Harvest was after 6.5 h at 2.9 x 108 cfu/ml.


title: E2a_MO_Smad2_Lib3

status: Public on Aug 01 2014

city: Stanford

first: Andrea

middle: E.

last: Wills

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford School of Medicine

library_source: genomic

data_processing:
ChIP-Seq reads are mapped to xenTro2 genome using the bwa-sw tool. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
ChIP-seq homer-output  as an excel file contains annotated peaks for Samples
Genome_build: UCSC XenTro2

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: E2a-depleted embryos

growth_protocol: Embryos were raised in 1/9 MR to stage 10.5 (Nieuwkoop and Faber staging criteria)

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.
Embryos were fixed for 1hr in 1% formaldehyde, glycine treated and frozen.  Embryos were then homogenized, sonicated, and centrifuged to remove yolk and cytoplasm.  Nuclei were complexed with antibody.

tag: embryonic stage

value: Stage 10.5

tag: chip characteristics

tag: barcode


title: heads-light_dark-ZeitgeberTime0

description: Wh_LD_0 hr light/dark

source_name: Wh_LD_0 hr light/dark


title: heads-light_dark-ZeitgeberTime4

description: Wh_LD_4 hr light/dark

source_name: Wh_LD_4 hr light/dark


title: WholeBlood_d5_Cs-137_rep1

status: Public on Aug 31 2014

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4846A) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1_107_Sep091 and Grid: 026655_D_F_20110722) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Well Above Background were excluded

organism: Mus musculus

source_name: mouse blood, day 5 after Cs-137 injection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the PAXgene Blood RNA Kit (Qiagen/BD) according to manufacturer’s instructions, followed by removal of globin transcripts using the GLOBINclear kit (Ambion Inc., Austin, TX) to remove both a- and b-globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were either injected intraperitoneally with 8.0 ± 0.3 MBq 137CsCl solution in a volume of 50 μL or kept as controls. At the time of sacrifice, blood was collected by cardiac puncture and 400 ul was placed in PAXgene blood RNA solution (PreAnalytiX GmbH, USA) and kept at 4-degrees C for shipping to Columbia for RNA isolation.

tag: gender

value: male

tag: accrued radiation dose

tag: tissue

value: whole blood


title: 9388306035_R04C02

status: Public on Jul 12 2014

type: genomic

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: IDAT files were analysed in using minfi package and subset-quantile within array normalization (SWAN).Probes on chromosomes X and Y, probes with a detection P-value >0.01 in one or more samples and probes with SNP in the 10 last bases or with two or more SNP in the probe sequence were excluded from analysis. The differential methylation analysis was performed using 402,566 autosomal CpGs using the ‘dmpFinder’ minfi function.

organism: Homo sapiens

source_name: Adjacent

label_protocol: Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays

value: pancreas

tag: cellularity

value: Adjacent

value: Female


title: 9388306035_R03C01

source_name: Tumor

value: Male


title: 9388306121_R06C01


title: 9388306035_R01C02


title: 9388306121_R06C02


title: 9388306035_R01C01


title: 9388306121_R04C02


title: 9388306121_R05C02


title: 9388306121_R04C01


title: 9388306035_R02C01


title: 8959312046_R06C02

status: Public on Jul 08 2014


title: 8959312046_R06C01


title: 9388306121_R01C01


title: 9388306121_R05C01


title: 8959312046_R04C02


title: 8959312046_R01C02


title: 9388306121_R01C02


title: 9388306121_R03C01


title: 8959312007_R04C02


title: 9388306035_R06C01


title: 9388306121_R02C02


title: 9388306121_R02C01


title: 8959312046_R05C01


title: 8959312046_R04C01


title: 9388306121_R03C02


title: 9388306035_R02C02


title: 9388306035_R05C01


title: 8959312046_R01C01


title: 8959312007_R05C01


title: 8959312007_R01C01


title: 8959312046_R03C01


title: 8959312046_R03C02


title: 8959312007_R03C01


title: 9388306035_R05C02


title: 9388306035_R06C02


title: 8959312001_R06C01


title: 8959312001_R03C02


title: 8959312007_R02C02


title: 8959312001_R06C02


title: 8959312007_R04C01


title: 8959312001_R04C02


title: 8959312001_R05C02


title: 8959312007_R02C01


title: 8959312007_R03C02


title: 8959312001_R02C02


title: 8959312001_R01C02


title: 8942351032_R05C01


title: 8942351064_R04C01


title: 8942351032_R05C02


title: 8942351032_R04C02


title: 8942351032_R06C01


title: 8942351064_R02C02


title: 8942351064_R05C01


title: 8942351064_R04C02


title: 8942351064_R01C02


title: 8942351032_R03C01


title: 8942351032_R02C02


title: 8942351032_R01C02


title: 8942351031_R05C02


title: 8942351031_R06C02


title: 8942351032_R03C02


title: 8942351031_R04C02


title: 8942351031_R06C01


title: 8942334138_R05C02


title: 8942351031_R05C01


title: 8942351031_R01C01


title: 8942351032_R01C01


title: 8942351032_R02C01


title: 8942351031_R01C02


title: 8942334138_R02C01


title: 8942334138_R06C01


title: 8942334138_R04C02


title: 8942334124_R05C02


title: 8942334124_R01C01


title: 8942334138_R04C01


title: 6285617095_R06C02


title: 6285617095_R03C02


title: 8942351031_R02C02


title: 6285617095_R05C02


title: 6285617095_R05C01


title: 8942351064_R01C01


title: 6285617095_R03C01


title: 6285617095_R01C02


title: 6285617095_R01C01


title: 6285617084_R06C02


title: 6285617093_R05C01


title: 6285617093_R01C02


title: 6285617093_R05C02


title: 6285617095_R02C01


title: 6285617095_R06C01


title: 6285617084_R05C01


title: 6285617084_R03C02


title: 6285617093_R06C02


title: 6285617093_R04C01


title: 6285617093_R02C01


title: 6285617084_R05C02


title: 6285617084_R01C01


title: 6285617084_R02C01


title: 6285617075_R06C02


title: 6285617075_R06C01


title: 6285617084_R02C02


title: 6285617075_R05C02


title: 6285617075_R04C02


title: 6285617093_R03C01


title: 6285617075_R03C02


title: 6285617084_R04C02


title: 6285617075_R05C01


title: 6285617093_R01C01


title: 6285617084_R04C01


title: 6285617075_R02C02


title: 6285617075_R03C01


title: 6285617073_R04C01


title: 6285617073_R03C01


title: 6285617075_R01C02


title: 6285617073_R01C01


title: 6285617065_R06C02


title: 6285617075_R04C01


title: 6285617065_R03C02


title: 6285617065_R06C01


title: 6285617065_R04C01


title: 6285617075_R02C01


title: 6285617073_R04C02


title: 6285617065_R05C01


title: 6285617075_R01C01


title: 6285617065_R02C01


title: 6285609013_R03C01


title: 6285609013_R05C01


title: 6285609013_R06C02


title: 6285609013_R02C02


title: 6285617073_R01C02


title: 6285609013_R05C02


title: 6285617065_R01C02


title: 6285617063_R06C02


title: 6285609013_R04C02


title: 6285609013_R03C02


title: 6285609013_R01C02


title: 6285617095_R04C02


title: 6229017151_R06C01


title: 6229017151_R06C02


title: 6229017151_R05C02


title: 6229017151_R01C01


title: 6229017151_R05C01


title: 6229017121_R06C02


title: 6285609013_R01C01


title: 6285617065_R02C02


title: 6285617084_R03C01


title: 6229017151_R01C02


title: 6229017121_R06C01


title: 6229017151_R04C02


title: 6285617073_R06C01


title: 6229017121_R05C02


title: 6229017151_R04C01


title: 6229017151_R02C01


title: 6285617073_R02C02


title: 6229017151_R02C02


title: 6285617073_R03C02


title: 6229017121_R03C02


title: 6229017121_R02C02


title: 6229017121_R01C02


title: 6229017121_R04C01


title: 6229017121_R05C01


title: 6229017121_R03C01


title: 6229017110_R06C01


title: 6229017110_R06C02


title: 6229017110_R05C01


title: 6229017110_R04C02


title: 6229017151_R03C02


title: 6229017110_R01C02


title: 6229017110_R03C02


title: 6229017110_R04C01


title: 6229017110_R03C01


title: 6229017121_R01C01


title: 6229017110_R02C02


title: 6229017109_R06C02


title: 6229017109_R05C01


title: 6229017109_R03C02


title: CTRL12

status: Public on Jun 22 2014

type: protein

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C.  Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to Pf or Pv proteins on the microarray, the following steps were taken: (i) the mean background signal of antibody binding to 24 control spots of in vitro transcription/translation reaction without DNA template (noDNA spots) were removed from each sera's raw values of antibody binding measured as the mean pixel intensity of spots of printed protein; (ii) After background subtraction, values were log2-transformed (data presented in Sample data tables).

