title: 1772066084_A12

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_E06

status: Public on Oct 06 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: EmbryoMoleculeCounts.cef

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10 and UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list. Mitochondrial genes and genes with less than 4 molecules have been omitted. The first two lines of each file are table metadata (see https://github.com/linnarsson-lab/ceftools)

molecule: polyA RNA

organism: Homo sapiens

source_name: ventral midbrain

growth_protocol: Wild-type CD1 mice were mated overnight and noon of the day was considered E0.5. Mothers were killed and embryos were dissected out of the uterine horn between the time points E11.5 and E18.5. Adult CD1 animals were dissected at P19 to P27. Human tissue was collected at Addenbrooke’s Hospital (Cambridge, UK) and dissected in HIBERNATE medium (Gibco). Samples were shipped overnight on ice (in HIBERNATE solution) to Sweden. For the embryonic stem cells (hES DA),  iCell DopaNeurons from Cellular Dynamics International (DNC-301030001, lot #6003358) were differentiated following the manufacturer’s recommendations and harvested at day 5 and 21.

extract_protocol:
Human embryo ventral midbrain dissection was performed on ice in neuronal N2 culturing media. 10-17  tissue pieces were collected for each experiment. The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3’ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

tag: tissue

value: ventral midbrain

tag: Sex

value: pooled male and female

tag: age

tag: inferred cell type

value: hProgM


title: 1772067089_E02

description: EmbryoMoleculeCounts.cef

value: hOMTN


title: 1772067089_E03

description: EmbryoMoleculeCounts.cef

value: Unk


title: 1772066084_A02

description: MouseEmbryoMoleculeCounts.cef

organism: Mus musculus

tag: strain

value: mSert


title: 1772066084_A01

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_E01

description: EmbryoMoleculeCounts.cef

value: hEndo


title: 1771013153_H11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_H09

description: MouseEmbryoMoleculeCounts.cef

value: mRN


title: 1771013153_H01

description: MouseEmbryoMoleculeCounts.cef

value: mUnclassified


title: 1772067089_D10

description: EmbryoMoleculeCounts.cef


title: 1772067089_D12

description: EmbryoMoleculeCounts.cef

value: hProgFPL


title: 1772067089_D08

description: EmbryoMoleculeCounts.cef

value: hProgBP


title: 1772067089_D09

description: EmbryoMoleculeCounts.cef


title: 1772067089_D07

description: EmbryoMoleculeCounts.cef


title: 1771013153_F09

description: MouseEmbryoMoleculeCounts.cef

value: mNProg


title: 1772067089_D06

description: EmbryoMoleculeCounts.cef


title: 1771013153_F06

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_D01

description: EmbryoMoleculeCounts.cef


title: 1771013153_F02

description: MouseEmbryoMoleculeCounts.cef

value: mEndo


title: 1772067089_D05

description: EmbryoMoleculeCounts.cef


title: 1771013153_E09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_E06

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_C12

description: EmbryoMoleculeCounts.cef


title: 1771013153_D11

description: MouseEmbryoMoleculeCounts.cef

value: mNbM


title: 1771013153_D09

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_C08

description: EmbryoMoleculeCounts.cef


title: 1772067089_C06

description: EmbryoMoleculeCounts.cef


title: 1772067089_C05

description: EmbryoMoleculeCounts.cef


title: 1771013153_D02

description: MouseEmbryoMoleculeCounts.cef

value: mPeric


title: 1771013153_D01

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_C04

description: EmbryoMoleculeCounts.cef


title: 1771013153_D03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_C09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_B08

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_B07

description: EmbryoMoleculeCounts.cef

value: hNbM


title: 1772067089_C02

description: EmbryoMoleculeCounts.cef


title: 1771013153_B05

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_B03

description: EmbryoMoleculeCounts.cef

value: hNProg


title: 1772067089_B06

description: EmbryoMoleculeCounts.cef

value: ventral midbrain


title: 1772067089_B01

description: EmbryoMoleculeCounts.cef

value: pooled male and female


title: 1771013153_A12

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_A11

description: EmbryoMoleculeCounts.cef


title: 1772067089_B05

description: EmbryoMoleculeCounts.cef


title: 1771013153_B07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_E08

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_C10

description: EmbryoMoleculeCounts.cef


title: 1771013153_A11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_A08

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_C11

description: EmbryoMoleculeCounts.cef


title: 1772067089_A08

description: EmbryoMoleculeCounts.cef


title: 1772067089_A05

description: EmbryoMoleculeCounts.cef


title: 1772067089_A06

description: EmbryoMoleculeCounts.cef

value: hProgM


title: 1771013153_A03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013153_A10

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_A04

description: EmbryoMoleculeCounts.cef


title: 1771013153_A02

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_A03

description: EmbryoMoleculeCounts.cef


title: 1771013118_H03

description: MouseEmbryoMoleculeCounts.cef


title: 1772067089_A02

description: EmbryoMoleculeCounts.cef


title: 1772067089_A01

description: EmbryoMoleculeCounts.cef

value: hMgl


title: 1771013118_F11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_F07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_G07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_F09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_F02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_E10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_E09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_E03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_D04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_E02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_C06

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_C12

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_C11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_B09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_C02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_A12

description: MouseEmbryoMoleculeCounts.cef


title: 1771013117_B10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_A11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013117_A07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_B11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_H01

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_G10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_G05

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013117_D04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_A04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_F10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013118_F03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_F07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_C08

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_C02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_H03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013113_B03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_G05

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_G09

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_G01

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_F10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_F03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_F01

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_E10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_D07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_E02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_D04

description: MouseEmbryoMoleculeCounts.cef

value: mMgl


title: 1771013111_D03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_D01

description: MouseEmbryoMoleculeCounts.cef

value: mNbDA


title: 1771013111_C11

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_C09

description: MouseEmbryoMoleculeCounts.cef

value: mOMTN


title: 1771013111_C05

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_C08

description: MouseEmbryoMoleculeCounts.cef


title: 1771013111_C04

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013110_H10

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_H03

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_G12

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_E05

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_D08

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_D04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013108_E06

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_D03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_C12

description: MouseEmbryoMoleculeCounts.cef


title: 1771013108_G07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013108_A03

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_C02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_C04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_C07

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_B12

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_B06

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_G10

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_H04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_A02

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_G04

description: MouseEmbryoMoleculeCounts.cef


title: 1771013013_A06

description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


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description: MouseEmbryoMoleculeCounts.cef


title: ChIPSeq WT CD8 T Input

status: Public on May 09 2016

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

description: Input control

library_source: genomic

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to BAM format using igvtools
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser. For RNA-Seq, raw counts are calculated using cuffdiff
Genome_build: mm9

molecule: genomic DNA

source_name: Pre-activated CD8+ T cells

growth_protocol: Cells of indicated phenotype were FACS-sorted from spleens and lymph nodes of WT or Bach2-deficient mice, or from mice reconstituted with WT and Bach2-deficient BM cells. Alternatively, where indicated, cells were harvested at day 5 following stimulation of naïve FACS-sorted cells with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of 100IU IL-2.

extract_protocol:
T cells were chemically crosslinked and sonicated cells to generate fragmented genomic DNA. DNA fragments purified from agarose gels and used for cluster generation and sequencing. Chromatin immunoprecipitation was performed using the following antibodies: BACH2, JunD, p300, H3K4me1, H3K27ac
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform or Genome Analyzer II platform.

treatment_protocol: Where relevant, cells were briefly stimulated ex vivo with plate-bound anti-CD3 and anti-CD28 antibodies for indicated times and harvested for RNA-Seq analysis.

value: Spleen

tag: genotype/variation

value: wild type


title: ChIPSeq WT CD8 T H3K4me1

description: ChIP against H3K4me1

tag: chip antibody

value: H3K4me1 (ab8895, Abcam)


title: Leishmania_control:wild type_rep2 [SAMPLE 1B]

status: Public on Jul 31 2016

type: RNA

city: New Delhi

first: Swati

last: Saha

state: Delhi

address: Benito Juarez Raod

department: Microbiology

country: India

institute: University of Delhi

description: SAMPLE 1B; gProcessedSignal_1B

hyb_protocol: Hybridization was done using Agilent's In situ Hybridization kit (5188-5242) according to manufacturer's instructions.

