title: MTB/TRAS tumor 5

city: Philadelphia

first: Lewis

middle: A.

last: Chodosh

state: PA

address: 421 curie blvd, BRB II/III 616

department: Cancer Biology

institute: University of Pennsylvania

description: Mammary gland tumors induced by Hras

hyb_protocol: Affymetrix Generic Hybrdization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: The data were analyzed with GCRMA using R and quantile normalized

label: Biotin

source_name: Mammary Gland tumor induced by oncogenic Hras

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: NMuMG, was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum, 1% penicillin/streptomycin, and 2 mM L-glutamine.

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

treatment_protocol: Mammary tissue was harvested at different post-induction time points and snap frozen.  To generate Ras-driven tumors, MTB/TRAS mice were administered 0.012 mg/ml doxycycline in their drinking water and monitored for tumor formation.  Tumors were harvested at 1-cm

tag: Genotype

value: MTB/TRAS; Gender:Female; Tissue:Mammary gland tumor; Strain:FVB


title: MTB/TRAS tumor 6

status: Public on Dec 22 2008

type: RNA

country: USA

description: Mammary gland tumors induced by Hras

molecule: total RNA

organism: Mus musculus


title: CD8_18_aGVHD(-)

city: Minato-ku

first: Naoyuki

last: Takahashi

state: Tokyo

address: 4-6-1, Shirokanedai

department: Research Hospital

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: The probes for 8 positive control genes (ACTB, ATP5F1, GAPD, GTF2B, PLA2G5, RPS5, TFRC, and K-ALPHA-1/TUBA1B) were spotted on a total of 24 spots and those for 4 negative control genes (lambda A, lambda B, Omp A1, and Omp A2) were spotted on a total of 12 spots, while nothing was spotted on 33 spots.  Therefore, a total of 69 spot data were already eliminated from the whole 684 spot data on the Genopal array IMS human 0.6K v.2.

hyb_protocol: Hybridization was performed according to Mitsubishi Rayon’s protocol ver. 2.  Briefly, 10 μg of biotin-modified aRNA, which was fragmented using Fragmentation Reagents (Ambion), was suspended in buffer A1 containing 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, and 0.05% Tween 20.  The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon).  Hybridization was carried out at 65°C for 16 hr with the chamber rotating slowly.  Microarrays were washed by soaking twice in buffer A1 at 65°C for 20 min, then once in buffer A2 containing 0.12 M Tris-HCl (pH 7.5) and 0.12 M NaCl, at 65°C for 10 min, and finally left at rest for 60 min at room temperature.  Microarrays were stained with 2 μg/ml Streptavidin-Cy5 (GE Healthcare) in buffer A2 at room temperature for 30 min, then washed 4 times by soaking in buffer A1 at room temperature each for 5 min.

scan_protocol: The arrays were then scanned to obtain images using a cooled CCD-type DNA chip image analyzer (Mitsubishi Rayon).  Fluorescent intensity of images was quantified automatically with the software developed by Mitsubishi Rayon Co., Ltd.

data_processing:
To identify differentially-expressed genes during acute GVHD versus recovery phase, the raw signal intensity data were processed as follows.
To obtain gene-specific signal intensity data, the raw value for lambda A (negative control) in the same block was subtracted.
Secondly, paired gene-specific data (aGVHD(+) vs. aGVHD(−)) were discarded, if both values were lower than a threshold of 100 counts/sec.  If only one of the paired gene-specific values was lower than 100 counts/sec, it was replaced by 100 counts/sec.
Thirdly, these filtered gene-specific data were normalized within each block.  Since each block on a microarray did not contain enough number of spots to justify an assumption that median log-ratio of all the genes within a block should be zero, we examined other normalization methods.  To this purpose, we compared M-A scatter plots (i.e., scatter plots of log-ratios (M) versus averages of log-intensities (A) for paired data) for each block, for the following normalization methods.  The first is median-centering of log-ratio for a selected set of housekeeping genes (GAPDH, ACTB, RPS5, and K-ALPHA-1/TUBA1B) which were abundantly expressed in every subset of PBMCs.  The second is normalization by GAPDH gene.  The third is lowess normalization using lowess function (‘stats’ package) in R language (http://www.r-project.org/), with the lowess smoothing parameter f set to 0.4.  Most of the M-A plots, especially for low intensity data spots, were distributed unequally around 0 value of M-axis, if normalization was performed by the selected housekeeping genes (first method) or GAPDH (second method).  It seemed, therefore, to be most appropriate to perform normalization by lowess method to avoid false positive results, especially for low intensity data spots.  Consequently, we used lowess normalized data in the subsequent analysis.
Finally, significance analysis of microarray (SAM) (Tusher VG et al. Proc Natl Acad Sci USA 98: 5116-5121, 2001) was carried out to evaluate differential gene expression during acute GVHD compared to recovery phase, with false discovery rate (FDR) lower than 10%, using 'samr' package in R language.

label: biotin

organism: Homo sapiens

source_name: CD8+ subsets, case IMS18, recovery

label_protocol: Total RNA of each subset of PBMCs derived from 10 ml of peripheral blood, was reverse-transcribed with oligo (dT) primer bearing a T7 promoter and transcribed in vitro to synthesize biotin-modified antisense RNA (aRNA) using MessageAmp II-Biotin Enhanced kit (Ambion), according to Mitsubishi Rayon’s protocol ver. 2.  For some specimens, which contained too few cells to obtain enough amount of aRNA for array hybridization by single round amplification, amplification was performed two rounds, using MessageAmp II aRNA Amplification Kit (Ambion) in addition to MessageAmp II-Biotin Enhanced kit, according to the manufacturer’s protocol.

extract_protocol:
Ten milliliter of peripheral blood was centrifuged over Histopaque 1077 (Sigma, St. Louis, USA) at 500 × g for 15 minutes to isolate mononuclear cells, which were then washed with RPMI 1640 media.  CD8+, CD56+, CD4+, and CD14+ cell subsets were isolated from the peripheral blood mononuclear cells (PBMCs) in this order by employing CD8 MicroBeads, CD56 MicroBeads, CD4 MicroBeads, and CD14 MicroBeads, respectively (Miltenyi Biotec GmbH, Germany), and then lyzed immediately in TRIZOL® reagent (Invitrogen, California, USA).  Total RNA was extracted and then purified using RNeasy® Micro kit (Qiagen, Valencia, CA) with on-column DNase digestion, according to the manufacturer’s protocol.
For each subset of PBMCs of a patient, paired samples (taken during acute GVHD (aGVHD(+)) versus taken upon discharge (aGVHD(−))) were handled in the same way and in parallel for every step of the following procedure, from total RNA extracting to scanning the arrays, according to Mitsubishi Rayon’s protocol ver. 2.