molecule: protein

source_name: serum

tag: sample collection site

value: Irvine, California, USA

tag: sample source

value: Healthy Blood Donor at UCI

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: Unexposed

tag: symptomatic or asymtomatic at sample collection

tag: qpcr screening for plasmodium

tag: qpcr plasmodium species


title: 6229017110_R05C02

tag: age


title: 6229017109_R05C02


title: CTRL8


title: CTRL10


title: CTRL11


title: 6229017110_R01C01


title: CTRL9


title: CTRL7


title: CTRL6


title: 6229017109_R04C02


title: 6229017110_R02C01


title: 6229017109_R02C01


title: 6042324127_R03C02


title: 6042324127_R04C01


title: 6042324127_R05C02


title: CTRL2


title: PCD 55

value: Tha Song Yang, Tak, Thailand

value: Hospital Outpatient (PCD)

value: Exposed

value: Symptomatic

value: Negative


title: PCD 56


title: PCD 58


title: 6229017109_R01C02


title: PCD 59


title: 6042324127_R04C02


title: 6229017109_R02C02


title: PCD 60


title: 6042324127_R06C02


title: 6042324127_R03C01


title: 6042324127_R06C01


title: PCD 57


title: PCD 52

value: Positive

value: P.falcip + P. vivax


title: 6042324127_R02C01


title: PCD 51

value: P. vivax


title: 6042324127_R01C01


title: PCD 50


title: 6229017109_R03C01


title: PCD 47


title: PCD 46


title: PCD 49

value: P. falciparum


title: CTRL5


title: PCD 45


title: PCD 48


title: PCD 41


title: PCD 40


title: PCD 39


title: PCD 44


title: CTRL4


title: PCD 42


title: PCD 38


title: PCD 36


title: PCD 37


title: PCD 34


title: PCD 35


title: 6229017109_R01C01


title: 6042324127_R05C01


title: PCD 33


title: PCD 32


title: PCD 54


title: PCD 31


title: PCD 30


title: PCD 24


title: PCD 29


title: PCD 20


title: PCD 25


title: PCD 26


title: PCD 21


title: PCD 23


title: PCD 16


title: PCD 19


title: PCD 18


title: PCD 17


title: CTRL3


title: PCD 27


title: PCD 14


title: PCD 15


title: PCD 22


title: PCD 10


title: PCD 11


title: PCD 13


title: PCD 9


title: PCD 28


title: PCD 12


title: PCD 53


title: ACD 86

value: Mae Salid Noi, Tak, Thailand

value: Community Mass Blood Survey (ACD)

value: Asymptomatic


title: ACD 87


title: ACD 88


title: ACD 89


title: ACD 92


title: ACD 93


title: PCD 3


title: PCD 2


title: PCD 6


title: ACD 84


title: ACD 85


title: PCD 5


title: ACD 90


title: ACD 82


title: ACD 81


title: ACD 80


title: ACD 76


title: ACD 79


title: PCD 8


title: ACD 75


title: PCD 4


title: PCD 7


title: ACD 91


title: PCD 1


title: ACD 83


title: ACD 78


title: ACD 73


title: ACD 72


title: ACD 70


title: ACD 62


title: ACD 74


title: ACD 64


title: ACD 65


title: ACD 63


title: ACD 60


title: ACD 66


title: ACD 61


title: ACD 77


title: ACD 67


title: ACD 59


title: ACD 68


title: ACD 56


title: ACD 58


title: ACD 55


title: ACD 57


title: ACD 52


title: ACD 54


title: ACD 51


title: ACD 53


title: ACD 69


title: ACD 71


title: ACD 50


title: PCD 43


title: ACD 49


title: ACD 47


title: ACD 48


title: ACD 45


title: ACD 46


title: ACD 43


title: ACD 44


title: ACD 40


title: ACD 39


title: ACD 41


title: ACD 38


title: ACD 37


title: CTRL1


title: ACD 33


title: ACD 24


title: ACD 35


title: ACD 31


title: ACD 30


title: ACD 36


title: ACD 34


title: ACD 42


title: ACD 25


title: ACD 29


title: ACD 26


title: ACD 23


title: ACD 21


title: ACD 27


title: ACD 28


title: ACD 22


title: ACD 32


title: ACD 17


title: ACD 16


title: ACD 18


title: ACD 19


title: ACD 20


title: ACD 15


title: ACD 14


title: ACD 12


title: ACD 13


title: ACD 3


title: ACD 5


title: ACD 4


title: ACD 8


title: ACD 2


title: ACD 6


title: ACD 1


title: ACD 7


title: ACD 10


title: ACD 9


title: PrTFB1 cells confronted with PC3 mRFP cells

status: Public on May 01 2014

city: Stockholm

first: Hayrettin

last: Guven

address: Nobels Vag 16

department: MTC

country: Sweden

institute: Karolinska Institute

description: PrTFB1 + PC3 mRFP

hyb_protocol: Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan scanner.

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.3.1) using the RMA method.

label: biotin

source_name: primary human prostate fibroblast of non-tumor area

label_protocol: 150ng total RNA was used to generate sense strand cDNA using Ambion WT Expression kit that was fragmented and biotinylated using Affymetrix Gene Chip WT Terminal Labeling Kit.

growth_protocol: Each fibroblast cell line were plated (0.5 X 106) in 10 cm dishes coated with collagen (Rat tail) (Corning) in IMDM medium for 5-7 days.

extract_protocol: Total RNA was prepared from 5-7day-old monolayers of fibroblasts using Ambion's RNAqueous-4PCR kit (Invitrogen).

treatment_protocol: Cells were trypsinized in trypsin-EDTA solution and then washed once with complete medium and once with PBS.

tag: cell line

tag: treatment

value: confronted with PC3 mRFP cells

tag: clone

value: polyclonal fibroblast like cells


title: PrTFB2 cells confronted with PC3 mRFP cells

description: PrTFB2 + PC3 mRFP

source_name: primary human prostate fibroblast cells of tumor area


title: PdHFB cells alone

description: PdHFB

source_name: primary human pediatric hernia fibroblast cells


title: ACD 11


title: PdHFB cells confronted with PC3 mRFP cells

description: PdHFB + PC3 mRFP


title: PrNFB1 cells confronted with PC3 mRFP cells

description: PrNFB1 + PC3 mRFP


title: HS68 skin cells alone

source_name: primary human adult skin fibroblast cells


title: swi6myc_DMSO_solid

status: Public on Nov 15 2013

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the sacCer3 genome assembly using BWA (Version: 0.5.9-r16) with default options
Non-uniquely mapped reads were filtered out in order to remove the reads with low mapping quality
Reads that mapped onto rRNA were filtered out
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig format

organism: Saccharomyces cerevisiae

source_name: SWI6 Myc-tagged yeast cells

growth_protocol: Normal growth conditions were 30°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8), and fixed with formaldehyde. For heat shock, mid-log phase yeast cells were collected and re-suspended in pre-warmed 39°C YPD media, then incubated for 15 min at 39°C.