scan_protocol: The hybridized and washed microarray slides were scanned on a G2565C scanner (Agilent Technologies).

data_processing:
Raw data were analysed using GeneSpring GX 12.1 Software. Normalization of the data was done using the same software using the 75th percentile shift method (included in the sample table; gProcessedSignal columns in the Complete_data_with_fold-changes.xls as well).
Fold change with respect to control (Samples 1A and 1B) calculated are GeneSpring-normalized, in terms of log base 2 (provided in the 'Complete_data_with_fold-changes.xls').

molecule: total RNA

organism: Leishmania donovani

source_name: Leishmania_control_wild type

label_protocol: Complementary RNA was labelled with Cy3 using Agilent's Quick-Amp labeling kit. Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).

growth_protocol: Grown in M199 medium supplemented with 10% FBS, hemin (5µg/ml), 100µM adenine at 26°C.

extract_protocol: RNA was isolated using the PureLink RNA mini-kit (Invitrogen).

treatment_protocol: RNA isolated from logarithmically growing cells.

value: L. donovani 1S

tag: cell type

value: promastigotes

tag: growth stage

value: logarithmically growing


title: ChIPSeq WT CD8 T H3K27ac

description: ChIP against H3K27ac

value: H3K27ac (ab4729, Abcam)


title: ChIPSeq WT CD8 T BACH2

description: ChIP against BACH2

value: BACH2 (N-2, Tohoku University)


title: Leishmania_HAT4-null_rep2 [SAMPLE 2B]

description: SAMPLE 2B; gProcessedSignal_2B


title: Leishmania_HAT4-null_rep1 [SAMPLE 2A]

description: SAMPLE 2A; gProcessedSignal_2A


title: HSG_negControl_04

status: Public on Jul 20 2016

first: John

middle: A

last: Chiorini

address: Building 10/Room 1A21

department: NIDCR

description: Gene expressio without BMP6 treatment.

hyb_protocol: in 1 mM Tris-HCl buffer containing 0.1% bovine serum albumin or human serum albumin, and stored at -20 0C.

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

data_processing: Normalization of sample signal intensity was performed using  quantile normalization.  Following normalization, the probes with values below the 20th percentile in >80% of the samples were removed.   Genes differentially expressed between the primary SS and healthy volunteers were identified using unpaired, asymptotic t-test (p < 0.05 following adjustment for multiple hypothesis testing using Benjamini-Hochberg FDR correction).

source_name: HSG, negative control, replicate 4

label_protocol: A total of 500 ng of RNA was labeled with Cy3-CTP, and the quality and yield of complementary RNA (cRNA) were then analyzed using a NanoDrop ND-1000 UV-VIS Spectrophotometer (version 3.2.1). Only cRNA with a total yield of >1.65 μg and a specific avidity of > 9.0 pmoles Cy3/μg cRNA was used in the hybridization step.

growth_protocol: The human salivary gland cell line (HSG) were cultured with 1 x Minimum Essential Medium (GIBCO) with 10% of FBS (Invitrogen) containing 1% antibiotics at 37 °C in 5% CO2. Recombinant human BMP-6 was purchased from R&D System. The stock solution was diluted

extract_protocol: MSGs were obtained from study participants and stored in RNAlater (Qiagen) until RNA extraction. Samples were homogenized with a Bullet-Blender (Next Advance) or an Omni TH (Omni International). Total RNA was extracted with an RNeasy Mini kit according to the instructions of the manufacturer (Qiagen). The quality of RNA was measured using a 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ribosomal RNA ratio of 1.7 and an RNA integrity number of ≥ 6.5 were used for the arrays.

treatment_protocol: Cells were treated for 72 hrs with the indicated concentration of BMP-6 throughout the manuscript.

value: salivary gland cell line (HSG)

tag: bmp6 treatment (ng/ml)


title: Leishmania_control:wild type_rep1 [SAMPLE 1A]

description: SAMPLE 1A; gProcessedSignal_1A


title: HSG_BMP0.1ng_02

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP 0.1 ng treatment, replicate 2


title: HSG_negControl_01

description: Gene expressio without BMP6 treatment.

source_name: HSG, negative control, replicate 1


title: HSG_BMP150ng_02

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP 150 ng treatment, replicate 2


title: HSG_BMP6ng_02

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP 6  ng treatment, replicate 2


title: HSG_BMP0.1ng_01

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP 0.1 ng treatment, replicate 1


title: HSG_BMP150ng_01

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP 150 ng treatment, replicate 1


title: HSG_negControl_05

description: Gene expressio without BMP6 treatment.

source_name: HSG, negative control, replicate 5


title: HSG_BMP6ng_01

description: Gene expression after BMP6 treatment.

source_name: HSG, BMP6 6 ng treatment, replicate 1


title: HSG_negControl_02

description: Gene expressio without BMP6 treatment.

source_name: HSG, negative control, replicate 2


title: HSG_negControl_03

description: Gene expressio without BMP6 treatment.

source_name: HSG, negative control, replicate 3


title: WT plants under drought stress condition, biological rep2

status: Public on Dec 31 2015

city: Yangling

first: Kunming

last: Chen

state: Shaanxi

address: Xinong Road 22#

department: College of Life Sciences

country: China

institute: Northwest A&F University

description: Gene expression data from leaves

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip rice genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (P/N 00-00212, Affymetrix)

data_processing:
The data were read with Command Console Software 3.1 (Affymetrix) and normalized using GeneSpring Software 11.0 (Agilent) and the MAS5.0 algorithm.
Data quality was assessed and statistical analysis was performed as described in the Affymetrix GeneChip Expression Analysis and Statistical Algorithms Description Documents. The data were analyzed using Student’s t-test.

label: biotin

organism: Oryza sativa

source_name: The youngest fully expanded leaves from 2.5-month-old WT plants under drought stress condition

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

growth_protocol: After germination, rice seeds were transferred into a tray and watered daily with Hoagland’s nutrient solution. After 2 weeks, when the fourth leaf of each seedling had fully expanded, every four seedlings was transferred into a plastic pot, which were each filled with 12.5 kg of soil from a paddy field and cultivated in a greenhouse with a day/night temperature cycle of 36 ◦C/28 ◦C, light intensity of 800 μmol m-1 s-1, 16 h day/8 h dark, and 60%–65% relative humidity. The seedlings were watered at 2–3 d intervals to keep the soil submerged in water until the drought treatments were applied.

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

treatment_protocol: For drought treatment, pairs of 10-week-old osnox2 and WT plants were each grown in the same pot to ensure an identical water-stress condition. The youngest fully expanded leaf from each osnox2 and WT plant was harvested 0 and 15 days after the commencement of the drought treatment. At these two time points, the soil moisture percentages were 47.3 ± 1.9% and 8.5 ± 2.1%, respectively.

tag: treatment

value: drought

value: fresh leaves

tag: genotype

value: Oryza sativa ssp. Japonica. cv. Dongjin


title: WT plants under drought stress condition, biological rep1

description: Gene expression data from leaves


title: LuCaP 145.2 PCa xenograft tumor

status: Public on Jun 24 2015

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice.

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.7.3.1 were used to grid and extract the data using the GE2_105_Jan09 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases.