tag: Subsets

tag: Status

value: during recovery phase

tag: Case

tag: AGE

tag: SEX

value: M

tag: Diagnosis

value: MDS (→AML)

tag: Grading of acute GVHD

value: 2 (skin; 3, gut; 0, liver; 0)


title: MTB/TRAS tumor 4

description: Mammary gland tumors induced by Hras


title: CD8_17_aGVHD(+)

source_name: CD8+ subsets, case IMS17, aGVHD

value: during acute GVHD

value: F

value: NHL (LBL)

value: 1 (skin; 2, gut; 0, liver; 0)


title: Lean_needle biopsy_subject 2

city: Paris

first: David

middle: M

last: Mutch

address: Centre de Recherche des Cordeliers (CRC), 15 rue de l'école de médecine

department: Nutrition and Metabolism

country: France

institute: INSERM UMRS U872 (Eq 7) Nutriomique

description: Lean_needle biopsy_subject 2

hyb_protocol: Agilent Low RNA Input Linear Amplification kit

scan_protocol: microarrays scanned using an AXON scanner and data visualized using GenePix software

data_processing: Lowess normalized using Goulphar software, background signal not removed

source_name: subcutaneous adipose tissue, lean needle biopsy

extract_protocol: Qiagen RNeasy total RNA Mini kit

treatment_protocol: tissue samples stored at -80°C until used

tag: Gender

source_name: In-house adipose tissue reference pool

tag: subjects all undergoing plastic surgery


title: CD8_17_aGVHD(-)

source_name: CD8+ subsets, case IMS17, recovery


title: CD8_13_aGVHD(+)

source_name: CD8+ subsets, case IMS13, aGVHD

value: AML (M3)


title: MTB/TRAS tumor 3

description: Mammary gland tumors induced by Hras


title: MTB/TRAS tumor 1

description: Mammary gland tumors induced by Hras


title: MTB/TRAS tumor 2

description: Mammary gland tumors induced by Hras


title: CD8_13_aGVHD(-)

source_name: CD8+ subsets, case IMS13, recovery


title: CD8_11_aGVHD(-)

source_name: CD8+ subsets, case IMS11, recovery

value: AML (M2)


title: CD8_11_aGVHD(+)

source_name: CD8+ subsets, case IMS11, aGVHD


title: CD4_25_aGVHD(-)

source_name: CD4+ subsets, case IMS25, recovery

value: ALL (L2)


title: NMuMG TGFB3 rep 1

description: NMuMG cells treated with TGFbeta3

source_name: Mammary Gland cell line 24hr TGFb3 treated

tag: Non-transformed mammary epithelial cells


title: CD4_25_aGVHD(+)

source_name: CD4+ subsets, case IMS25, aGVHD


title: NMuMG TGFB3 rep2

description: NMuMG cells treated with TGFbeta3


title: CD4_18_aGVHD(+)

source_name: CD4+ subsets, case IMS18, aGVHD


title: NMuMG TGFB3 rep3

description: NMuMG cells treated with TGFbeta3


title: NMuMG TGFB1 rep2

description: NMuMG cells treated with TGFbeta1

source_name: Mammary Gland cell line 24hr TGFb1 treated


title: CD4_18_aGVHD(-)

source_name: CD4+ subsets, case IMS18, recovery


title: NMuMG TGFB1 rep3

description: NMuMG cells treated with TGFbeta1


title: NMuMG control rep2

description: NMuMG cells untreated

source_name: Mammary Gland cell line untreated


title: NMuMG TGFB1 rep 1

description: NMuMG cells treated with TGFbeta1


title: CD4_17_aGVHD(+)

source_name: CD4+ subsets, case IMS17, aGVHD


title: NMuMG control rep 1

description: NMuMG cells untreated


title: CD4_17_aGVHD(-)

source_name: CD4+ subsets, case IMS17, recovery


title: CD4_13_aGVHD(-)

source_name: CD4+ subsets, case IMS13, recovery


title: CD4_13_aGVHD(+)

source_name: CD4+ subsets, case IMS13, aGVHD


title: CD4_11_aGVHD(+)

source_name: CD4+ subsets, case IMS11, aGVHD


title: CD4_11_aGVHD(-)

source_name: CD4+ subsets, case IMS11, recovery


title: MTB/TRAS 8d rep2

description: MTB/TRAS induced for 8 day

source_name: Mammary Gland 8d Ras induction

value: MTB/TRAS; Gender:Female; Tissue:Mammary gland; Strain:FVB


title: MTB/TRAS 14d rep2

description: MTB/TRAS induced for 14day

source_name: Mammary Gland 14d Ras induction


title: NMuMG control rep3

description: NMuMG cells untreated


title: MTB/TRAS 14d rep 1

description: MTB/TRAS induced for 14day


title: MTB/TRAS 8d rep3

description: MTB/TRAS induced for 8 day


title: Endometriosis-15

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChipHuman U133A arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 2500 Scanner (Affymetrix).

source_name: endometriosis, broard ligament

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

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy purification were performed according to the manufacturer's instructions.