extract_protocol:
Cross-linked chromatins were sheared using a sonicator, and immunoprecipitated using the following beads or anti-body: IgG Sepharose 6 Fast Flow (GE Healthcare Life Sciences) to pull-down all TAP-tagged proteins used in this study, anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654) to pull-down Swi6 in the SWI6-13XMyc strains, and RNAPII Ser5P antibody (Abcam, cat.# ab5131) to pull-down active RNAPII. Mock ChIP DNA was prepared by immunoprecipitation with IgG Sepharose in the wild type strain with no TAP-tagged protein expression. Input DNA was prepared in parallel with the SWI6-TAP ChIP sample but leaving out the immunoprecipitation step.
The NEB ChIP-seq library preparation for Illumina (New England BioLabs) and the SOLiD V3 barcoded fragment library preparation protocol (Applied Biosystems) were used to sequence the samples using Illumina HiSeq 2000 and SOLiD V4, respectively

treatment_protocol: For rapamycin treatment, either DMSO or rapamycin was added to mid-log phase yeast cells and incubated for 30 min at 30°C. Since DMSO is a solvent for rapamycin, control and rapamycin-added cells were treated with DMSO and rapamycin to be a final concentration of 0.1% and 100 nM, respectively

tag: chip antibody

value: anti-Myc

tag: chip antibody manufacturer

value: Sigma Aldrich

tag: chip antibody catalog #

tag: cell type

value: SWI6 Myc-tagged yeast cells

tag: strain

value: DMSO

tag: temperature


title: PrTFB2 cells alone


title: PrTFB1 cells alone

source_name: primary human prostate fibroblast cells of non-tumor area


title: PdSFB cells confronted with PC3 mRFP cells

description: PdSFB + PC3 mRFP

source_name: primary human pediatric skin fibroblast cells


title: crossy cells confronted with PC3 mRFP cells

description: BJhTERT Crossy + PC3 mRFP

source_name: Immortalized human foreskin fibroblast cells

value: BJhTERT

value: crossy


title: swi6_DMSO_solid

source_name: SWI6 TAP-tagged yeast cells

value: IgG

value: GE Healthcare Life Sciences

value: SWI6 TAP-tagged yeast cells


title: input_DMSO_solid

value: input DNA


title: HS68 skin cells confronted with PC3 mRFP cells

description: HS68 + PC3 mRFP


title: crossy cells alone

description: BJhTERT Crossy


title: whirly cells confronted with PC3 mRFP cells [re-analysis]

description: BJhTERT Whirly + PC3 mRFP

value: whirly


title: PrNFB1 cells alone


title: Piri_Athal_14dpi_R2

status: Public on Jul 22 2013

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

description: A. thaliana plants were pre-grown for 14 days prior to inoculation

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).

organism: Serendipita indica

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica was cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Barley seeds (Hordeum vulgare cv. Golden Promise) were surface sterilized with 70% ethanol for 1 minute, 12% sodium hypochlorite for 1.5 hours and sterile distilled water for 3 hours. Sterilized seeds were kept in the dark for 3 days on sterile wet filter paper at room temperature. Incubation was performed in a Conviron phytochamber with a day/night cycle of 16/8 hours (light intensity: 110 µmol m-2 s-1) and temperature 22/18°C. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4‹C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23‹C (350 µmol/m-2s-1); night: 8 h, 18‹C; 60% humidity).

extract_protocol: Barley root samples from four to five plants per jar were collected 14 dpi and carefully washed in distilled water. The differentiation zone (four cm below the seed) of the roots was excised and immediately frozen in liquid nitrogen. Arabidopsis root material was harvested in liquid nitrogen 3 and 14 dpi. For each time point roots from 80 to 100 plants were pooled. P. indica hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturerfs instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For barley studies, three-day-old barley germlings were transferred into sterile jars containing 1/10 PNM medium and inoculated with 3 ml chlamydospore suspension (5×105 ml-1 in 0.002% TWEEN20). For inoculation of Arabidopsis roots with P. indica chlamydospores, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or mock treated.

tag: host

value: A. thaliana

tag: host tissue

value: root

tag: time (dpi)

tag: symbiont

value: P. indica


title: Piri_Athal_3dpi_R2

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 2


title: Normal_brain_3

status: Public on Sep 26 2013

city: shanghai

first: Yong

last: Yan

address: 415# of Fengyang street

department: neurosurgery

country: China

institute: changzheng hospital

description: long noncoding RNA expression in normal brain tissue 3

hyb_protocol: Hybridization Procedure: 1. Add 500 uL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube: For 1*244K array Amount cyanine 3-labeled, linearly amplified cRNA 1.5ug 10X Blocking Agent 50ul Nuclease-free water ul 25X Fragmentation Buffer 10ul Total volume 250ul  For 2*105K array Amount cyanine 3-labeled, linearly amplified cRNA 1. 5ug 10X Blocking Agent 25ul Nuclease-free water ul 25X Fragmentation Buffer 5ul Total volume 125ul  For 4*44K array Amount cyanine 3-labeled, linearly amplified cRNA 1.65ug 10X Blocking Agent 11ul Nuclease-free water ul 25X Fragmentation Buffer 2.2ul Total volume 55ul  For 8*15K array Amount cyanine 3-labeled, linearly amplified cRNA 0.6ug 10X Blocking Agent 5ul Nuclease-free water ul 25X Fragmentation Buffer 1ul Total volume 25ul  For 8*60K array Amount cyanine 3-labeled, linearly amplified cRNA 0.6ug 10X Blocking Agent 5ul Nuclease-free water ul 25X Fragmentation Buffer 1ul Total volume 25ul   4. Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA.  6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K 8*60k cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul 2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul  7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible.  10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11. Slowly dispense the volume of hybridization sample onto the gasket well in a "drag and dispense" manner. Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K 8*60K Volume Prepared 500ul 250ul 110ul 50ul 50ul Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul  12. Slowly place an array "active side" down onto the SureHyb gasket slide, so that the "Agilent"-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14. Hand-tighten the clamp onto the chamber. 15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: Scanning Procedure: 1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: normal brain

label_protocol: Purify the labeled/amplified RNA and labeled cRNA QC 1. Add 20 uL of nuclease-free water to your cRNA sample, for a total volume of 100 uL. 2. Add 350 uL of Buffer RLT and mix well by pipetting. 3. Add 250 uL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge. 4. Transfer the 700 uL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube. 5. Transfer the RNeasy column to a new collection tube and add 500 uL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube. 6. Add another 500 uL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube. 7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report "Labeling Efficiency-QC") directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. 8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column. 9. Take 1.5 ul of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report "Labeling Efficiency-QC"). - From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50. - Blank the instrument with 1.5 uL of 1x labeling solution. - Use 1.5 uL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3). - The specific activity (pmol dyes per ug genomic DNA) of the labeled genomic DNA can be obtained by the following calculation: (Concentration of Cy3) Specific Activity = pmol Cy3 per ug cRNA (Concentration of cRNA) * 1000 * If the yield is <1.65 ug and the specific activity is <9.0 pmol Cy3 per ug cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: Prepare the tissue RNA Sample 1. Homogenization - Cryopulverization of tissue using the Biopulverizer - Place the BioPulverizer in a shallow container and cool thoroughly with either liquid nitrogen. - Place prefrozen tissue in the well of the mortar. - Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS). - Empty the powdered contents for subsequent homogenization or extraction procedures. b) Homogenization using the Mini-Bead-Beater-16 - Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.  - Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten. - Set the timer depending on the type of sample. Start the machine. 2. Phase Separation Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000  g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. 3. RNA Precipitation Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000  g for 10 minutes at 4°C.  4. RNA Wash Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500  g for 5 minutes at 4°C. 5. Redissolving the RNA At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

extract_protocol: Prepare labeling reaction:1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.  2. Add 1.2 uL of T7 Promoter Primer.  3. Use nuclease-free water to bring the total reaction volume to 11.5 uL. 4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. 5. Place the reactions on ice and incubate for 5 minutes. 6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.  Volume(ul) per reaction 5First Strand Buffer 4 0.1M DTT 2 10mM dNTP mix 1 MMLV-RT 1 RNaseOut 0.5 Total volume 8.5 7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. 8. Add 8.5 uL of cDNA Master Mix to each sample tube and mix by pipetting up and down. 9. Incubate samples at 40°C in a circulating water bath for 2 hours. 10. Move samples to a 65°C circulating water bath and incubate for 15 minutes. 11. Move samples to ice. Incubate for 5 minutes. 12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. 13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.  Volume(ul) per reaction Nuclease-free water 15.3 4X Transcription Buffer 20 0.1 M DTT 6 NTP mix 8 50% PEG 6.4 RNaseOUT 0.5 Inorganic pyrophosphatase 0.6 T7 RNA Polymerase 0.8 Cyanine-3-CTP 2.4 Total volume 60 14. Add 60 uL of Transcription Master Mix to each sample tube. Gently mix by pipetting. 15. Incubate samples in a circulating water bath at 40°C for 2 hours.