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

tag: tissue type

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: molecule

value: second round aRNA

extract_protocol: Flash frozen LuCaP PCa xenograft tissue was histologically evaluated for regions of viable tumor. RNA was isolated from 15, 10-micron sections from xenografts with ≥80% tumor content. For xenografts with <80% tumor, stroma and necrotic tissue were removed using an 18-guage needle prior to sectioning. RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.) according to the manufacturer's protocol with on-column DNase digestion followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: LuCaP 145.2 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group

tag: batch

value: no batch normalization applied

tag: ne group

value: first round aRNA


title: WT plants under normal growth condition, biological rep3

description: Gene expression data from leaves

source_name: The youngest fully expanded leaves from 2.5-month-old WT plants under normal growth condition

value: control

tag: tissue


title: LuCaP 147 PCa xenograft tumor

description: LuCaP 147 PCa xenograft tumor

value: LuCaP 147 PCa xenograft tumor, CHGA negative group

value: CHGA negative group

tag: erg group

value: ERG negative group


title: LuCaP 86.2 PCa xenograft tumor

description: LuCaP 86.2 PCa xenograft tumor

value: LuCaP 86.2 PCa xenograft tumor, CHGA negative group

value: ERG positive group


title: LuCaP 96CR PCa xenograft tumor

description: LuCaP 96CR PCa xenograft tumor

value: LuCaP 96CR PCa xenograft tumor, CHGA negative group


title: LuCaP 145.1 PCa xenograft tumor

value: LuCaP 145.1 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group


title: LuCaP 81 PCa xenograft tumor

description: LuCaP 81 PCa xenograft tumor

value: LuCaP 81 PCa xenograft tumor, CHGA negative group


title: LuCaP 96 PCa xenograft tumor

description: LuCaP 96 PCa xenograft tumor

value: LuCaP 96 PCa xenograft tumor, CHGA negative group


title: LuCaP 141 PCa xenograft tumor

description: LuCaP 141 PCa xenograft tumor

value: LuCaP 141 PCa xenograft tumor, CHGA negative group


title: LuCaP 93 PCa xenograft tumor

value: male

value: LuCaP 93 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group


title: HSG_negControl_06

description: Gene expressio without BMP6 treatment.

source_name: HSG, negative control, replicate 6

value: salivary gland cell line (HSG)


title: WT plants under normal growth condition, biological rep1

description: Gene expression data from leaves

value: fresh leaves

value: Oryza sativa ssp. Japonica. cv. Dongjin

tag: age


title: LuCaP 115 PCa xenograft tumor

description: LuCaP 115 PCa xenograft tumor

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: second round aRNA

value: LuCaP 115 PCa xenograft tumor, CHGA negative group

value: no batch normalization applied

value: first round aRNA


title: WT plants under normal growth condition, biological rep2

description: Gene expression data from leaves

value: control


title: LuCaP 105 PCa xenograft tumor

description: LuCaP 105 PCa xenograft tumor

value: LuCaP 105 PCa xenograft tumor, CHGA negative group

value: CHGA negative group

value: ERG negative group


title: LuCaP 92 PCa xenograft tumor

description: LuCaP 92 PCa xenograft tumor

value: LuCaP 92 PCa xenograft tumor, CHGA negative group

value: ERG positive group


title: LuCaP 49 PCa xenograft tumor

value: LuCaP 49 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group


title: LuCaP 35 PCa xenograft tumor

description: LuCaP 35 PCa xenograft tumor

value: male

value: LuCaP 35 PCa xenograft tumor, CHGA negative group


title: WT plants under drought stress condition, biological rep3

description: Gene expression data from leaves

value: drought


title: LuCaP 35CR PCa xenograft tumor

description: LuCaP 35CR PCa xenograft tumor

value: LuCaP 35CR PCa xenograft tumor, CHGA negative group


title: LuCaP 136 PCa xenograft tumor

description: LuCaP 136 PCa xenograft tumor

value: LuCaP 136 PCa xenograft tumor, CHGA negative group


title: LuCaP 78 PCa xenograft tumor

description: LuCaP 78 PCa xenograft tumor

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: LuCaP 78 PCa xenograft tumor, CHGA negative group


title: LuCaP 77 PCa xenograft tumor

description: LuCaP 77 PCa xenograft tumor

value: second round aRNA

value: LuCaP 77 PCa xenograft tumor, CHGA negative group


title: LuCaP 58 PCa xenograft tumor

description: LuCaP 58 PCa xenograft tumor

value: LuCaP 58 PCa xenograft tumor, CHGA negative group

value: no batch normalization applied

value: first round aRNA


title: LuCaP 23.1CR PCa xenograft tumor

description: LuCaP 23.1CR PCa xenograft tumor

value: LuCaP 23.1CR PCa xenograft tumor, CHGA negative group

value: CHGA negative group


title: LuCaP 23.1 PCa xenograft tumor

description: LuCaP 23.1 PCa xenograft tumor

value: LuCaP 23.1 PCa xenograft tumor, CHGA negative group


title: PFC_120hr_treated_4

status: Public on May 26 2015

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.

source_name: prefrontal cortex, ethanol vapor treated, 120 hr

label_protocol: Biotinylated cRNAs were prepared with the Illumina® TotalPrep-96™ RNA Amplification kit from Ambion according to manufacturer's instructions.

extract_protocol:
Whole brains were cryosectioned at 300um. Specific brain regions were isolated using a 1.25 mm (AMY) or 2.0 mm (NAC, PFC) micropunch. Eight, 6 and 5-8 micropunces were collected from AMY, NAC and PFC, respectively.
Total RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion, Austin, TX) using the manufacturer supplied modification to collect both mRNAs and small RNAs. Quality control was performed with the Agilent Tape Station.

value: adult (10-12 weeks)