tag: endometriosis, broard ligament


title: Endometriosis-18


title: MTB/TRAS 8d rep 1

description: MTB/TRAS induced for 8 day


title: Endometriosis-16


title: MTB/TRAS 48hr rep3

description: MTB/TRAS induced for 48hr

source_name: Mammary Gland 48hr Ras induction


title: MTB/TRAS 96hr rep2

description: MTB/TRAS induced for 96hr

source_name: Mammary Gland 96hr Ras induction


title: MTB/TRAS 96hr rep3

description: MTB/TRAS induced for 96hr


title: MTB/TRAS 96hr rep 1

description: MTB/TRAS induced for 96hr


title: MTB/TRAS 48hr rep2

description: MTB/TRAS induced for 48hr


title: MTB/TRAS 48hr rep 1

description: MTB/TRAS induced for 48hr


title: Endometriosis-14


title: MTB/TRAS 24hr rep3

description: MTB/TRAS induced for 24 hr

source_name: Mammary Gland 24hr Ras induction


title: Endometriosis-5

source_name: endometriosis, peritoneal

tag: endometriosis, peritoneal


title: Endometriosis-6


title: Endometriosis-7


title: Endometrium-18

source_name: eutopic endometrium

tag: eutopic endometrium


title: Endometriosis-3


title: Endometrium-16


title: MTB/TRAS 24hr rep2

description: MTB/TRAS induced for 24 hr


title: MTB/TRAS 24hr rep 1

description: MTB/TRAS induced for 24 hr


title: Endometriosis-12


title: MTB/TRAS 0hr rep3

description: MTB/TRAS uninduced

source_name: Mammary Gland uninduced


title: MTB/TRAS 0hr rep2

description: MTB/TRAS uninduced


title: Endometrium-14


title: Gingival tissue sample 1 from patient 95, Affected site

city: New York

first: Ryan

middle: T

last: Demmer

state: NY

department: Epidemiology

institute: Columbia University

description: A total of 90 subjects with moderate to severe periodontitis (63 with chronic and 27 with aggressive periodontitis) were recruited among the patients referred for periodontal therapy to the Clinic for Post-doctoral Periodontics, Columbia University College of Dental Medicine. Eligible patients were (i) at least 13 yr old; (ii) had a minimum of 24 teeth present; (iii) had no past history of systematic periodontal therapy other than occasional prophylaxis provided by the referring general dentist, (iv) had received no systemic antibiotics or anti-inflammatory drugs for at least 6 months, (v) harbored a minimum of 4 teeth with radiographic bone loss, (vi) did not suffer from diabetes mellitus, (vii) did not suffer from any of the systemic conditions or genetic disorders that entail a diagnosis of 'Periodontitis as a manifestation of systemic diseases', (viii) were not pregnant, and (ix) were not current users of tobacco products or of nicotine replacement medication. Signed informed consent was obtained prior to enrollment. All participants underwent a full-mouth examination of the periodontal tissues at six sites per tooth, using a manual probe. The examination included assessments of presence/absence of dental plaque and bleeding on probing (BoP), and linear measurements of probing pocket depth (PPD) and clinical attachment level (CAL).  'Diseased' sites showed BoP, had an interproximal PPD of>3 mm, and a concomitant CAL of>2 mm. 'Healthy' sites showed no BoP, had PPD of<5 mm and CAL of<3 mm. A software program identified (i) maxillary 'diseased' and 'healthy' interdental papillae, based on the above criteria and (ii) pairs of diseased interdental papillae with similar clinical presentation, i.e., with PPD and CAL within 2 mm of each other. A posterior maxillary sextant encompassing a pair of qualifying 'diseased' interdental papillae was identified.  Periodontal surgery was performed at the identified sextant without any prior supra- or subgingival instrumentation. After infiltration with an appropriate local anesthetic, submarginal incisions were performed, mucoperiosteal flaps were reflected, and the portion of each interproximal gingival papilla that adhered to the root surface was carefully dissected. This section comprised the ulcerated epithelial lining of the interproximal periodontal pockets and a portion of the underlying connective tissue.

hyb_protocol: According to the manufacturer's instructions.

data_processing: All CEL files in the series were processed using RMA in R using justRMA with default parameters.

source_name: Patient 95 gingival tissue sample collected as Affected

label_protocol: Synthesis of Biotin-Labeled cRNA was performed using the GeneChip Expression 3'-Amplification Reagents for IVT labeling kit (Affymetrix). The cRNA yield was determined spectrophotometrically at 260 nm. Finally, the cRNA was fragmented by incubation in fragmentation buffer  at 94 0C for 35 min and stored at –80 0C until hybridizations.

extract_protocol: Gingival tissue specimens were homogenized in Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA collected in the upper aqueous phase was precipitated by mixing with isopropyl alcohol and additional centrifugation and washed in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The purified RNA was quantitated spectrophotometrically, and 7.5 micrograms of total RNA was reverse transcribed using GeneChip Expression 3' amplification one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.

treatment_protocol: After collection gingival tissue specimens were thoroughly rinsed with sterile normal saline solution and transferred into Eppendorf tubes containing 5 volumes of a RNA stabilization reagent (RNAlater, Ambion, Austin, TX, USA).  Specimens were stored in RNAlater overnight at 4.0 C and thereafter snap-frozen and stored in liquid nitrogen. All further processing occurred simultaneously for gingival biopsies originating from the same donor.

tag: Gingival tissue phenotype

value: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)

tag: Tissue

value: Gingival


title: Endometrium-15


title: xenograft  14 day mouse array replicate 2

data_processing: MAS5.0 was used for initial data extraction, raw data normalised to the internal spikes using R.  Human and mouse orthologues and homologues were identified using Netaffix and only those transcripts used for further analysis.

organism:
Homo sapiens
Mus musculus

tag: xenograft, day 14 post implantation on mouse chip


title: Gingival tissue sample 2 from patient 95, Affected site

scan_protocol: According to the manufacturer's instructions.


title: Endometrium-12


title: MTB/TRAS 0hr rep 1

description: MTB/TRAS uninduced

tag: Genotype


title: Gingival tissue sample 2 from patient 94, Affected site

source_name: Patient 94 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 94, Unaffected site

source_name: Patient 94 gingival tissue sample collected as Unaffected

value: Healthy (no BoP + PPD of<5 mm + CAL of<3 2 mm


title: Lean_surgical biopsy_subject 3

description: Lean_surgical biopsy_subject 3

source_name: subcutaneous adipose tissue, lean surgical biopsy

label_protocol: Agilent Low RNA Input Linear Amplification kit

value: Female, Biopsy Technique:surgical

source_name: In-house adipose tissue reference pool


title: xenograft  14 day mouse array replicate 1


title: xenograft  10 day mouse array replicate 2

tag: xenograft, day 10 post implantation on mouse chip


title: Endometrium-7


title: Gingival tissue sample 1 from patient 93, Affected site

source_name: Patient 93 gingival tissue sample collected as Affected


title: Endometrium-6


title: Gingival tissue sample 1 from patient 94, Affected site


title: Gingival tissue sample 2 from patient 93, Affected site


title: Gingival tissue sample 3 from patient 92, Unaffected site

source_name: Patient 92 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 93, Unaffected site