treatment_protocol: Total RNA Clean-up and RNA QC: 1. Mix the following in a microcentrifuge tube:  Redissolved RNA ≤85ul  10×Reaction buffer 10ul  Baseline-ZERO DNase 5ul  RNase-free water X ul  Total volume 100ul  2. Incubate at 37°C for 30 minutes.  3. Add 350 μl Buffer RLT, and mix well.  4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5.  5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through.  6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through.  7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane.  8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min.  9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA.  10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

tag: disease state

value: normal

tag: gender

value: male


title: GBM_tumor_3

description: long noncoding RNA expression in glioblastoma tissue 3

source_name: glioblastoma multiforme

value: glioblastoma multiforme


title: Normal_brain_1

description: long noncoding RNA expression in normal brain tissue 1


title: Normal_brain_2

description: long noncoding RNA expression in normal brain tissue 2


title: GBM_tumor_1

description: long noncoding RNA expression in glioblastoma tissue 1


title: GBM_tumor_2

description: long noncoding RNA expression in glioblastoma tissue 2


title: Piri_Athal_14dpi_R3

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 3


title: GBM_tumor_4

description: long noncoding RNA expression in glioblastoma tissue 4


title: NJ020055

status: Public on Jun 21 2013

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Intensity data were log2-transformed, quantile normalized using RMA, and expression levels were summarized on a transcript level using the mean value of all probesets mapping to a transcript.  Non-expressed and invariant transcripts were removed using a median variance filter, corrected by a Benjamini-Hochberg false discovery rate (FDR) of 0.10, resulting in a final dataset of 11950 transcript measurements across 217 samples

source_name: Lung tissue

label_protocol: mRNA microarray target labeling was conducted using 300 ng of total RNA and the Message Amp II kit.

extract_protocol: Total RNA including small RNA species was isolated from approximately 100 mg of snap-frozen lung tissue using the mirVana kit (AB/Ambion, Austin TX).

value: Male

tag: final diagnosis

value: control

tag: repository

value: IIAM/NJH

tag: tissue source

value: R Lower

tag: preservative

value: Frozen

tag: rin

tag: smoking status

value: nonsmoker

tag: quit how many years ago

tag: pack years

tag: st. george's total score

tag: fvc pre-bronchodilator % predicted

tag: dlco % predicted


title: NJ020056

tag: age

value: Aliquot 1/RLL-P


title: NJ020064

value: Female

value: Aliquot 30/RLL

value: current


title: NJ020081

value: Aliquot 24/RML


title: NJ020066


title: NJ020063


title: NJ020343

value: Aliquot 1


title: Normal_brain_4

description: long noncoding RNA expression in normal brain tissue 4


title: NJ020077


title: GBM_tumor_5

description: long noncoding RNA expression in glioblastoma tissue 5


title: Piri_Athal_3dpi_R1

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 1

tag: host

value: A. thaliana

tag: host tissue

value: root


title: NJ020083

value: Aliquot 10/RML-C

value: former


title: NJ020061


title: Piri_Athal_14dpi_R1

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 1

tag: time (dpi)

tag: symbiont

value: P. indica


title: Piri_Athal_3dpi_R3

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 3


title: NJ020053

tag: gender

value: Male


title: NJ020045

tag: final diagnosis

value: control

value: Aliquot 3/RLL-P


title: NJ020051

tag: repository

value: IIAM/NJH

value: Aliquot 74/RLL


title: NJ020042

tag: tissue source

value: Aliquot 2/RLL-P

value: Frozen

value: nonsmoker


title: NJ020032

value: Aliquot 62/RLL-P

tag: preservative


title: NJ020079

value: Aliquot 1/RLL-C

tag: rin

value: current


title: NJ020027

value: Aliquot 67/RLL

tag: smoking status


title: NJ020007

value: Female

value: Aliquot 1/RLL-P

tag: quit how many years ago


title: NJ020011

tag: pack years


title: NJ020044

tag: st. george's total score


title: NJ020015

value: Aliquot 7/LLL-P

tag: fvc pre-bronchodilator % predicted


title: NJ020028

value: Aliquot 37/RLL-P

tag: dlco % predicted


title: NJ020080

tag: age

value: Aliquot 14/RML-P


title: NJ020022

value: Male

value: Aliquot 37/LLL


title: NJ020016

value: control

value: former


title: NJ020040

value: IIAM/NJH

value: Aliquot 7/RLL-C


title: NJ020026

value: Aliquot 1/LLL-P

value: Frozen


title: NJ020017


title: NJ020003

value: nonsmoker


title: NJ020006


title: NJ020025


title: NJ020005


title: NJ020036

value: Aliquot 70/LLL-P


title: NJ020049

value: current


title: PdSFB cells alone

description: PdSFB

tag: cell line

tag: clone

value: polyclonal fibroblast like cells


title: NJ020002

value: Female


title: genomic DNA from liver sample 82

status: Public on Aug 08 2013

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: NAFLD

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

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

data_processing: GenomeStudio V2011.1; methylation module 1.9.0

label: Cy5 and Cy3

source_name: liver tissue 82

label_protocol: Standard Illumina Protocol

extract_protocol: For homogenisation of five to ten milligram frozen tissue and subsequent nucleic acid isolation, tubes with 1.4 mm ceramic beads (Precellys, Villeurbanne, France) and the AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) were used.

tag: group

value: NAFLD

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue

value: liver


title: NJ020001

tag: gender

tag: final diagnosis

tag: repository

tag: tissue source

value: R Lower


title: NJ004863

value: Aliquot 52/RLL-P

tag: preservative

tag: rin

tag: smoking status

tag: quit how many years ago


title: NJ020000

value: Male

value: Aliquot 6/LLL-P

tag: pack years

tag: st. george's total score

tag: fvc pre-bronchodilator % predicted

tag: dlco % predicted


title: NJ004851

tag: age

value: control

value: Aliquot 1/LLL-C


title: NJ004860

value: IIAM/NJH

value: Aliquot 1/RLL-P


title: NJ004840

value: Aliquote 66/RLL-P


title: LT282601

value: IPF/UIP

value: LTRC

value: L Upper

value: RNAlater


title: NJ004830

value: Aliquot 47/RLL-P

value: Frozen

value: current


title: LT284326

value: Female

value: nonsmoker


title: NJ004803

value: Aliquot 85/RLL-P


title: LT284489

value: L Lower


title: NJ004824

value: Aliquot 48/LLL-P

value: former


title: NJ004804

value: Male

value: control

value: Aliquot 70/LLL-P


title: LT275751

value: R Lower


title: NJ004818

value: IIAM/NJH

value: Aliquot 73/RLL-P


title: LT275526

value: IPF/UIP

value: LTRC

value: R Middle


title: LT295133

value: Frozen


title: NJ004847

value: Aliquot 41/LLL-P


title: NJ004827

value: Female

value: Aliquot 92/RLL-P


title: NJ004819

value: Aliquot 65/LLL-P

value: current


title: LT286644

value: UF

value: R Upper

value: nonsmoker


title: LT275655

value: NSIP


title: NJ004808

value: Male

value: control

value: Aliquot 91/RLL-P


title: LT269763

value: R Lower

value: former


title: LT287196

value: IPF/UIP

value: LTRC

value: L Lower


title: LT287909

value: L Ling

value: RNAlater


title: LT277811

value: Frozen


title: LT280851

value: Female


title: LT264690

value: L Upper


title: LT266377


title: LT263234


title: LT266817


title: LT264518

value: UF


title: LT269381

value: R Upper


title: LT259072


title: LT262773


title: LT258372


title: LT235441


title: LT219681

value: nonsmoker


title: LT231101

value: DIP

value: current


title: LT214473

value: Male

value: NSIP


title: LT219896

value: R Middle


title: LT230142

value: R Lower

value: former


title: LT231373

value: IPF/UIP

value: LTRC


title: LT231890

value: RB-ILD


title: LT211455


title: LT245763

value: COP


title: LT217339

value: Frozen


title: LT228897

value: L Lower


title: LT211379


title: LT207236

value: Female


title: LT239116


title: LT205601


title: LT221381

value: RNAlater


title: LT205707


title: LT206005


title: LT242161


title: LT203446

value: UF


title: LT201831

value: R Upper

value: nonsmoker


title: LT211015


title: LT197381

value: L Ling


title: LT201348

value: L Upper


title: LT197286


title: LT195192


title: LT182636

value: Male


title: LT196309


title: LT188467


title: LT194091


title: LT182067


title: LT187987


title: LT185396


title: LT189721


title: LT170158

value: NSIP


title: LT171776

value: R Lower


title: LT175399

value: former


title: LT188524

value: IPF/UIP


title: LT185066

value: LTRC


title: LT184241


title: LT173946


title: LT180758

value: R Middle


title: LT168219


title: LT168352


title: LT195188

value: RB-ILD


title: LT159825

value: Frozen


title: whirly cells alone [re-analysis]