value: prefrontal cortex


title: LuCaP 70 PCa xenograft tumor

description: LuCaP 70 PCa xenograft tumor

value: male

value: LuCaP 70 PCa xenograft tumor, CHGA negative group

value: ERG negative group


title: PFC_120hr_control_3

description: Replicate 3

source_name: prefrontal cortex, saline control, 120 hr


title: PFC_120hr_control_2

description: Replicate 2


title: PFC_120hr_treated_1

description: Replicate 1


title: PFC_120hr_control_6

description: Replicate 6


title: PFC_120hr_treated_3

description: Replicate 3


title: PFC_120hr_treated_5

description: Replicate 5


title: PFC_120hr_treated_2

description: Replicate 2


title: PFC_120hr_treated_8

description: Replicate 8


title: PFC_120hr_control_4

description: Replicate 4


title: PFC_120hr_control_1

description: Replicate 1


title: PFC_120hr_control_7

description: Replicate 7


title: PFC_8hr_treated_5

description: Replicate 5

source_name: prefrontal cortex, ethanol vapor treated, 8 hr


title: PFC_8hr_treated_6

description: Replicate 6


title: PFC_8hr_treated_7

description: Replicate 7


title: PFC_120hr_control_8

description: Replicate 8


title: PFC_120hr_treated_6

description: Replicate 6


title: PFC_120hr_control_5

description: Replicate 5


title: PFC_8hr_treated_8

description: Replicate 8


title: PFC_8hr_treated_4

description: Replicate 4


title: PFC_120hr_treated_7

description: Replicate 7


title: PFC_8hr_treated_3

description: Replicate 3


title: LuCaP 23.12 PCa xenograft tumor

description: LuCaP 23.12 PCa xenograft tumor

value: LuCaP 23.12 PCa xenograft tumor, CHGA negative group

value: ERG positive group


title: PFC_8hr_control_7

description: Replicate 7

source_name: prefrontal cortex, saline control, 8 hr


title: PFC_8hr_control_8

description: Replicate 8


title: PFC_8hr_control_4

description: Replicate 4


title: PFC_8hr_control_6

description: Replicate 6


title: PFC_8hr_treated_2

description: Replicate 2


title: PFC_8hr_control_3

description: Replicate 3


title: PFC_0hr_treated_5

description: Replicate 5

source_name: prefrontal cortex, ethanol vapor treated, 0 hr


title: PFC_8hr_treated_1

description: Replicate 1


title: PFC_8hr_control_5

description: Replicate 5


title: PFC_8hr_control_1

description: Replicate 1


title: PFC_0hr_control_5

description: Replicate 5

source_name: prefrontal cortex, saline control, 0 hr


title: PFC_0hr_control_3

description: Replicate 3


title: PFC_8hr_control_2

description: Replicate 2


title: PFC_0hr_treated_6

description: Replicate 6


title: PFC_0hr_treated_4

description: Replicate 4


title: PFC_0hr_control_1

description: Replicate 1


title: NAC_120hr_treated_5

description: Replicate 5

source_name: nucleus accumbens, ethanol vapor treated, 120 hr

value: nucleus accumbens


title: PFC_0hr_treated_8

description: Replicate 8


title: PFC_0hr_treated_3

description: Replicate 3


title: NAC_120hr_treated_6

description: Replicate 6


title: NAC_120hr_treated_4

description: Replicate 4


title: PFC_0hr_treated_2

description: Replicate 2


title: PFC_0hr_treated_1

description: Replicate 1


title: NAC_120hr_control_8

description: Replicate 8

source_name: nucleus accumbens, saline control, 120 hr


title: NAC_120hr_control_7

description: Replicate 7


title: PFC_0hr_control_7

description: Replicate 7


title: PFC_0hr_control_8

description: Replicate 8


title: NAC_120hr_control_4

description: Replicate 4


title: PFC_0hr_control_2

description: Replicate 2


title: PFC_0hr_control_4

description: Replicate 4


title: NAC_8hr_treated_8

description: Replicate 8

source_name: nucleus accumbens, ethanol vapor treated, 8 hr


title: NAC_8hr_treated_7

description: Replicate 7


title: NAC_120hr_treated_7

description: Replicate 7


title: NAC_120hr_treated_3

description: Replicate 3


title: NAC_120hr_treated_2

description: Replicate 2


title: NAC_8hr_treated_4

description: Replicate 4


title: NAC_120hr_control_5

description: Replicate 5


title: NAC_8hr_treated_2

description: Replicate 2


title: NAC_120hr_treated_1

description: Replicate 1


title: NAC_8hr_treated_5

description: Replicate 5


title: NAC_120hr_control_6

description: Replicate 6


title: NAC_120hr_treated_8

description: Replicate 8


title: NAC_8hr_control_5

description: Replicate 5

source_name: nucleus accumbens, saline control, 8 hr


title: NAC_8hr_control_7

description: Replicate 7


title: NAC_120hr_control_3

description: Replicate 3


title: NAC_8hr_control_4

description: Replicate 4


title: NAC_120hr_control_2

description: Replicate 2


title: NAC_120hr_control_1

description: Replicate 1


title: NAC_8hr_treated_6

description: Replicate 6


title: NAC_8hr_treated_3

description: Replicate 3


title: NAC_0hr_treated_8

description: Replicate 8

source_name: nucleus accumbens, ethanol vapor treated, 0 hr


title: NAC_8hr_control_8

description: Replicate 8


title: NAC_8hr_treated_1

description: Replicate 1


title: NAC_0hr_treated_6

description: Replicate 6


title: NAC_8hr_control_6

description: Replicate 6


title: NAC_8hr_control_3

description: Replicate 3


title: NAC_0hr_treated_7

description: Replicate 7


title: NAC_0hr_control_2

description: Replicate 2

source_name: nucleus accumbens, saline control, 0 hr


title: NAC_0hr_treated_4

description: Replicate 4


title: NAC_0hr_control_7

description: Replicate 7


title: NAC_0hr_treated_3

description: Replicate 3


title: NAC_0hr_control_1

description: Replicate 1


title: NAC_0hr_treated_5

description: Replicate 5


title: LuCaP 73 PCa xenograft tumor

description: LuCaP 73 PCa xenograft tumor

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: LuCaP 73 PCa xenograft tumor, CHGA negative group


title: NAC_0hr_treated_1

description: Replicate 1


title: NAC_0hr_control_5

description: Replicate 5


title: AMY_120hr_treated_4

description: Replicate 4

source_name: amygdala, ethanol vapor treated, 120 hr

value: amygdala


title: AMY_120hr_treated_7

description: Replicate 7


title: AMY_120hr_treated_8

description: Replicate 8


title: NAC_0hr_control_4

description: Replicate 4


title: NAC_0hr_control_6

description: Replicate 6


title: AMY_120hr_treated_5

description: Replicate 5


title: AMY_120hr_treated_3

description: Replicate 3


title: AMY_120hr_treated_2

description: Replicate 2


title: AMY_120hr_treated_6

description: Replicate 6


title: AMY_120hr_control_8

description: Replicate 8

source_name: amygdala, saline control, 120 hr


title: AMY_120hr_treated_1

description: Replicate 1


title: AMY_120hr_control_6

description: Replicate 6


title: AMY_120hr_control_5

description: Replicate 5


title: NAC_0hr_control_8

description: Replicate 8


title: AMY_120hr_control_3

description: Replicate 3


title: NAC_0hr_control_3

description: Replicate 3


title: AMY_120hr_control_1

description: Replicate 1


title: AMY_8hr_treated_7

description: Replicate 7

source_name: amygdala, ethanol vapor treated, 8 hr


title: AMY_8hr_treated_6

description: Replicate 6


title: AMY_120hr_control_4

description: Replicate 4


title: AMY_120hr_control_2

description: Replicate 2


title: AMY_8hr_treated_4

description: Replicate 4


title: AMY_8hr_treated_5

description: Replicate 5


title: PFC_0hr_treated_7

description: Replicate 7


title: AMY_8hr_treated_8

description: Replicate 8


title: AMY_8hr_treated_2

description: Replicate 2


title: AMY_8hr_treated_1

description: Replicate 1


title: AMY_8hr_control_8

description: Replicate 8

source_name: amygdala, saline control, 8 hr


title: AMY_8hr_control_4

description: Replicate 4


title: AMY_8hr_control_7

description: Replicate 7


title: AMY_0hr_treated_7

description: Replicate 7

source_name: amygdala, ethanol vapor treated, 0 hr


title: AMY_8hr_treated_3

description: Replicate 3


title: AMY_8hr_control_1

description: Replicate 1


title: AMY_0hr_treated_8

description: Replicate 8


title: AMY_8hr_control_3

description: Replicate 3


title: AMY_8hr_control_2

description: Replicate 2


title: AMY_0hr_treated_3

description: Replicate 3


title: AMY_8hr_control_6

description: Replicate 6


title: AMY_0hr_control_8

description: Replicate 8

source_name: amygdala, saline control, 0 hr


title: AMY_0hr_control_6

description: Replicate 6


title: AMY_0hr_treated_4

description: Replicate 4


title: AMY_0hr_treated_6

description: Replicate 6


title: AMY_0hr_control_3

description: Replicate 3


title: AMY_0hr_control_7

description: Replicate 7


title: AMY_0hr_treated_1

description: Replicate 1


title: AMY_0hr_control_2

description: Replicate 2


title: AMY_0hr_control_5

description: Replicate 5


title: AMY_0hr_treated_2

description: Replicate 2


title: AMY_0hr_control_4

description: Replicate 4


title: AMY_8hr_control_5

description: Replicate 5


title: AMY_0hr_control_1

description: Replicate 1


title: Ctrl1 TNF 24h rep2

status: Public on Oct 01 2014

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

institute: AstraZeneca, IMED RIA

description:
Ctrl1_TNF_24h_rep2
X5854953036_H

data_processing:
The data were normalised using quantile normalisation with in R. PALO (p<0.05 present in at least one) were used to filter the data.
Following background subtraction, the raw signal values extracted with Illumina Beadstudio version 2 software were quantile normalized

label: Biotin

source_name: Fibroblasts from healthy control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Cells were lysed in RLT + 1% β-Mercaptoethanol, RNA were isolated using Qiagen Rneasy mini kit

value: 5ng/ml TNF

tag: time (hours)

tag: disease type

value: healthy control

value: fibroblast


title: Ctrl1 NS 24h rep2

description:
Ctrl1_NS_24h_rep2
X5854953036_I

value: Non-stimulated


title: RBCK1-/- 2 IL1B 8h

description:
RBCK1-/- 2_IL1B_8h
X5854953036_A

source_name: Fibroblasts from RBCK1 deficient patient

value: 5ng/ml IL1B

value: RBCK1 deficient patient


title: AMY_0hr_treated_5

description: Replicate 5

tag: strain

value: adult (10-12 weeks)