source_name: Patient 93 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 92, Affected site

source_name: Patient 92 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 92, Affected site


title: Gingival tissue sample 3 from patient 91, Unaffected site

source_name: Patient 91 gingival tissue sample collected as Unaffected


title: Endometrium-5


title: xenograft  10 day mouse array replicate 1


title: Gingival tissue sample 3 from patient 95, Unaffected site

source_name: Patient 95 gingival tissue sample collected as Unaffected


title: xenograft  7 day mouse array replicate 1

description: xenograft  7 day mouse array replicate 1

source_name: xenograft  7 day mouse array replicate 1

tag: xenograft, day 7 post implantation on mouse chip


title: xenograft  7 day mouse array replicate 2

description: xenograft  7 day mouse array replicate 2

source_name: xenograft  7 day mouse array replicate 2


title: CD56_8_aGVHD(+)

description: The probes for 8 positive control genes (ACTB, ATP5F1, GAPD, GTF2B, PLA2G5, RPS5, TFRC, and K-ALPHA-1/TUBA1B) were spotted on a total of 48 spots and those for 4 negative control genes (lambda A, lambda B, Omp A1, and Omp A2) were spotted on a total of 24 spots, while nothing was spotted on 17 spots.  Therefore, a total of 89 spot data were already eliminated from the whole 684 spot data on the Genopal array IMS human 0.6K v.1.

hyb_protocol: Hybridization was performed according to Mitsubishi Rayon’s protocol ver. 1.  Briefly, 10 μg of biotin-modified aRNA, which was fragmented using Fragmentation Reagents (Ambion), was suspended in 2×SSC and 0.2% SDS.  The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon).  Hybridization was carried out at 65°C for 16 hr with the chamber rotating slowly.  Microarrays were washed by soaking twice in 1×SSC and 0.2% SDS at 45°C for 20 min, then once in 0.1×SSC at 45°C for 10 min, and finally left at rest for 60 min at room temperature.  Microarrays were stained with 2 μg/ml Streptavidin-Cy5 (GE Healthcare) in 0.1 M Tris-HCl (pH 7.5) and 0.15 M NaCl at room temperature for 30 min, then washed 4 times by soaking in 0.1 M Tris-HCl (pH 7.5), 0.15 M NaCl, and 0.05% Tween 20, at room temperature each for 5 min.

data_processing:
To identify differentially-expressed genes during acute GVHD versus recovery phase, the raw signal intensity data were processed as follows.
To obtain gene-specific signal intensity data, the raw value for lambda A (negative control) in the same block was subtracted.
Secondly, paired gene-specific data (aGVHD(+) vs. aGVHD(−)) were discarded, if both values were lower than a threshold of 100 counts/sec.  If only one of the paired gene-specific values was lower than 100 counts/sec, it was replaced by 100 counts/sec.
Thirdly, these filtered gene-specific data were normalized within each block.  Since each block on a microarray did not contain enough number of spots to justify an assumption that median log-ratio of all the genes within a block should be zero, we examined other normalization methods.  To this purpose, we compared M-A scatter plots (i.e., scatter plots of log-ratios (M) versus averages of log-intensities (A) for paired data) for each block, for the following normalization methods.  The first is median-centering of log-ratio for a selected set of housekeeping genes (GAPDH, ACTB, RPS5, and K-ALPHA-1/TUBA1B) which were abundantly expressed in every subset of PBMCs.  The second is normalization by GAPDH gene.  The third is lowess normalization using lowess function (‘stats’ package) in R language (http://www.r-project.org/), with the lowess smoothing parameter f set to 0.4.  Most of the M-A plots, especially for low intensity data spots, were distributed unequally around 0 value of M-axis, if normalization was performed by the selected housekeeping genes (first method) or GAPDH (second method).  It seemed, therefore, to be most appropriate to perform normalization by lowess method to avoid false positive results, especially for low intensity data spots.  Consequently, we used lowess normalized data in the subsequent analysis.

source_name: CD56+ subsets, case IMS8, aGVHD

label_protocol: Total RNA of each subset of PBMCs derived from 10 ml of peripheral blood, was reverse-transcribed using T7-Oligo(dT)24 Promoter Primer (Ambion) and SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen).  In order to synthesize enough amount of biotin-modified antisense RNA (aRNA) for array hybridization, 2 rounds of amplification was performed, using T7-Oligo(dT)24 Promoter Primer, SuperScript™ Double-Stranded cDNA Synthesis kit, QIAquick PCR Purification kit (QIAGEN), BioArray™ HighYield™ RNA Transcript Labeling kit (T7) (ENZO), Rneasy MinElute Cleanup kit (QIAGEN), and random primer (Invitrogen), according to Mitsubishi Rayon’s protocol ver. 1.

extract_protocol:
Ten milliliter of peripheral blood was centrifuged over Histopaque 1077 (Sigma, St. Louis, USA) at 500 × g for 15 minutes to isolate mononuclear cells, which were then washed with RPMI 1640 media.  CD8+, CD56+, CD4+, and CD14+ cell subsets were isolated from the peripheral blood mononuclear cells (PBMCs) in this order by employing CD8 MicroBeads, CD56 MicroBeads, CD4 MicroBeads, and CD14 MicroBeads, respectively (Miltenyi Biotec GmbH, Germany), and then lyzed immediately in TRIZOL® reagent (Invitrogen, California, USA).  Total RNA was extracted and then purified using RNeasy® Micro kit (Qiagen, Valencia, CA) with on-column DNase digestion, according to the manufacturer’s protocol.
For each subset of PBMCs of a patient, paired samples (taken during acute GVHD (aGVHD(+)) versus taken upon discharge (aGVHD(−))) were handled in the same way and in parallel for every step of the following procedure, from total RNA extracting to scanning the arrays, according to Mitsubishi Rayon’s protocol ver. 1.