description: BJhTERT Whirly

tag: cell line

value: BJhTERT

tag: clone

value: whirly


title: LT163657

value: Female


title: LT163953


title: LT166493

value: RNAlater


title: LT165736

value: L Lower


title: LT167906


title: LT174813

value: nonsmoker


title: LT159457


title: LT157253


title: LT156276


title: LT157856


title: LT150445


title: LT118629

value: DIP


title: LT154455

value: UF

value: R Upper


title: LT112491

value: Male


title: LT151949

value: R Lower


title: LT119242


title: LT137431

value: former


title: LT134302

value: IPF/UIP


title: LT130861

value: LTRC


title: LT142933


title: LT139601


title: LT134776


title: LT104717


title: LT134279


title: LT135791


title: LT107185

value: COP


title: LT144921


title: LT148511

value: L Upper


title: LT128262


title: LT106561

value: NSIP

value: Frozen


title: LT139008


title: LT109321


title: LT118098

value: RB-ILD

value: current


title: LT128191


title: LT154952


title: LT116459


title: LT118519


title: LT103266


title: LT102695

value: Female


title: LT092669

value: L Lower


title: LT095103


title: LT093665

value: L Ling

value: nonsmoker


title: LT090283


title: LT089958


title: LT069422

value: RNAlater


title: LT087826


title: LT099826


title: LT074868


title: LT067836


title: LT072789

value: R Upper


title: LT077082

value: Male


title: LT082092

value: R Lower


title: LT062911

value: former


title: LT098394

value: IPF/UIP


title: LT081225

value: UF

value: LTRC


title: LT100434

value: L Upper


title: LT063974


title: LT067200


title: LT080836

value: R Middle


title: LT071706

value: Frozen


title: LT078404

value: RB-ILD


title: LT091552


title: LT059846


title: LT101536


title: LT243646


title: LT094331

value: NSIP


title: LT062141


title: LT077317


title: LT059736


title: LT056301


title: LT039091


title: LT041723


title: LT030385


title: LT031688

value: Female


title: LT006946


title: LT020259

value: L Lower


title: LT009429


title: LT008331


title: LT019699


title: LT025724


title: LT049193


title: LT046539


title: LT017495

value: current


title: LT008069


title: LT012680

value: nonsmoker


title: LT056464


title: LT047521


title: LT002902


title: LT001600


title: LT007259

value: RNAlater


title: LT026534


title: LT000216


title: LT004173


title: NJ020343

data_processing: Intensity data were log2-transformed, quantile normalized using RMA, and expression levels were summarized on a miRNA level using the median-polished value of all probesets mapping to each miRNA. Non-human miRNA probesets were removed, resulting in a final dataset of 1801 miRNA transcript measurements across 192 samples.

label_protocol: miRNA microarray target labeling was conducted using 1000 ng of total RNA and the FlashTag kit (Genisphere, Hatfield, PA)