title: Ctrl5 TNF 8h

description:
Ctrl5_TNF_8h
X5854953036_E


title: Myd88-/- IL1B 24h

description:
Myd88-/-_IL1B_24h
X5854953017_H

source_name: Fibroblasts from MyD88 deficient patient

value: MyD88 deficient patient


title: Myd88-/- TNF 8h

description:
Myd88-/-_TNF_8h
X5854953036_D


title: Nemo-/- TNF 24h rep2

description:
Nemo-/-_TNF_24h_rep2
X5854953036_K

source_name: Fibroblasts from NEMO deficient patient

value: NEMO deficient patient


title: Myd88-/- NS 24h rep2

description:
Myd88-/-_NS_24h_rep2
X5854953036_J


title: Myd88-/- NS 8h

description:
Myd88-/-_NS_8h
X5854953017_L


title: Ctrl1 IL1B 24h

description:
Ctrl1_IL1B_24h
X5854953036_B


title: Myd88-/- TNF 24h

description:
Myd88-/-_TNF_24h
X5854953036_C


title: Ctrl6 TNF 24h

description:
Ctrl6_TNF_24h
X5854953017_I


title: RBCK1-/- 2 NS 24h

description:
RBCK1-/- 2_NS_24h
X5854953017_K


title: Ctrl6 TNF 8h

description:
Ctrl6_TNF_8h
X5854953036_F


title: Ctrl6 NS 24h

description:
Ctrl6_NS_24h
X5854953017_J


title: Ctrl5 TNF 24h

description:
Ctrl5_TNF_24h
X5854953017_G


title: Ctrl6 IL1B 24h

description:
Ctrl6_IL1B_24h
X5854953017_F


title: Nemo-/- TNF 24h

description:
Nemo-/-_TNF_24h
X5854953017_E


title: RBCK1-/- 1 NS 8h

description:
RBCK1-/- 1_NS_8h
X5846793056_J


title: Ctrl5 NS 8h

description:
Ctrl5_NS_8h
X5854953017_D


title: RBCK1-/- 1 NS 24h

description:
RBCK1-/- 1_NS_24h
X5854953017_A


title: Ctrl5 IL1B 24h

description:
Ctrl5_IL1B_24h
X5854953017_C


title: Nemo-/- IL1B 24h

description:
Nemo-/-_IL1B_24h
X5854953017_B


title: Nemo-/- NS 24h

description:
Nemo-/-_NS_24h
X5846793056_E


title: Myd88-/- NS 24h

description:
Myd88-/-_NS_24h
X5846793056_I


title: RBCK1-/- 1 TNF 24h

description:
RBCK1-/- 1_TNF_24h
X5846793056_C


title: Nemo-/- NS 8h

description:
Nemo-/-_NS_8h
X5846793056_L


title: Myd88-/- IL1B 8h

description:
Myd88-/-_IL1B_8h
X5846793056_G


title: RBCK1-/- 1 IL1B 24h

description:
RBCK1-/- 1_IL1B_24h
X5846793006_I


title: Ctrl1 IL1B 8h

description:
Ctrl1_IL1B_8h
X5846793056_K


title: RBCK1-/- 1 TNF 8h

description:
RBCK1-/- 1_TNF_8h
X5846793056_F


title: Ctrl5 IL1B 8h

description:
Ctrl5_IL1B_8h
X5846793006_J


title: Ctrl5 NS 24h

description:
Ctrl5_NS_24h
X5846793006_K


title: Nemo-/- IL1B 8h

description:
Nemo-/-_IL1B_8h
X5846793056_D


title: RBCK1-/- 2 TNF 8h

description:
RBCK1-/- 2_TNF_8h
X5846793056_H


title: RBCK1-/- 2 TNF 24h

description:
RBCK1-/- 2_TNF_24h
X5846793006_L


title: Ctrl6 NS 8h

description:
Ctrl6_NS_8h
X5846793006_G


title: Ctrl1 NS 8h

description:
Ctrl1_NS_8h
X5846793056_A


title: RBCK1-/- 2 NS 8h

description:
RBCK1-/- 2_NS_8h
X5846793006_D


title: Ctrl6 IL1B 8h

description:
Ctrl6_IL1B_8h
X5846793006_H


title: Ctrl1 NS 24h

description:
Ctrl1_NS_24h
X5846793006_F


title: Nemo-/- TNF 8h

description:
Nemo-/-_TNF_8h
X5846793056_B


title: Ctrl1 TNF 24h

description:
Ctrl1_TNF_24h
X5846793006_C


title: UNIVREP_40610

status: Public on Dec 31 2012

city: Changsha

first: Chao

address: 110 Xiangya Road

institute: Central South University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed by RMA using Affymetrix Expression Console with default analysis settings.

source_name: parietal cortex from brain

label_protocol: GeneChip® WT Sense Target Labeling and Control Reagents.

extract_protocol: RNAs were extracted from the parietal cortex of 168 samples using the RNeasy Mini kit (Qiagen, Valencia, CA). The concentration and A260/A280 ratio were measured on the NanoDrop spectrophotometer. The 28S:18S rRNA ratio and RNA Integrity Number (RIN) were measured using an RNA LabChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Only RNA samples with a RIN >7 were used for the expression profiling.

value: parietal cortex

tag: disease status

tag: post-mortem interval (pmi)

tag: Sex

tag: ph


title: RBCK1-/- 1 IL1B 8h

description:
RBCK1-/- 1_IL1B_8h
X5846793006_B

tag: treatment

tag: cell type


title: UNIVREP_51210


title: RBCK1-/- 2 IL1B 24h

description:
RBCK1-/- 2_IL1B_24h
X5846793006_E

source_name: Fibroblasts RBCK1 deficient patient

value: Fibroblasts RBCK1 deficient patient


title: CC301_51110

source_name: parietal cortex from brain, unaffected control

value: unaffected

value: M


title: Ctrl1 TNF 8h

description:
Ctrl1_TNF_8h
X5846793006_A


title: UNIVREP_51310


title: CC303_51110

source_name: parietal cortex from brain, depression

value: depression

value: F


title: CC305_51110


title: UNIVREP_51110


title: UNIVREP_40910


title: UNIVREP_40710


title: CC302_51310


title: CC304_51110


title: CC296_51310


title: CC300_51310


title: UNIVREP_40810


title: CC297_51310


title: CC292_51310


title: CC299_51310

source_name: parietal cortex from brain, schizophrenia

value: schizophrenia


title: CC291_51310

source_name: parietal cortex from brain, bipolar

value: bipolar


title: CC288_51310


title: CC298_51310


title: CC287_51310


title: CC295_51310


title: CC289_51310


title: CC281_51310


title: CC279_51110


title: CC290_51110


title: CC283_51310


title: CC276_51210


title: CC285_51310


title: CC277_51210


title: CC278_51310


title: CC282_51310


title: CC280_51310


title: CC284_51310


title: CC274_51210


title: CC273_51210


title: CC275_51210


title: CC260_51110


title: CC261_51210


title: CC263_51210


title: CC293_51310


title: CC272_51210


title: CC271_51210


title: CC258_51210


title: CC268_51210


title: CC269_51110


title: CC267_51210


title: CC266_51210


title: CC257_51210


title: CC264_51210


title: CC250_51110


title: CC262_51210


title: CC286_51310


title: CC247_51310


title: CC265_51210


title: CC249_51110


title: CC294_51310


title: CC256_51210


title: CC270_51210


title: CC255_51210


title: CC251_51110


title: CC254_51210


title: CC248_51110


title: CC252_51210


title: CC244_40910


title: CC246_40910


title: CC241_40910


title: CC259_51210


title: CC234_40810


title: CC238_40610


title: CC252_51110


title: CC239_40910


title: CC240_40910


title: CC228_40810


title: CC242_40910


title: CC225_40810


title: CC243_40910


title: CC237_40910


title: CC236_40910


title: CC232_40810


title: CC229_40810


title: CC227_40610


title: CC226_40810


title: CC233_40810


title: CC220_40810


title: CC222_40810


title: CC218_40610


title: CC221_40810


title: CC217_40810


title: CC231_40810


title: CC215_40810


title: CC213_40810


title: CC212_40810


title: CC224_40810


title: CC210_40810


title: CC234_40910


title: CC216_40810


title: CC219_40810


title: CC209_40610


title: CC205_40710


title: CC207_40710


title: CC208_40710


title: CC204_40710


title: CC211_40810


title: CC206_40710


title: CC230_40810


title: CC245_40910


title: CC223_40810


title: CC198_40710


title: CC203_40710


title: CC201_40710


title: CC195_40710


title: CC196_40710


title: CC194_40710


title: CC193_40710

source_name: parietal cortex from brain, bipolar (not bipolar)

value: bipolar (not bipolar)


title: CC197_40710


title: CC189_40710


title: CC186_40710


title: CC184_40710


title: CC183_40610


title: CC177_40610


title: CC184_40610


title: CC180_40610


title: CC192_40610


title: CC190_40710


title: CC179_40610


title: CC182_40610


title: CC178_40610


title: CC188_40710


title: CC191_40710


title: CC175_40610


title: CC176_40610


title: CC172_40610


title: CC168_51110


title: CC174_40610


title: CC214_41410


title: CC199_40710


title: CC164_40610


title: CC173_40610


title: CC167_40610


title: CC181_40610


title: CC169_51110


title: CC187_40710


title: CC166_51110


title: CC163_51110


title: CC157_40910


title: CC202_40710


title: CC159_51110


title: CC158_40910


title: CC162_51110


title: CC155_40910


title: CC165_51110


title: CC171_40610


title: CC160_51110


title: CC170_51110


title: CC153_40910


title: CC154_40910


title: CC152_40910


title: CC156_40610


title: CC151_40910


title: CC161_51110


title: CC200_40710


title: CC150_40910


title: CC148_40910


title: CC149_40910


title: CC147_40910


title: CC145_40610


title: CC143_111109

source_name: cerebellum from brain, bipolar

extract_protocol: RNAs were extracted from the cerebellum of 144 samples using the RNeasy Mini kit (Qiagen, Valencia, CA). The concentration and A260/A280 ratio were measured on the NanoDrop spectrophotometer. The 28S:18S rRNA ratio and RNA Integrity Number (RIN) were measured using an RNA LabChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Only RNA samples with a RIN >7 were used for the expression profiling.