tag: Subsets

tag: Status

tag: Case

value: 2 (skin; 2, gut; 1, liver; 0)


title: Endometrium-3


title: Gingival tissue sample 1 from patient 91, Affected site

source_name: Patient 91 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 91, Affected site


title: Gingival tissue sample 2 from patient 90, Affected site

source_name: Patient 90 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 90, Unaffected site

source_name: Patient 90 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 9, Unaffected site

source_name: Patient 9 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 90, Affected site


title: wt collar chip

city: Beijing

first: Lei

last: Wang

state: Beijing

address: Nanxincun 20, Development center 214,Haidian district

country: China

institute: Institute of Botany, CAS

description: All the processes for cDNA and cRNA synthesis, cRNA fragmentation, hybridization, washing and staining, and scanning, were conducted according to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix). Poly-A RNA Control Kit and the One-Cycle cDNA Synthesis kit were used in this experiment as described in the website: http://www.affymetrix.com/products/arrays/specific/rice.affx.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix TeraGenomics; GCOS software (Affymetrix GeneChip Operating Software) was used for data collection and normalization.

molecule: polyA RNA

organism: Oryza sativa

source_name: Collars from wild type rice

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: After seeds germination 2 weeks in MS media, transfer the seedling in the field to grow until heading stage.

extract_protocol: 30 collars were taken from wild type plants or antiOsLIC transgenic plants respectively. One collar from one plant only. The leaves are just sprout 2-3 cm (about 1-2 days) from the stem. For measuring the genes expression level, Wild type plants were taken as control. The developing collar from both line2 of OsLIC antisense transgenic plants and wild type were harvested at the heading stage. The position of the collar was about 1cm above the last developed collar. Total RNA was extracted from the collars using TRIzol regeant (Invitrogen, P/N 15596-018, USA) and purified by using Qiagen RNeasy columns (QIAGEN, Cat. NO. 74104).

treatment_protocol: The wild type palnts and transgenic plants treat in same conditions (same field and same temperature condition).

tag: wild type plants

tag: Developing collar about 2-3 mm length in tillering stage (90-100 days after germination)


title: Gingival tissue sample 2 from patient 9, Affected site

source_name: Patient 9 gingival tissue sample collected as Affected


title: antiOsLIC collar chip

source_name: Collars from antiOsLIC transgenic rice

extract_protocol: 30 collars were taken from wild type plants and antiOsLIC transgenic plants respectively. One collar from one plant only. The leaves are just sprout 2-3 cm (about 1-2 days) from the stem. For measuring the genes expression level, Wild type plants were taken as control. The developing collar from both line2 of OsLIC antisense transgenic plants and wild type were harvested at the heading stage. The position of the collar was about 1cm above the last developed collar. Total RNA was extracted from the collars using TRIzol regeant (Invitrogen, P/N 15596-018, USA) and purified by using Qiagen RNeasy columns (QIAGEN, Cat. NO. 74104).

tag: antiOsLIC transgenic plants


title: mouse peritoneum time 0 mouse array replicate 1

description: mouse on mouse control

tag: time 0 control


title: human endometrium time 0 mouse array replicate 1

description: human on mouse control


title: human endometrium time 0 mouse array replicate 2

description: human on mouse control


title: Gingival tissue sample 1 from patient 89, Affected site

source_name: Patient 89 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 88, Affected site

source_name: Patient 88 gingival tissue sample collected as Affected


title: CD8_18_aGVHD(+)

source_name: CD8+ subsets, case IMS18, aGVHD

tag: AGE

tag: SEX

tag: Diagnosis

tag: Grading of acute GVHD


title: Gingival tissue sample 1 from patient 9, Affected site

tag: Gingival tissue phenotype


title: kernel_susceptible2_water stress_vs_well watered_rep2

city: Milano

first: Rosanna

last: Marino

state: Milano

address: Via celoria 26

department: Department of biomolecular sciences and biothecnology

country: Italy

institute: Universita' degli studi di Milano

description: ch2/ch1 (water stress/well watered)

hyb_protocol: The slides were hybridized using the procol described in the MWG Array manual (http://ecom2.mwgdna.com/services/array/download)

scan_protocol: Images were acquired at 5µm resolution by ScanArray v3.1 software on SA4000 Scanner (Packard Bioscience, Wellesley, MA) and quantified using Quantarray v3.0 software (Packard Bioscience, Wellesley, MA)

data_processing: Local background subtraction, per chip LOWESS and 50th percentile within array normalization function were performed by Genespring (Agilent Techonologies, Palo Alto,CA)

organism: Zea mays

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in well watered field condition and labeled with cyanine 3

label_protocol: 1µg of purified poly(A+) RNA was labeled according to the protocol of the Amersham CyScribe Post-Labeling Kit (GE Healthcare, NJ, USA)

growth_protocol: All plants were grown in open field in Foggia (Southern Italy) where in late spring and summer the temperature is high and the rainfall is usually very limited or absent. Therefore the water supply was tightly controlled by differential irrigation.

extract_protocol: Total RNA was extracted, from a pool of 6-9 kernels (2-3 seeds from 3 different ears) at 10 DAP, using LiCl based method. RNA quality was evaluated on agarose gels and assorbance 260/280 ratios between 1.8 and 2.2 were typically obtained. Poly(A+) RNA was purfied using the Amersham mRNA Purification Kit (GE Healthcare, NJ, USA).

treatment_protocol: Two levels of drought treatment were applied, well watered and water stress, with two randomized blocks for each level. For each block, two rows of fifteen plants per genotype were grown at a plant density of four plants/square meter. All trials were well irrigated from sowing to the start of the treatment. Thereafter, the well-watered trials received additional full irrigations maintaining soil moisture at about 30% expressed on a dry weight basis, while stressed plants received just enough water for surviving (soil moisture about 16%). The stress was applied strarting three weeks before flowering time.

tag: RIL from B73xH99

tag: phenotypically recorded as susceptible (RIL68)

tag: organ

value: 10days after pollination kernels

tag: well watered

value: 30% (expressed on a dry weight basis) soil moisture was maintained for the treatment