value: Control

value: IIAM/NJH

value: Aliquot 1


title: LT002410

value: Male

value: former


title: LT006783

value: IPF/UIP

value: R Lower


title: LT033422

value: LTRC


title: LT011501

value: DIP


title: LT012417


title: NJ020081

value: Aliquot 24/RML

value: Frozen


title: NJ020083

value: Aliquot 10/RML-C


title: NJ020080

value: Aliquot 14/RML-P


title: NJ020061

value: Aliquot 1/RLL-P


title: NJ020065

value: Female

value: Aliquot 1/LLL-P


title: NJ020053

value: current


title: NJ020051

value: Control

value: Aliquot 74/RLL


title: NJ020056

value: IIAM/NJH

value: nonsmoker


title: NJ020066

value: Male

value: Aliquot 30/RLL


title: NJ020063


title: NJ020044

value: Aliquot 2/RLL-P


title: NJ020064


title: NJ020042


title: NJ020040

value: Aliquot 7/RLL-C

value: former


title: NJ020049


title: NJ020032

value: Aliquot 62/RLL-P


title: NJ020045

value: Aliquot 3/RLL-P

value: Frozen


title: NJ020036

value: Aliquot 70/LLL-P


title: NJ020026


title: NJ020028

value: Aliquot 37/RLL-P


title: NJ020027

value: Aliquot 67/RLL


title: NJ020016

value: Female

value: Aliquot 1/RLL-P


title: NJ020022

value: Control

value: Aliquot 37/LLL


title: NJ020025

value: IIAM/NJH

value: Aliquot 1/LLL-P


title: NJ020012

value: Aliquot 6/LLL-P

value: current


title: NJ020015

value: Male

value: Aliquot 7/LLL-P

value: nonsmoker


title: NJ020055

value: R Lower


title: NJ020007


title: NJ020005

value: former


title: NJ020011

value: Frozen


title: NJ020003


title: NJ020006


title: NJ020002


title: NJ020001


title: NJ004863

value: Aliquot 52/RLL-P


title: NJ004860


title: NJ004851

value: Aliquot 1/LLL-C


title: NJ020000


title: NJ004827

value: Aliquot 92/RLL-P


title: NJ004830

value: Female

value: Aliquot 47/RLL-P


title: NJ004818

value: Control

value: Aliquot 73/RLL-P


title: NJ004824

value: IIAM/NJH

value: Aliquot 48/LLL-P


title: NJ004840

value: Aliquote 66/RLL-P


title: NJ004847

value: Aliquot 41/LLL-P


title: NJ004808

value: Male

value: Aliquot 91/RLL-P

value: current


title: NJ004804

value: Aliquot 70/LLL-P


title: LT295133

value: IPF/UIP

value: LTRC

value: L Lower

value: nonsmoker


title: LT298606

value: R Middle

value: RNAlater


title: LT287909

value: Female

value: L Ling

value: former


title: LT284326

value: R Lower


title: LT286644

value: UF

value: R Upper

value: Frozen


title: LT284489


title: LT280851


title: LT269381


title: LT275751


title: LT269763

value: Male


title: LT275655

value: NSIP

value: IIAM/NJH


title: NJ004803

value: Control

value: Aliquot 85/RLL-P

value: current


title: LT282601

value: IPF/UIP

value: LTRC

value: L Upper


title: LT266817

value: L Lower


title: NJ004819

value: Female

value: Aliquot 65/LLL-P


title: LT266377

value: RNAlater

value: nonsmoker


title: LT264518

value: UF

value: R Lower

value: former


title: LT264690

value: Male


title: LT258372

value: Frozen


title: LT259072

value: NSIP

value: IIAM/NJH


title: LT263234


title: LT245763

value: COP


title: LT239116


title: LT242161


title: LT231373


title: LT235441


title: LT230142


title: LT219681


title: LT221381


title: LT228897


title: LT217339

value: R Middle


title: LT211455

value: IPF/UIP


title: LT206005

value: LTRC


title: LT211379


title: LT207236


title: LT214473


title: LT205707

value: RB-ILD


title: LT203446

value: L Lower


title: LT211015

value: Female


title: LT205601


title: LT201348

value: L Upper


title: LT196309


title: LT231101

value: DIP

value: current


title: LT194091


title: LT198096


title: LT195192


title: LT197286


title: LT244824

value: RNAlater


title: LT188524

value: R Lower

value: nonsmoker


title: LT187987

value: Male


title: LT185066

value: Frozen


title: LT188467

value: former


title: LT189721

value: UF


title: LT201831

value: IIAM/NJH

value: R Upper


title: LT180758

value: IPF/UIP

value: R Middle


title: LT182636

value: LTRC


title: LT182067


title: LT175399


title: LT168352

value: L Lower


title: LT173946

value: Female


title: LT167906


title: LT163953


title: LT163657

value: NSIP


title: LT184241


title: LT168219


title: LT157253


title: LT159457


title: LT185396


title: LT154952


title: LT154455


title: LT156276


title: LT150445


title: LT139008

value: L Upper


title: LT144921


title: LT137431


title: LT134776


title: LT135791


title: LT134302


title: LT134279


title: LT128262


title: LT165736


title: LT119242


title: LT118519

value: DIP


title: LT103266


title: LT118098

value: RB-ILD

value: current


title: LT104717

value: R Lower


title: LT107185

value: COP


title: LT106561

value: Male

value: Frozen


title: LT099826

value: former


title: LT101536

value: RNAlater


title: LT098394


title: LT100434


title: LT094331

value: IIAM/NJH


title: LT090283

value: IPF/UIP


title: LT092669


title: LT109321


title: LT082092


title: LT091552


title: LT089958


title: LT095103


title: LT087826

value: nonsmoker


title: LT116459

value: LTRC


title: LT081225

value: UF

value: R Upper


title: LT077317

value: NSIP

value: L Lower


title: LT074868


title: LT128191


title: LT067836


title: LT069422


title: LT071706

value: R Middle


title: LT093665

value: L Ling


title: LT067200

value: L Upper


title: LT062911


title: LT059846

value: R Lower


title: LT063974

value: Female


title: LT080836

value: Male


title: LT059736

value: Frozen


title: LT072789


title: LT031688

value: former


title: LT039091


title: LT033422


title: LT056301


title: LT030385

value: RNAlater


title: LT056464


title: LT019699


title: LT025724


title: LT047521


title: LT062796


title: LT046539


title: LT077082

value: RB-ILD

value: IIAM/NJH


title: LT006783

value: IPF/UIP


title: LT006946

value: LTRC

value: nonsmoker


title: LT008069


title: LT002902


title: LT011501

value: DIP


title: LT007259


title: LT001600


title: LT004173


title: LT008331

value: NSIP


title: LT000216

value: L Lower


title: NJ020079

value: Control

value: Aliquot 1/RLL-C

value: current


title: SScReg_1269_LA

status: Public on Apr 09 2013

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

hyb_protocol: Hyb using Agilent Hyb Kit

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro analysis software.

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

label_protocol: Labeled using Agilent Quick Amp Labeling Kit

extract_protocol: Total RNA isolated using Qiagen Fibrous Tissue Mini Kit

tag: sample type

value: Registry Patient

tag: disease state

value: Systemic Sclerosis

value: skin biopsy

tag: subject

source_name: Strategene Universal Human Reference

extract_protocol: Total RNA isolated by stratagene

treatment_protocol: Total RNA isolated by stratagene

tag: reference

value: Strategene Universal Human Reference


title: SScReg_1096_LA

tag: tissue


title: SScMH_14_base_LF

value: SSc MMF patient

tag: treatment

value: mycophenolate mofetil


title: SScMH_14_6mo_LA


title: SScMH_10_base_LF


title: SScMH_16_06mo_LF


title: LT009429

tag: gender

value: Female

tag: final diagnosis

tag: repository

tag: tissue source

value: R Lower

tag: preservative

value: Frozen


title: SScReg_1213_LA


title: SScReg_1004_base_LA


title: SScMH_12_base_RF


title: SScMH_16_6mo_LA


title: SScMH_16_base_LF


title: LT100821

value: Male

value: IPF/UIP

value: LTRC

value: HOPE

tag: rin

tag: smoking status

value: former

tag: quit how many years ago

tag: pack years

tag: st. george's total score


title: SScMH_14_6mo_LF


title: SScMH_14_base_LA


title: SScMH_16_base_LA


title: SScReg_1103_base_LA


title: SScReg_1002_base_LA


title: SScReg_1213_LF


title: SScMH_12_6mo_LA


title: SScReg_1156_base_LA


title: SScMH_12_base_LA


title: SScReg_1067_LA


title: SScReg_1066_LA


title: SScReg_1080_LA


title: LT195188

tag: age

value: RB-ILD

value: IIAM/NJH

tag: fvc pre-bronchodilator % predicted

tag: dlco % predicted


title: SScMH_12_6mo_RF

tag: sample type

tag: disease state

tag: subject


title: SScMH_10_06mo_LF

tag: tissue

tag: treatment

tag: reference


title: SScMH_08_06mo_LA


title: SScMH_10_06mo_LA


title: SScMH_08_base_LF


title: SScMH_08_base_LA


title: SScMH_07_base_LF


title: LT078404

tag: gender

tag: final diagnosis

tag: repository

value: R Middle


title: SScMH_10_12mo_LA


title: SScMH_10_12mo_LF


title: SScMH_07_base_LA


title: SScMH_06_base_RF


title: SScMH_07_12mo_LF


title: SScMH_07_12mo_LA


title: SScMH_06_06mo_RA


title: SScMH_05_06mo_RA


title: SScMH_08_06mo_LF


title: SScMH_07_06mo_LF


title: SScMH_05_base_RA


title: SScMH_07_06mo_LA


title: SScMH_06_12mo_RF


title: SScMH_06_12mo_RA


title: SScMH_05_06mo_RF


title: SScMH_06_06mo_RF


title: SScMH_04_base_LF


title: SScMH_05_base_RF


title: SScMH_04_base_LA


title: SScMH_06_base_RA


title: SScMH_04_12mo_LA


title: SScMH_04_12mo_LF


title: SScMH_03_12mo_LF


title: SScMH_03_base_LF


title: SScMH_03_base_LA


title: SScMH_03_06mo_LA


title: SScMH_03_12mo_LA


title: LT002410

value: UF

tag: tissue source

tag: preservative

tag: rin


title: SScMH_02_base_LA

value: Registry Patient

value: Systemic Sclerosis


title: SScMH_04_06mo_LA

value: skin biopsy

value: Strategene Universal Human Reference


title: MH_Norm_08_LA

value: Normal Control

value: normal


title: SScMH_03_06mo_LF

value: SSc MMF patient

value: mycophenolate mofetil


title: SScMH_02_base_LF


title: MH_Norm_09_RA


title: MH_Norm_1004


title: MH_Norm_05_LA


title: MH_Norm_08_LF


title: MH_Norm_09_RF


title: MH_Norm_06_LF


title: MH_Norm_03_RF


title: MH_Norm_04_RA


title: MH_Norm_07_LF


title: MH_S1001


title: MH_Norm_04_RF


title: SScMH_10_base_LA


title: MH_Norm_07_LA


title: MH_Norm_03_RA


title: MH_Norm_02_LA


title: MH_Norm_01_LF


title: MH_Norm_01_LA


title: genomic DNA from frontal cortex_6055432066_R04C02_Cohort2B

status: Public on Jan 24 2013

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

country: United Kingdom

institute: King's College London

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

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2011.1 used to generate the raw intensity file (unmethylated and methylated signal intensities).
Data used in the development of the R wateRmelon package for analysis of Illumina Infinium450 Human Methylation data.
The GenomeStudio v2011.1-computed Average Betas (normalized) is betaqn_geo_all cohorts.csv.
Thirteen other wateRmelon-generated normalized beta matrices include:
danen_geo_all cohorts.csv
danes_geo_all cohorts.csv
danet_geo_all cohorts.csv
daten1_geo_all cohorts.csv
daten2_geo_all cohorts.csv
fuks_geo_all cohorts.csv
nanes_geo_all cohorts.csv
nanet_geo_all cohorts.csv
nasen_geo_all cohorts.csv
naten_geo_all cohorts.csv
swan_geo_all cohorts.csv
tost_geo_all cohorts.csv
dasen_geo_all cohorts.csv

extract_protocol: Genomic DNA was extracted and purified from post-mortem brain or blood samples using phenol-chloroform protocol according to standard instructions

tag: subjectid

tag: barcode

tag: lunnonetal

value: FALSE

tag: Sex

tag: source tissue

value: frontal cortex


title: genomic DNA from frontal cortex_6055432066_R02C01_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R05C01_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R04C01_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R02C02_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R01C02_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R05C02_Cohort2B


title: HDD-2

status: Public on Feb 27 2013

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Gene expression in forebrain of high-dose dexamethasone-treated pups.
Replicate 2.

hyb_protocol: 825 ng from each of the Cy3- or Cy5-labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume was adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rabbit (4x44k 60-mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the sandwich firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and assess the mobility of the bubbles. The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979), and then immediately scanned.

scan_protocol: The arrays were scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through the use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house-developed algorithms described in Iacobas et al., Mol Genet Genomics 2012 (PMID 22246408).
This experiment used the multiple yellow strategy in which Cy3- and Cy5-labeled biological replicates are cohybridized with a two-color array and each channel is processed independently.