value: cerebellum


title: CC144_100909

source_name: cerebellum from brain, schizophrenia


title: CC142_100909

source_name: cerebellum from brain, depression


title: CC139_100909


title: CC136_100909


title: CC137_102309


title: CC138_102109


title: CC146_40910


title: CC135_100909


title: CC131_100909


title: CC129_102109


title: CC126_102109


title: CC116_102109


title: CC130_111109


title: CC114_102309


title: CC127_103009


title: CC112_102309


title: CC115_102309


title: CC110_102309


title: CC128_102109


title: CC110_103009


title: CC103_100909


title: CC95_100909


title: CC113_102309


title: CC102_103009


title: CC106_102309


title: CC103_111809


title: CC91_102309


title: CC107_111809


title: CC85_103009


title: CC86_103009


title: CC83_111809


title: CC89_103009


title: CC84_111809


title: CC133_102109


title: CC76_103009


title: CC70_111109


title: CC71_111809


title: CC79_111809


title: CC99_102109


title: CC65_111809


title: CC66_110409


title: CC63_102309


title: CC90_103009


title: CC72_111809


title: CC74_111109


title: CC69_111809


title: CC78_111109


title: CC63_102109


title: CC61_102109


title: CC56_102309


title: CC52_111809


title: CC58_111109


title: CC54_100909


title: CC57_111109


title: CC59_111109


title: CC51_111109


title: CC49_111109


title: CC43_111109


title: CC52_111109


title: CC41_111109


title: CC37_111809


title: CC40_111809


title: CC36_111809


title: CC35_111809


title: CC38_111809


title: CC34_103009


title: CC30_103009


title: CC28_103009


title: CC33_103009


title: CC24_102309


title: CC25_102309


title: CC42_111809


title: CC22_103009


title: CC20_102309


title: CC19_102309


title: CC21_102309


title: CC7_100909


title: CC14_102109


title: CC16_102109


title: CC18_102309


title: CC31_103009


title: CC10_102109


title: CC15_102109


title: CC12_102109


title: CC9_100909


title: CC5_102309


title: CC1_100909


title: CC5_102109


title: P1_IFNa_2h, rep

status: Public on Jul 30 2012

description:
Duplicate of 6116768041_A
6142069027_H

data_processing: The data were normalised using quantile normalisation with in R. PALO (p<0.05 present in at least one) were used to filter the data.

source_name: Fibroblasts from patient with TBK1 deficiency

tag: gender

value: female

tag: stimulation

value: IFNa

tag: concentration

tag: timepoints


title: CC3_100909


title: CC11_102109


title: TLR3p_IL1b_2h

source_name: Fibroblasts from patient with partial TLR3 deficiency


title: CC2_100909


title: STAT1_IL1b_2h

source_name: Fibroblasts from patient with STAT1 deficiency

value: male


title: TLR3p_PIC_2h

value: Poly I:C


title: TLR3_IL1b_2h

source_name: Fibroblasts from patient with TLR3 deficiency


title: CC5_100909


title: TLR3_PIC_2h, rep

description:
Duplicate of 6116768041_C
6142069027_J


title: TLR3p_PIC_8h


title: P2_IFNa_8h


title: STAT1_IFNa_2h


title: C16_IFNa_8h

source_name: Fibroblasts from healthy control


title: C8_PIC_2h


title: CC105_111109


title: P1_PIC_8h


title: P2_PIC_8h


title: P2_IL1b_8h


title: TLR3p_IFNa_8h


title: C8_IL1b_2h


title: C1_IFNa_2h


title: TLR3p_IFNa_2h


title: TLR3p_NS_

source_name: Fibroblasts from patient with partial TLR deficiency

value: NS


title: CC98_103009


title: P2_NS_


title: C8_PIC_8h


title: P1_IFNa_8h


title: C8_IFNa_2h


title: TLR3_PIC_8h


title: P2_IL1b_2h


title: C16_IL1b_2h


title: C8_NS_


title: C8_IFNa_8h


title: TLR3_NS_


title: C1_NS_


title: TLR3_IL1b_8h


title: C1_IFNa_8h


title: C16_NS_


title: STAT1_IL1b_8h


title: C16_PIC_2h


title: C16_IL1b_8h


title: P1_IL1b_2h


title: C8_IL1b_8h


title: C1_PIC_8h


title: STAT1_PIC_2h


title: STAT1_IFNa_8h


title: C16_IFNa_2h


title: P2_PIC_2h


title: C1_IL1b_2h


title: P1_PIC_2h


title: P2_IFNa_2h


title: TLR3p_IL1b_8h


title: P1_NS_


title: C16_PIC_8h


title: P1_IL1b_8h


title: C1_IL1b_8h


title: TLR3_IFNa_2h


title: C1_PIC_2h


title: TLR3_PIC_2h


title: STAT1_NS_


title: MIC3

status: Public on Mar 27 2012

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description:
tissue: synovial biopsy tissue (15–20 synovial samples per patient) was obtained by needle arthroscopy of the affected knee of patients with systemic lupus erythematosus (SLE n = 4), patients with rheumatoid arthritis (RA n = 7), patients with osteoarthritis (OA n = 5), patients with seronegative arthritis (SA, n = 4) and patients with microcrystalline arthritis (MIC n = 5). For each patient, 4–6 synovial samples were snap-frozen in liquid nitrogen and stored at −80° for later RNA extraction. The same amount of tissue was also kept at −80° for future immunostaining experiments on frozen sections. The remaining material was stored in formaldehyde and paraffin-embedded for conventional optical evaluation and immunostaining of selected cell markers.
patients: all patients with SLE met the American College of Rheumatology (ACR; formerly, the American Rheumatism Association) revised classification criteria for SLE (5), all were female, and the mean age was 32 years (range 19–40 years). All SLE patients had active articular disease at the time of synovial tissue sampling, and none had received immunosuppressive therapy; some of the SLE patients were receiving nonsteroidal antiinflammatory drugs. All patients with RA met the ACR classification criteria for RA (6) and all had early (<1 year's duration) active disease at the time of tissue sampling. Among the patients with RA, 2 were female and 5 were male, and the mean age was 51 years (range 37–69 years). In these patients, the mean C-reactive protein (CRP) level was 25 mg/liter (range 9–96 mg/liter), and the mean Disease Activity Score in 28 joints (including the CRP) (7) was 5.08 (range 3.76–5.82). None of the RA patients had received any treatment, except with nonsteroidal antiinflammatory drugs. Among the patients with OA, 5 were female and 1 was male, and the mean age was 63.2 years (range 51–73 years). The diagnosis of seronegative arthritis was based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement). The diagnosis of microcrystalline arthritis was based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid.

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts and originating from 39,000 genes; Affymetrix UK) were hybridized overnight at 45°C in monoplicate cultures with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the GeneChip Fluidics Station (Affymetrix UK).

scan_protocol: The slides were scanned on a GeneChip Scanner 3000.

data_processing:
For the initial normalization and data analysis steps, data were retrieved using Affymetrix GCOS software. The frequency of positive genes on each slide was 48–55%. After scaling of all probe sets to a value of 100, the amplification scale was reported to be between 1.1 and 2.5 for all slides. The signals yielded by the poly(A)-RNA, hybridization, and housekeeping controls (GAPDH 3′:5′ ratio <2) were indicative of the good quality of the amplification and hybridization procedures.
Statistical analyses of the microarray data were further performed using GeneSpring software (Agilent, Palo Alto, CA). For each slide, scaled data were normalized to the 50th percentile value for each chip and to the median value for each gene. The data were assessed by analysis of variance (ANOVA) with or without Benjamini-Hochberg corrections for multiple comparisons.