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in water stress field condition and labeled with cyanine 5

tag: water stress

value: 16% (expressed on a dry weight basis) soil moisture was maintained for the treatment


title: CD56_5_aGVHD(-)

source_name: CD56+ subsets, case IMS5, recovery

tag: Subsets

value: during recovery phase

value: 2 (skin; 3, gut; 1, liver; 0)


title: CD56_5_aGVHD(+)

source_name: CD56+ subsets, case IMS5, aGVHD

tag: Status

value: during acute GVHD

value: F


title: CD56_8_aGVHD(-)

source_name: CD56+ subsets, case IMS8, recovery

tag: Case


title: Gingival tissue sample 3 from patient 88, Unaffected site

source_name: Patient 88 gingival tissue sample collected as Unaffected

tag: Tissue


title: Gingival tissue sample 2 from patient 89, Affected site


title: Lung_CD40L-KO_14 days unexposed to P. murina_rep5

city: Bethesda

first: Joseph

last: Kovacs

state: MD

department: CCMD

institute: NIH

hyb_protocol: Twenty mg of fragmented cRNA was used to prepare the hybridization cocktail as described by Affymetrix. Hybridization cocktail containing 15 µg of fragmented cRNA were added to an MG-U74Av2 array (Affymetrix) and hybridized for 16 hours at 45˚C in a Hybridization Oven 640 (Affymetrix). The arrays were stained and washed using the GeneChip® Fluidics Station 400 using R-Phycoerythrin Streptavidin (Molecular Probes) and a biotinylated goat anti-Streptavidin antibody (Vector Laboratories, Burlingame, CA).

scan_protocol: Experiments 1 and 2 were scanned using the GeneArray® 2500 scanner. The GeneChip® Scanner 3000 was used to scan Experiments 3 and 4. The signal intensity was quantitated using GeneChip® Operating Software v1.2 (GCOS 1.2)

data_processing: Data were first normalized to the median value of each chip, then logarithmically transformed after the addition of a small value (1% of the median) to dampen the influence of extremely small data values.  A one-way ANOVA was performed to determine the significance of changes within each experiment.  Affymetrix genes were selected if the P-value was less than 0.001 and the  fold change (FC) between the exposed compared to the unexposed animals was at least 1.5 fold or at most 1/1.5 fold .

source_name: Mouse lung homogenate

label_protocol: The cDNA was purified following the procedures described by Affymetrix and was transcribed in vitro and biotin-labeled using the BioArrayHigh Yield RNA Transcript Labeling Kit (ENZO Life Science Inc., Farmingdale, NY).

growth_protocol: Animals were cohoused with a seeder mouse highly infected with Pneumocystis murina and sacrificed at the corresponding day of exposure, and lungs were harvested at that time. Unexposed animals (controls) were sacrificed at the corresponding time points and lungs were harvested.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.

tag: Strain

value: CD40L-KO, Gender:female, Age:8 weeks


title: Lung_CD40L-KO_14 days unexposed to P. murina_rep4


title: Gingival tissue sample 1 from patient 88, Affected site


title: Gingival tissue sample 3 from patient 87, Unaffected site

source_name: Patient 87 gingival tissue sample collected as Unaffected


title: CD56_1_aGVHD(+)

source_name: CD56+ subsets, case IMS1, aGVHD

value: M


title: CD56_1_aGVHD(-)

source_name: CD56+ subsets, case IMS1, recovery

value: AML (M2)


title: Gingival tissue sample 1 from patient 87, Affected site

source_name: Patient 87 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 87, Affected site


title: Gingival tissue sample 3 from patient 86, Unaffected site

source_name: Patient 86 gingival tissue sample collected as Unaffected


title: CD14_8_aGVHD(-)

source_name: CD14+ subsets, case IMS8, recovery


title: CD14_5_aGVHD(+)

source_name: CD14+ subsets, case IMS5, aGVHD

value: AML (M3)


title: Lung_CD40L-KO_14 days unexposed to P. murina_rep2


title: Lung_CD40L-KO_14 days unexposed to P. murina_rep3


title: CD14_5_aGVHD(-)

source_name: CD14+ subsets, case IMS5, recovery


title: Lung_CD40L-KO_14 days unexposed to P. murina_rep1


title: Gingival tissue sample 2 from patient 86, Affected site

source_name: Patient 86 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 85, Affected site

source_name: Patient 85 gingival tissue sample collected as Affected


title: CD14_8_aGVHD(+)

source_name: CD14+ subsets, case IMS8, aGVHD


title: Lung_CD40L-KO_35 days exposed to P. murina_rep4


title: Gingival tissue sample 1 from patient 86, Affected site


title: Lung_CD40L-KO_35 days exposed to P. murina_rep3


title: CD8_8_aGVHD(+)

source_name: CD8+ subsets, case IMS8, aGVHD


title: CD8_8_aGVHD(-)

source_name: CD8+ subsets, case IMS8, recovery


title: Gingival tissue sample 3 from patient 83, Unaffected site

source_name: Patient 83 gingival tissue sample collected as Unaffected


title: Lung_CD40L-KO_35 days exposed to P. murina_rep2


title: CD8_5_aGVHD(+)

source_name: CD8+ subsets, case IMS5, aGVHD


title: Gingival tissue sample 2 from patient 83, Affected site

source_name: Patient 83 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 83, Affected site


title: Lung_CD40L-KO_35 days exposed to P. murina_rep1

source_name: Mouse lung homogenate


title: CD8_1_aGVHD(-)

source_name: CD8+ subsets, case IMS1, recovery


title: Lung_C57BL_7 days unexposed to P. murina_rep4

value: C57BL, Gender:female, Age:8 weeks


title: Gingival tissue sample 1 from patient 82, Affected site

source_name: Patient 82 gingival tissue sample collected as Affected

value: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)


title: Gingival tissue sample 1 from patient 81, Affected site

source_name: Patient 81 gingival tissue sample collected as Affected

value: Gingival


title: Gingival tissue sample 2 from patient 82, Affected site


title: Gingival tissue sample 2 from patient 80, Affected site

source_name: Patient 80 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 8, Affected site

source_name: Patient 8 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 78, Affected site

source_name: Patient 78 gingival tissue sample collected as Affected


title: Lung_C57BL_7 days unexposed to P. murina_rep3


title: CD8_1_aGVHD(+)

source_name: CD8+ subsets, case IMS1, aGVHD


title: CD8_5_aGVHD(-)

source_name: CD8+ subsets, case IMS5, recovery


title: Gingival tissue sample 2 from patient 81, Affected site


title: Gingival tissue sample 1 from patient 84, Affected site

source_name: Patient 84 gingival tissue sample collected as Affected


title: CD4_8_aGVHD(+)