organism: Oryctolagus cuniculus

source_name: High-dose dexamethasone rabbit pup forebrain

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike-in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3)- or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Timed pregnant New Zealand rabbits were purchased from Charles River Laboratories, Inc. (Wilmington, Mass., USA). The premature pups were delivered by C-section at day 29 of gestational age (term = 32 days). Pups were dried with pre-warmed towels and placed in an infant incubator at 35C. The pups were gavage-fed with puppy formula (Esbilac, Petag, IL) in a volume of 2 ml every 12 h (100 ml /kg/day) starting at 2 h age. Subsequently, feeds were advanced to 125, 150, 200, 250, and 280 ml/kg at postnatal days 3, 5, 7, 10, and 14 respectively. The pups were euthanized at 14 postnatal days.

extract_protocol: Total RNA extraction was performed using an RNeasy Mini kit (Qiagen, Germantown, MD, USA) following the manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: Dexamethasone (West-Ward, Eatontown, NJ) was administered in high dose (0.25 mg/kg twice daily) for a maximum duration of 5 days. The dose of GC was based on its use in premature infants at risk of chronic lung disease in neonatal intensive care units. All medications were administered intramuscularly.

tag: breed

value: New Zealand

value: forebrain

tag: developmental stage

value: P14 of preterm (GD29)

value: high-dose dexamethasone


title: MH_Norm_02_RF

tag: sample type

tag: disease state

tag: subject


title: CTR-2

description:
Gene expression in forebrain of vehicle-treated pups.
Replicate 2.

source_name: Control (saline exposed) rabbit pup forebrain

tag: tissue

tag: treatment

value: saline vehicle


title: MH_Norm_05_LF

tag: reference


title: genomic DNA from frontal cortex_6055432066_R03C02_Cohort2B


title: CTR-3

description:
Gene expression in forebrain of vehicle-treated pups.
Replicate 3.


title: HDD-3

description:
Gene expression in forebrain of high-dose dexamethasone-treated pups.
Replicate 3.


title: HDD-1

description:
Gene expression in forebrain of high-dose dexamethasone-treated pups.
Replicate 1.


title: HDD-4

description:
Gene expression in forebrain of high-dose dexamethasone-treated pups.
Replicate 4.


title: CTR-1

description:
Gene expression in forebrain of vehicle-treated pups.
Replicate 1.


title: genomic DNA from frontal cortex_6055432060_R06C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R06C02_Cohort2B


title: genomic DNA from frontal cortex_6055432066_R01C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R05C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R03C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R04C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R01C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R06C02_Cohort2B


title: SScMH_04_06mo_LF


title: genomic DNA from frontal cortex_6055432060_R02C01_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R06C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R02C02_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R05C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R05C02_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R03C02_Cohort2B


title: CTR-4

description:
Gene expression in forebrain of vehicle-treated pups.
Replicate 4.


title: genomic DNA from frontal cortex_6055432029_R04C01_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R02C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R05C01_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R03C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R03C01_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R02C01_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R06C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R01C02_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R01C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R04C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R06C01_Cohort2B


title: genomic DNA from frontal cortex_6055432060_R01C01_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R05C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R04C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R03C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R05C01_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R03C01_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R02C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R01C01_Cohort2B


title: genomic DNA from frontal cortex_6055432029_R04C02_Cohort2B


title: genomic DNA from frontal cortex_6055432012_R01C02_Cohort2B


title: genomic DNA from cerebellum_6042316047_R05C02_Cohort2A

value: cerebellum


title: genomic DNA from cerebellum_6042316047_R06C01_Cohort2A


title: genomic DNA from cerebellum_6042316047_R04C02_Cohort2A


title: genomic DNA from cerebellum_6042316047_R04C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R06C02_Cohort2A


title: genomic DNA from cerebellum_6042316042_R06C01_Cohort2A


title: genomic DNA from cerebellum_6042316047_R02C02_Cohort2A


title: genomic DNA from cerebellum_6042316047_R05C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R05C02_Cohort2A


title: genomic DNA from cerebellum_6042316042_R04C02_Cohort2A


title: genomic DNA from cerebellum_6042316042_R05C01_Cohort2A


title: genomic DNA from cerebellum_6042316047_R02C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R03C02_Cohort2A


title: genomic DNA from cerebellum_6042316047_R01C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R04C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R03C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R02C01_Cohort2A


title: genomic DNA from cerebellum_6042316042_R02C02_Cohort2A


title: genomic DNA from cerebellum_6042316042_R01C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R05C02_Cohort2A


title: genomic DNA from cerebellum_6042316031_R06C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R06C02_Cohort2A


title: genomic DNA from cerebellum_6042316042_R01C02_Cohort2A


title: genomic DNA from cerebellum_6042316031_R04C02_Cohort2A


title: genomic DNA from cerebellum_6042316031_R03C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R04C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R03C02_Cohort2A


title: genomic DNA from cerebellum_6042316031_R01C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R01C02_Cohort2A


title: genomic DNA from cerebellum_6042316031_R02C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R02C02_Cohort2A


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML245T)

status: Public on Feb 12 2013

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

description:
MIAML245T
Unable to perform LOH analysis on 245 due to poor quality.

hyb_protocol: The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturer’s recommendations. Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in .txt format. Call rates for the entire group of samples included in this report were between 94.02% and 99.35%, with a mean call rate of 98.06%; none of the tumor DNA samples gave out-of-bounds results.
Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip, adapted to run on a 64-bit computer environment. To generate functional and practical displays of LOH, a two-step, internally developed, Java-based software analysis system was employed.  The Pre-LOH Unification Tool (PLUT) served to align all individual patient SNP calls to their respective dbSNP rs ID numbers and genomic physical positions prior to incorporation into the LOH tool version 2, an updated version of the LOH tool able to accommodate Affy SNP 6.0 array data.
Primary data description: dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol:
Purification_protocol: AML blast DNA used for SNP 6.0 profiling was extracted from negatively column enriched AML cell samples as described30 that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter31. CD33 and CD13 were then used in order to further discriminate myeloid blasts versus contaminating erythroid lineage or other non-myeloid cells.  Cells forming a dense population cloud on the CD33 versus CD13 plots that were either single marker positive or double positive were sorted.  Aliquots of final cell preparations were made for the majority of sorted samples and manually analyzed for cell composition using cytospins and blast counts.
Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

tag: tumor-enrollment or tumor-relapse or tumor-persistent vs normal

value: tumor-enrollment

tag: cell type

value: purified AML blasts


title: MH_Norm_06_LA


title: genomic DNA from cerebellum_6042316024_R06C01_Cohort2A


title: genomic DNA from cerebellum_6042316024_R06C02_Cohort2A


title: genomic DNA from cerebellum_6042316024_R05C01_Cohort2A


title: primary human: buccal (MIAML245N_BU_091411)

description:
MIAML245N_BU_091411
Unable to perform LOH analysis on 245 due to poor quality.

source_name: primary human: buccal

value: buccal cells


title: genomic DNA from cerebellum_6042316024_R05C02_Cohort2A


title: genomic DNA from cerebellum_6042316024_R04C02_Cohort2A


title: genomic DNA from cerebellum_6042316024_R03C01_Cohort2A


title: genomic DNA from cerebellum_6042316024_R01C02_Cohort2A


title: genomic DNA from cerebellum_6042316024_R04C01_Cohort2A


title: genomic DNA from cerebellum_6042316031_R05C01_Cohort2A


title: genomic DNA from cerebellum_6042316024_R02C01_Cohort2A


title: genomic DNA from cerebellum_6042316024_R01C01_Cohort2A


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML245T_PERSIST_091411)

description:
MIAML245T_PERSIST_091411
Unable to perform LOH analysis on 245 due to poor quality.

value: tumor-persistent


title: genomic DNA from cerebellum_6042316024_R02C02_Cohort2A


title: c_D_1152

status: Public on Sep 12 2012

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E06_609608

hyb_protocol: Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix MAS5 summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100. Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.

source_name: fresh frozen tumor sample

label_protocol: PCR products were labeled with a single biotin according to the Affymetrix protocol.

extract_protocol: For total RNA, frozen tissue sections were homogenized in Trizol and RNA was extracted according to standard protocols. For high molecular weight genomic DNA,  frozen tissue sections were homogenized in 1 ml of G2-buffer supplemented with 2 ml RNase (Qiagen). Subsequently, DNA was extracted  using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

treatment_protocol: 10-20 x 20mm sections from frozen tumor specimens from newly diagnosed previously untreated diffuse large B-cell lymphomas and peripheral blood lymphocytes from normal donors were directly transferred to extraction buffers.