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with microcrystalline arthritis

label_protocol: Labeling of RNA (complementary RNA [cRNA] synthesis) was performed according to a standard Affymetrix procedure (One-Cycle Target Labeling kit; Affymetrix UK, High Wycombe, UK). Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using a T7-Oligo(dT) Promoter Primer kit (Affymetrix UK) and Superscript II reverse transcriptase. RNase H was then added together with Escherichia coli DNA polymerase I and E coli DNA ligase, followed by a short incubation with T4-DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated cRNA was cleaned and fragmented by a 35-minute incubation at 95°C.

extract_protocol: Total RNA was extracted from synovial biopsy tissue using the Nucleospin RNA II extraction kit (Macherey-Nagel, Düren, Germany), which included DNase treatment of the samples.

value: synovial biopsies

tag: disease

value: Microcrystalline arthritis

value: m


title: SA4

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with seronegative arthritis

tag: tissue

value: Seronegative arthritis


title: P1_IFNa_2h


title: SA1

value: f


title: MIC2

value: NSAIDs/colchicine


title: SLE4

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with lupus arthritis

value: Systemic lupus erythematosus


title: SLE2

value: NSAIDs


title: MIC5


title: SLE3


title: RA5

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with rheumatoid arthritis

value: Rheumatoid arthritis


title: SA3


title: RA4


title: SA2


title: MIC4

value: colchicine


title: RA3


title: OA2

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with osteoarthritis

value: Osteoarthritis


title: OA3


title: OA5


title: Patient 25

status: Public on Nov 17 2011

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

institute: University of Namur

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA)

data_processing: SDS files were processed in RQ manager software and raw data were then exported in XLS file

label: FAM

source_name: peritoneum

label_protocol: cDNA was prepared but no labelling was performed as TaqMan-based qRT-PCR was performed subsequently.

growth_protocol: The material was fresh-frozen at -70°C in RPMI1640 medium supplemented with 50% FCS and 20% DMSO at a ratio of 1:1 (Invitrogen, Carlsbad, CA, USA)

extract_protocol: Material was thawed and centrifuged at 1200rpm for 5 minutes in 15ml PBS. After an additional wash in 15ml PBS, total RNA was prepared using the Trizol method (Invitrogen, Carlsbad, CA, USA).

tag: disease state

value: peritoneal serous carcinoma

tag: figo stage

tag: grade

tag: residual disease (cm)

tag: chemotherapy prior to tapping

value: no

tag: sample type

value: effusion sample


title: SLE1

tag: age


title: RA7


title: RA2


title: RA1


title: MIC1


title: TLR3_IFNa_8h

value: male

value: IFNa


title: Patient 24

source_name: ovary

value: serous ovarian carcinoma

value: yes


title: Patient 7


title: Patient 3


title: Patient 22

value: unknown


title: Patient 23


title: Patient 6


title: Patient 5


title: Patient 2

source_name: fallopian tube

value: tubal serous carcinoma


title: Patient 18

value: not evaluated


title: RA6

value: synovial biopsies

value: m


title: Patient 16


title: Patient 17


title: OA1

value: f


title: Patient 15


title: Patient 20


title: Patient 30


title: Patient 13


title: Patient 21


title: Patient 4


title: Patient 12


title: Patient 11


title: Patient 1


title: Patient 10


title: Patient 9


title: Patient 32


title: Patient 14


title: Patient 8


title: Patient 19


title: OA4

value: NSAIDs


title: STAT1_PIC_8h

value: Poly I:C


title: Patient 27


title: Patient 31


title: Patient 29


title: Patient 28


title: Patient 26


title: PBMC MYD88-/- R848

status: Public on Oct 20 2011

source_name: PBMC from MYD88 deficient patient

tag: time point

value: PBMC

value: herpes simplex virus type 1 (HSV1) encephalitis (HSE) MYD88 deficient patient


title: PBMC TRIF-/- LPS

source_name: PBMC from TRIF deficient patient

value: LPS

value: herpes simplex virus type 1 (HSV1) encephalitis (HSE) TRIF deficient patient


title: PBMC MYD88-/- NS

value: Non stimulated


title: PBMC Ctrl NS

source_name: PBMC from healthy control

value: healthy control


title: PBMC Ctrl LPS


title: PBMC TRIF-/- R848


title: PBMC MYD88-/- LPS


title: PBMC Ctrl R848


title: Fibroblasts C2-/- PIC

value: Fibroblasts


title: Fibroblasts C3 NS


title: Fibroblasts C2 IL1B


title: Fibroblasts MYD88-/- IL1B

source_name: Fibroblasts from MYD88 deficient patient


title: Fibroblasts TLR3 PIC

source_name: Fibroblasts from TLR3 deficient patient

value: herpes simplex virus type 1 (HSV1) encephalitis (HSE) TLR3 deficient patient


title: PBMC TRIF-/- NS


title: Fibroblasts MYD88-/- PIC


title: Fibroblasts C1 IL1B


title: Fibroblasts C2 NS


title: Fibroblasts P1TRIF-/- PIC

source_name: Fibroblasts from TRIF deficient patient


title: Fibroblasts TLR3-/- IL1B


title: Fibroblasts C1 NS


title: Fibroblasts C1 PIC


title: Fibroblasts C3 IL1B


title: Fibroblasts C3 PIC


title: Fibroblasts MYD88-/- NS

value: NS


title: Fibroblasts P1TRIF-/- NS


title: Fibroblasts TLR3-/- NS


title: Fibroblasts P1TRIF-/- IL1B


title: T023, human gonadotrope/null cell tumor, biological rep 5

status: Public on Jan 31 2011

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures, using the Affy GCS3000

data_processing: Hybridization intensities were quantified and normalized across all arrays using the RMA algorithm with GC adjust available as an array processing tool on Partek® Genomics Suite™ 6.5 software (St.Louis, MS).  Data were filtered to remove all genes considered absent, as determined by the Affymetrix GeneChip Operating Software (GCOS), in greater than 95% of all the samples (22 out of 23 total samples).  Remaining transcripts (38,932 of 54,675) were used for all subsequent statistical and visual analysis.  A mixed model ANOVA was employed to estimate the batch effect and the data were adjusted using the Partek Batch Remover™ tool available on Partek Genomics Suite.

source_name: Human gonadotrope/null cell tumor collected at the time of transsphenoidal surgery

label_protocol: Microarray targets were prepared and labeled from 300ng of total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) following the manufactures instructions.

treatment_protocol: With informed consent, pituitary tumor samples were obtained from patients at University of Colorado Hospital at the time of transsphenoidal surgery. Portions of the specimens not used for histology and immunohistochemistry were placed in RNAlater and stored at -80C. Gonadotrope tumors were defined as demonstrating positive immunostaining for FSH, LH, or alpha subunit in greater than 5-10% of cells.  Null cell adenomas were defined by gonadotropic staining for FSH, LH, or alpha subunit in less than 5-10% of cells. Normal pituitary glands used as controls were obtained at autopsy within 2 - 18 hours of death from University of Colorado Denver Pathology Department.

tag: tissue (group)

value: Gonadotrope tumor

value: F

tag: subclass

tag: invasive

value: No

tag: recurrent


title: T149, human gonadotrope/null cell tumor, biological rep 13

tag: gender

value: M

value: Gonadotrope

value: Yes


title: T003, human gonadotrope/null cell tumor, biological rep 3


title: N029, normal pituitary, biological rep 8

source_name: Normal human pituitary obtained at autopsy within 2 - 18 hours of death

value: Normal pituitary


title: T018, human gonadotrope/null cell tumor, biological rep 4


title: T078, human gonadotrope/null cell tumor, biological rep 11


title: N028, normal pituitary, biological rep 7


title: T028, human gonadotrope/null cell tumor, biological rep 7


title: T001, human gonadotrope/null cell tumor, biological rep 1


title: N036, normal pituitary, biological rep 9


title: T176, human gonadotrope/null cell tumor, biological rep 14


title: T119, human gonadotrope/null cell tumor, biological rep 12


title: T034, human gonadotrope/null cell tumor, biological rep 10


title: T002, human gonadotrope/null cell tumor, biological rep 2


title: T032, human gonadotrope/null cell tumor, biological rep 9


title: N022, normal pituitary, biological rep 4


title: N025, normal pituitary, biological rep 5


title: N010, normal pituitary, biological rep 1


title: N019, normal pituitary, biological rep 3


title: N018, normal pituitary, biological rep 2


title: N027, normal pituitary, biological rep 6


title: 16MB IRF1 chip-chip in 6 hours IFNg-treated human Hela cells-rep2 of 3

status: Public on Jan 15 2009

type: genomic

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

description: Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucleotide probes at 30bp intervals tiling over non-repetitive 16MB selected genes (HG17).