source_name: CD4+ subsets, case IMS8, aGVHD


title: Lung_C57BL_7 days unexposed to P. murina_rep2


title: Gingival tissue sample 3 from patient 8, Unaffected site

source_name: Patient 8 gingival tissue sample collected as Unaffected

value: Healthy (no BoP + PPD of<5 mm + CAL of<3 2 mm


title: Lung_C57BL_21 days unexposed to P. murina_rep5


title: Gingival tissue sample 3 from patient 78, Unaffected site

source_name: Patient 78 gingival tissue sample collected as Unaffected


title: Lung_C57BL_7 days unexposed to P. murina_rep1


title: Lung_C57BL_21 days unexposed to P. murina_rep4


title: Gingival tissue sample 1 from patient 8, Affected site


title: Gingival tissue sample 1 from patient 78, Affected site


title: CD4_5_aGVHD(+)

source_name: CD4+ subsets, case IMS5, aGVHD


title: CD4_8_aGVHD(-)

source_name: CD4+ subsets, case IMS8, recovery


title: CD4_5_aGVHD(-)

source_name: CD4+ subsets, case IMS5, recovery


title: Gingival tissue sample 1 from patient 80, Affected site


title: Gingival tissue sample 1 from patient 77, Affected site

source_name: Patient 77 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 76, Affected site

source_name: Patient 76 gingival tissue sample collected as Affected


title: Lung_C57BL_14 days unexposed to P. murina_rep4

source_name: Mouse lung homogenate


title: Gingival tissue sample 2 from patient 76, Affected site


title: Gingival tissue sample 2 from patient 77, Affected site


title: Lung_C57BL_14 days unexposed to P. murina_rep5


title: Gingival tissue sample 2 from patient 73, Affected site

source_name: Patient 73 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 74, Unaffected site

source_name: Patient 74 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 77, Unaffected site

source_name: Patient 77 gingival tissue sample collected as Unaffected


title: Lung_C57BL_21 days unexposed to P. murina_rep1


title: Lung_C57BL_21 days unexposed to P. murina_rep3


title: Lung_C57BL_21 days unexposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 74, Affected site

source_name: Patient 74 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 75, Affected site

source_name: Patient 75 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 73, Affected site


title: Gingival tissue sample 3 from patient 76, Unaffected site

source_name: Patient 76 gingival tissue sample collected as Unaffected


title: Lung_C57BL_14 days unexposed to P. murina_rep6


title: Gingival tissue sample 3 from patient 72, Affected site

source_name: Patient 72 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 72, Affected site


title: Gingival tissue sample 2 from patient 71, Affected site

source_name: Patient 71 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 74, Affected site


title: Gingival tissue sample 1 from patient 75, Affected site


title: Gingival tissue sample 2 from patient 72, Unaffected site

source_name: Patient 72 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 85, Affected site

source_name: Patient 85 gingival tissue sample collected as Affected


title: Lung_C57BL_14 days unexposed to P. murina_rep1


title: Lung_C57BL_14 days unexposed to P. murina_rep2


title: Lung_C57BL_7 days exposed to P. murina_rep8


title: Gingival tissue sample 2 from patient 70, Affected site

source_name: Patient 70 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 7, Affected site

source_name: Patient 7 gingival tissue sample collected as Affected


title: Lung_C57BL_7 days exposed to P. murina_rep7


title: Gingival tissue sample 1 from patient 70, Affected site


title: Lung_C57BL_7 days exposed to P. murina_rep6


title: Gingival tissue sample 3 from patient 69, Unaffected site

source_name: Patient 69 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 7, Affected site


title: Gingival tissue sample 2 from patient 69, Affected site

source_name: Patient 69 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 7, Affected site


title: Gingival tissue sample 2 from patient 84, Affected site

source_name: Patient 84 gingival tissue sample collected as Affected


title: expt 15 CONTROL 24H

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: This study compares mouse trophoblast cells isolated from placentas and treated at two different time points 1 and 24 hr with recombinant mouse leptin or control (serum-free medium).

hyb_protocol: The aRNA was hybridized to Illumina Sentrix MouseRef-8 Expression BeadChip arrays at 58 C for 20 h. After hybridization, the chips were washed and stained with streptavidin-C3.

scan_protocol: The image data were acquired by a BeadArray reader (Illumina, San Diego, CA)

data_processing: Summary intensities of 24,886 probesets on 19 arrays  of three BeadChips (excluding one outlier array -expt 28 CONTROL 24 which was removed from the statistical analysis) were obtained using Illumina’s BeadStudio(Illumina, San Diego CA)   and then quantile normalized using beadarray software (Illumina). Three paired t-tests were applied to the base 2 logarithm transformed normalized data using limma software to identify differentially expressed genes between control and leptin treated samples at 1 h, between leptin treatments of 1 h and 6 h, and between the 1 and 24 hour samples in the presence of leptin and absence of leptin.

source_name: primary trophoblast cells treated for 24 hours on serum-free medium

label_protocol: The total RNA was reverse transcribed to first strand cDNA with an a oligo(dT) primer bearing a 5’-T7 promoter by using ArrayScript  reverse transcriptase.  The first strand cDNA then underwent second-strand synthesis and clean-up to become the template for in vitro transcription.  The biotin-labeled aRNA was synthesized by using T7 RNA polymerase with biotin-NTP mix and purified.

growth_protocol: Placentas were separated from the underlying endometrium by using dissecting forceps in a sterile dish containing wash medium (Medium 199, 20mM Hepes, 10mM NaHCO3, penicillin/streptomycin). The placentas were then incubated in dissociation medium (wash medium containing 1 mg/ml collagenase, 20 µg/ml DNase) for up to 1 h at 37°C, with periodic pipetting to separate cells. Cells were washed to remove dissociation medium, then collected and filtered to remove undigested tissue. The cells were separated on an isotonic 40% Percoll gradient at 30,000 x g for 30 min. The trophoblast cell layer was transferred to a new tube, washed in wash buffer, and plated in NCTC-135 medium, with 20mM Hepes, 10 mM NaHCO3, 1.65 mM cysteine, 10% fetal calf serum, and penicillin/streptomycin on matrigel coated plastic wells. Cells were incubated in this medium for 14-18 h for optimal adherence before experiments were begun.