tag: type

value: primary DLBCL


title: Lymphoma_P02_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C10_40984


title: old_c503

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H04_41090


title: old_c514

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H11_41202


title: old_c490

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G05_41104


title: c_D_1126

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D03_609896


title: old_c486

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G04_41088


title: Lymphoma_P07_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D04_40890


title: Lymphoma_P10_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D12_41018


title: old_c484

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G02_41056


title: old_c482

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F12_41214


title: Lymphoma_P08_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D06_40922


title: old_c491

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G06_41120


title: Lymphoma_P01_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C08_40952


title: Lymphoma_P04_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D02_40858


title: old_c497

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G12_41216


title: Lymphoma_P11_Dx

description: MYOID_g_Kuni2newsamples_GenomeWideSNP_6_H10_41784


title: old_c496

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G11_41200


title: old_c502

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H03_41074


title: old_c495

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G10_41184


title: old_c504

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H05_41106


title: old_c481

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F10_41182


title: old_c501

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H02_41058


title: Lymphoma_P03_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C12_41016


title: old_c506

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H06_41122


title: old_c479

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F09_41166


title: old_c492

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G08_41152


title: Lymphoma_P09_Dx

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D09_40970


title: old_c498

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H01_41042


title: old_c494

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G09_41168


title: old_c478

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F08_41150


title: old_c476

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F06_41118


title: old_c475

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F05_41102


title: old_c466

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E08_41148


title: old_c474

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F04_41086


title: old_c472

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F02_41054


title: old_c470

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E12_41212


title: old_c464

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E06_41116


title: old_c449

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D07_41130


title: old_c458

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E02_41052


title: old_c453

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D11_41194


title: old_c473

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E03_41068


title: old_c451

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D09_41162


title: old_c448

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D06_41114


title: old_c468

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E10_41180


title: old_c447

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D05_41098


title: old_c445

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D04_41082


title: old_c469

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E11_41196


title: old_c461

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E04_41084


title: old_c465

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E07_41132


title: old_c471

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F01_41038


title: old_c443

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D03_41066


title: old_c450

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D08_41146


title: old_c477

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F07_41134


title: old_c460

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F03_41070


title: old_c467

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E09_41164


title: old_c437

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C12_41208


title: old_c433

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C09_41160


title: old_c432

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C08_41144


title: old_c436

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C11_41192


title: old_c462

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E05_41100


title: old_c430

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C07_41128


title: old_c429

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C06_41112


title: old_c428

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C05_41096


title: old_c426

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C04_41080


title: old_c287

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B02_41046


title: old_c304

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B06_41110


title: old_c277

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B01_41030


title: old_c438

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D01_41034


title: old_c408

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B11_41190


title: old_c411

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B12_41206


title: old_c407

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B10_41174


title: old_c291

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B03_41062


title: old_c404

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B09_41158


title: old_c422

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C02_41048


title: old_c295

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B04_41078


title: old_c307

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B07_41126


title: old_c274

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A12_41204


title: old_c268

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A11_41188


title: old_c267

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A10_41172


title: old_c251

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A06_41108


title: old_c425

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C03_41064


title: old_c254

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A07_41124


title: old_c261

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A09_41156


title: old_c242

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A04_41076


title: old_c250

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A05_41092


title: old_c230

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A02_41044


title: old_c300

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B05_41094


title: c_D_1158

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H10_609544


title: c_D_1048

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H07_609672


title: c_D_1051

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H03_609548


title: c_D_1004

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_F02_609646


title: c_D_1054

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H01_609694


title: c_D_1151

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G05_609600


title: c_D_1130

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_F05_609650


title: c_D_1049

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G01_609606


title: c_D_1129

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E08_609638


title: old_c239

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A03_41060


title: c_D_1053

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D05_609560


title: c_D_1103

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G10_609622


title: c_D_1108

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G04_609576


title: c_D_1127

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C06_609712


title: c_D_1106

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C04_609698


title: c_D_1046

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C12_609588


title: c_D_1112

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C08_609680


title: c_D_1124

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D10_609676


title: c_D_1135

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D12_609590


title: c_D_1118

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_B11_609534


title: c_D_1025

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H08_566346


title: c_D_1134

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A07_609592


title: c_D_1153

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_B10_609714


title: c_D_1047

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A08_609596


title: c_D_1043

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A12_609586


title: c_D_1109

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E04_609538


title: c_D_1041

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G11_566358


title: c_D_1012

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G08_566338


title: c_D_1029

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G09_566512


title: c_D_1020

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F07_566334


title: c_D_1036

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F03_566380


title: c_D_1050

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H02_566404


title: c_D_1010

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G06_566424


title: c_D_1017

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G02_566506


title: c_D_1005

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F02_566410


title: c_D_1008

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E04_566456


title: c_D_1002

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D11_566344


title: c_D_1028

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D10_566386


title: c_D_1030

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E12_566518


title: c_D_1023

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E09_566348


title: c_D_1027

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F06_566382


title: c_D_1019

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F10_566430


title: c_D_1035

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A11_566370


title: c_D_1034

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D12_566356


title: c_D_1016

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_C08_566398


title: c_D_1001

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B08_566408


title: c_D_1039

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D02_566520


title: c_D_1037

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A05_566444


title: c_D_1006

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D01_566500


title: c_D_1003

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D07_566388


title: c_D_1024

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A03_566342


title: c_D_1164

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G03_609836


title: c_D_1022

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A04_566454


title: c_D_1166

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G05_609800


title: c_D_1162

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G01_609754


title: c_D_1163

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G02_609752


title: c_D_1156

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F07_609882


title: c_D_1032

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A10_566480


title: c_D_1155

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F06_609786


title: c_D_1154

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F05_609740


title: c_D_1145

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E08_609858


title: c_D_1136

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E01_609742


title: c_D_1149

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E12_609724


title: c_D_1146

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E09_609788


title: c_D_1159

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F10_609758


title: c_D_1133

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D10_609722


title: c_D_1131

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D08_609908


title: c_D_1132

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E11_609730


title: c_D_1140

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E04_609818


title: c_D_1142

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E06_609900


title: c_D_1139

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E03_609912


title: c_D_1141

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E05_609756


title: c_D_1147

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E10_609732


title: ozone/Pam3Cys 24 hours O3/P3C/24h rep3

status: Public on Aug 01 2012

hyb_protocol: standard Agilent hyb protocol

scan_protocol: standard protocol on the Agilent scanner

data_processing:
Agi4x44PreProcess
RMA by Partek

source_name: lung tissue

label_protocol: 0.5-1.0 microgram of Total RNA was used as a template for synthesis of cDNA utilizing the One Color Low input Agilent Quick Amp Labeling Kit.

treatment_protocol: Mice were exposed to either 2ppm ozone or filtered air (FA) for 3 hours.  24 hours following ozone exposure, mice from either the ozone or FA group were treated intratracheally with either 100ug of Pam3CYS in saline or saline alone. Animals were euthanized 4 or 24 hours post-Pam3CYS exposure.

tag: time

value: 24 hours

tag: strain

value: lung


title: ozone/Pam3Cys 24 hours O3/P3C/24h rep2


title: free air/Pam3Cys 24 hours FA/P3C/24h rep4

value: free air/Pam3Cys


title: ozone/Pam3Cys 24 hours O3/P3C/24h rep4


title: c_D_1138

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E02_609764


title: free air/Pam3Cys 24 hours FA/P3C/24h rep2


title: free air/Pam3Cys 24 hours FA/P3C/24h rep1


title: O3/saline 24 hours O3/sal/24h rep4


title: c_D_1125

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D02_609826


title: O3/saline 24 hours O3/sal/24h rep3


title: free air/Pam3Cys 24 hours FA/P3C/24h rep3


title: O3/saline 24 hours O3/sal/24h rep2


title: ozone/Pam3Cys 24 hours O3/P3C/24h rep1


title: c_D_1128

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D05_609782


title: O3/saline 24 hours O3/sal/24h rep1


title: free air/saline 24 hours FA/sal/24h rep3

value: free air/saline


title: free air/saline 24 hours FA/sal/24h rep4


title: c_D_1150

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F01_609808


title: c_D_1120

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C09_609864


title: free air/saline 24 hours FA/sal/24h rep2