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: log_2(Signal for Cy5 / Signal for Cy3)

source_name: Chromatin immunoprecipitated DNA using IRF1 antibody, HeLa cells with IFNg treatment for 6 hours

label_protocol: For NimbleGen arrays, ChIP DNA prepared from LM-PCR was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers or Cy3 (ChIP DNA isolated from different antibody immunoprecipitated cells) per manufacturer's protocol.

extract_protocol: HeLa cells were human IFNg-induced for 6 hrs, cross-linked with 1% formaldehyde at room temperature for 10 min, washed twice with ice-cold PBS, collected in 1 ml of PBS (3 x 107 cells per tube) and centrifuged in a bench-top microfuge for 5 min at 5000 r.p.m. Cells were resuspended in 1ml lysis buffer (50mM Tris-Cl pH 8.1, 10mM EDTA, 1% SDS) plus protease inhibitors, incubated on ice for 10 min and sonicated to an average size of 500 bp. Immunoprecipitation (IP) was performed overnight at 4°C with no antibody, anti-STAT1, anti-IRF1, anti-H3ac or anti-H4ac antibody. A aliquot of blocked Staph A cells (Calbiochem, 507862) were added per IP and incubated at RT for 15 min. Precipitates were washed sequentially with 1X dialysis buffer (2 mM EDTA, 50 mM Tris-Cl pH 8.0, 0.2% Sarkosyl) twice, IP wash buffer (100 mM Tris-Cl pH 9.0, 500 mM LiCl, 1% NP40, 1% deoxycholic acid) four times. Samples were extracted with IP elution buffer (50 mM NaHCO3 and 1% SDS), heated at 65°C overnight to reverse cross-links, and DNA fragments purified with QIAEX II gel extraction Kit. LM-PCR was performed using the annealed linker primers oJW102 (5'-GCGGTGACCCGGGAGATCTGAATTC-3') and oJW103 (5'-GAATTCAGATC-3'). Chromatin DNA was blunted using T4 DNA polymerase at 37oC for 45~60 min, and purified using Qiaquick PCR purification kit. Blunted chromatin DNA was ligated to the linker at 16oC over night and purified. The sample was amplified with the following conditions: one cycle at 55oC for 2 min, 72oC for 5 min and 95oC for 2 min; followed by 20 cycles at 95oC for 30 seconds, 55oC for 30 seconds and 72oC for 1 min and one cycle at 72oC for 4 min. DNA was finally purified using Qiaquick.

tag: cell type

value: Hela

source_name: Input DNA from HeLa cells with IFNg treatment for 6 hours


title: 16MB STAT1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipitated DNA using STAT1 antibody, HeLa cells without IFNg treatment for 6 hours

source_name: Input DNA from HeLa cells without IFNg treatment for 6 hours


title: 16MB IRF1 chip-chip in 6 hours IFNg-treated human Hela cells-rep3 of 3


title: 16MB IRF1 chip-chip in 6 hours IFNg-treated human Hela cells-rep1 of 3


title: Moderate 1037

status: Public on Jul 19 2004

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description:
Moderate AD (MMSE14-19); correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray

source_name: hippocampal CA1 tissue

tag: ref #

tag: group

value: Moderate

tag: nft

tag: braak

tag: mmse

tag: Sex

tag: pmi


title: Control 1040

description:
Control (MMSE>25); correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray

value: Control


title: 16MB IRF1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep2 of 3

source_name: Chromatin immunoprecipitated DNA using IRF1 antibody, HeLa cells without IFNg treatment for 6 hours


title: 16MB IRF1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep3 of 3


title: Control 1039


title: Incipient 1043

description:
Incipient AD (MMSE 20-26); correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray

value: Incipient


title: 16 MB H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep2 of 3

description: Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 16MB selected locus(HG17)

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells without IFNg treatment for 6 hours


title: T030, human gonadotrope/null cell tumor, biological rep 8


title: Severe 1036

description:
Severe AD (MMSE<14); correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray

value: Severe


title: Incipient 1034


title: T024, human gonadotrope/null cell tumor, biological rep 6


title: 16MB STAT1 chip-chip in 6 hours IFNg-treated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipitated DNA using STAT1 antibody, HeLa cells with IFNg treatment for 6 hours


title: 16MB STAT1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep2 of 3


title: 16MB H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells without IFNg treatment for 6 hours


title: 16 MB H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep2 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells with no IFNg treatment for 6 hours


title: 16MB IRF1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep1 of 3


title: Moderate 1020


title: 16MB STAT1 chip-chip in 6 hours IFNg-untreated human Hela cells-rep1 of 3

description: Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucleotide probes at 30bp intervals tiling over non-repetitive 16MB selected locus (HG17).


title: 16MB H4 acetylation in 6 hours IFNg-treated human Hela cells-rep3 of 3

description: Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 16MB selected genes(HG17)

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells with IFNg treatment for 6 hours


title: 16MB H4 acetylation in 6 hours IFNg-treated human Hela cells-rep2 of 3


title: 16 MB H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep1 of 3


title: 16MB H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep2 of 3


title: 16MB STAT1 chip-chip in 6 hours IFNg-treated human Hela cells-rep1 of 3


title: 16MB H3 acetylation in 6 hours IFNg-treated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells with IFNg treatment for 6 hours


title: 16MB H4 acetylation in 6 hours IFNg-treated human Hela cells-rep1 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells with IFNg treated for 6 hours


title: 16MB STAT1 chip-chip in 6 hours IFNg-treated human Hela cells-rep2 of 3


title: H3 acetylation in 6 hours IFNg-treated human Hela cells-rep1 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells treated with IFNg for 6 hours

source_name: Input DNA from HeLa cells IFNg treated for 6 hours


title: H3 acetylation in 6 hours IFNg-treated human Hela cells-rep2 of 3


title: 16 MB H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep1 of 3


title: Moderate 1031


title: Moderate 965

description:
Moderate AD (MMSE14-19); correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores
Keywords = bioinformatics
Keywords = gene expresion
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray


title: Control 1015


title: Severe 723


title: Control  976


title: Control 1018


title: Incipient 715


title: Severe 819


title: Incipient 1019


title: Incipient 720


title: Moderate 856


title: Severe 701


title: Moderate 826


title: Control 1012


title: Incipient 994


title: Moderate 832


title: Moderate 1025


title: Control 1008


title: Severe 872


title: Control 1003


title: Severe 867


title: Severe 807


title: Incipient 1029


title: Control 1030


title: Sensitive stage x-ray treated No.3

status: Public on Jun 29 2004

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

description: X-ray treated, 15-20 minutes after treatment

organism: Drosophila melanogaster

source_name: C-S embryos at stage 9-11


title: Resistant stage control No.2

description: Control

source_name: C-S embryos at stage 13-15


title: resistant stage x-ray treated No.3


title: Sensitive stage control (No.3)

description: Control


title: Sensitive stage x-ray No. 2

description: x-ray treated, 15-20 minutes after treatment


title: resistant stage control No3

description: Control


title: Resistant stage x-ray 1

description: X-ray treated, 15-20minutes after treatment


title: Sensitive stage control 2

description: Control


title: Resistant stage control 1

description: Control


title: sensitive stage control 1

description: control for x-ray

source_name: C-S embryo at stage 9-11


title: Sensitive stage X-ray treated 1


title: resistant stage x-ray treated, No.2