extract_protocol: Cells were then collected by scraping in TRI Reagent  at 1h (CON and LEP), 6h (LEP), and 24h (CON and LEP) after treatment.  After phase separation, the aqueous phase was removed and mixed with an equal volume of ethanol.  This mixture was applied to an RNEasy column (Qiagen, Valencia, CA) and RNA purified according to manufacturer’s instructions.

treatment_protocol: One well was used for each treatment group.  After overnight culture, cells were exposed to either control serum-free medium (CON) or medium with  50 ng/mL recombinant mouse leptin (LEP).

tag: isolated from placentas on day 10 pregnant mouse


title: Gingival tissue sample 1 from patient 69, Affected site


title: Lung_C57BL_7 days exposed to P. murina_rep5

source_name: Mouse lung homogenate


title: Gingival tissue sample 3 from patient 68, Unaffected site

source_name: Patient 68 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 68, Affected site

source_name: Patient 68 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 68, Affected site


title: expt 15 LEPTIN 6H

source_name: primary trophoblast cells treated for 6 hours with recombinant mouse leptin


title: expt 15 LEPTIN 24H

source_name: primary trophoblast cells treated for 24 hours with recombinant mouse leptin


title: Gingival tissue sample 2 from patient 67, Affected site

source_name: Patient 67 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 67, Affected site


title: Gingival tissue sample 3 from patient 66, Unaffected site

source_name: Patient 66 gingival tissue sample collected as Unaffected


title: Lung_C57BL_7 days exposed to P. murina_rep2


title: Lung_C57BL_7 days exposed to P. murina_rep4


title: Lung_C57BL_7 days exposed to P. murina_rep1


title: Gingival tissue sample 2 from patient 66, Affected site

source_name: Patient 66 gingival tissue sample collected as Affected


title: Lung_C57BL_7 days exposed to P. murina_rep3


title: expt 15 CONTROL 1H

source_name: primary trophoblast cells treated for 1 hour on serum-free medium


title: Lung_C57BL_14 days unexposed to P. murina_rep3


title: expt 28 LEPTIN 24H


title: Gingival tissue sample 4 from patient 65, Unaffected site

source_name: Patient 65 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 71, Affected site

source_name: Patient 71 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 66, Affected site


title: Gingival tissue sample 2 from patient 65, Affected site

source_name: Patient 65 gingival tissue sample collected as Affected


title: Lung_C57BL_21 days exposed to P. murina_rep5


title: Gingival tissue sample 1 from patient 64, Affected site

source_name: Patient 64 gingival tissue sample collected as Affected


title: Lung_C57BL_21 days exposed to P. murina_rep6


title: expt 15 LEPTIN 1H

source_name: primary trophoblast cells treated for 1 hour with recombinant mouse leptin


title: Lung_C57BL_21 days exposed to P. murina_rep4


title: Gingival tissue sample 2 from patient 64, Affected site


title: expt 28 LEPTIN 6H


title: Gingival tissue sample 3 from patient 64, Unaffected site

source_name: Patient 64 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 63, Unaffected site

source_name: Patient 63 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 63, Affected site

source_name: Patient 63 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 63, Affected site


title: Gingival tissue sample 1 from patient 65, Affected site


title: expt 28 CONTROL 1H


title: expt 28 LEPTIN 1H


title: Lung_C57BL_21 days exposed to P. murina_rep3

source_name: Mouse lung homogenate


title: Lung_C57BL_14 days exposed to P. murina_rep8


title: Lung_C57BL_21 days exposed to P. murina_rep1


title: Lung_C57BL_14 days exposed to P. murina_rep7


title: Gingival tissue sample 1 from patient 61, Affected site

source_name: Patient 61 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 61, Unaffected site

source_name: Patient 61 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 62, Unaffected site

source_name: Patient 62 gingival tissue sample collected as Unaffected


title: Lung_C57BL_21 days exposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 62, Affected site

source_name: Patient 62 gingival tissue sample collected as Affected


title: expt 27 LEPTIN 24H

source_name: primary trophoblast cells treated for 24 hours with recombinant mouse leptin


title: Gingival tissue sample 2 from patient 61, Affected site


title: Gingival tissue sample 1 from patient 62, Affected site


title: expt 27 CONTROL 24H

source_name: primary trophoblast cells treated for 24 hours on serum-free medium


title: Gingival tissue sample 1 from patient 60, Affected site

source_name: Patient 60 gingival tissue sample collected as Affected


title: Lung_C57BL_14 days exposed to P. murina_rep6


title: expt 27 CONTROL 1H

source_name: primary trophoblast cells treated for 1 hour on serum-free medium


title: expt 27 LEPTIN 1H


title: Gingival tissue sample 1 from patient 59, Affected site

source_name: Patient 59 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 60, Affected site


title: Gingival tissue sample 2 from patient 59, Affected site


title: Gingival tissue sample 2 from patient 58, Affected site

source_name: Patient 58 gingival tissue sample collected as Affected


title: expt 19 CONTROL 24H


title: Gingival tissue sample 3 from patient 58, Unaffected site

source_name: Patient 58 gingival tissue sample collected as Unaffected


title: Lung_C57BL_14 days exposed to P. murina_rep5


title: expt 27 LEPTIN 6H

source_name: primary trophoblast cells treated for 6 hours with recombinant mouse leptin


title: Gingival tissue sample 1 from patient 58, Affected site


title: Gingival tissue sample 4 from patient 59, Unaffected site

source_name: Patient 59 gingival tissue sample collected as Unaffected


title: expt 19 LEPTIN 24H


title: Lung_C57BL_14 days exposed to P. murina_rep3


title: expt 19 LEPTIN 6H


title: Gingival tissue sample 2 from patient 56, Affected site

source_name: Patient 56 gingival tissue sample collected as Affected


title: Lung_C57BL_14 days exposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 55, Affected site

source_name: Patient 55 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 54, Unaffected site

source_name: Patient 54 gingival tissue sample collected as Unaffected


title: expt 19 CONTROL 1H


title: Lung_C57BL_14 days exposed to P. murina_rep4

source_name: Mouse lung homogenate


title: Gingival tissue sample 2 from patient 54, Affected site

source_name: Patient 54 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 56, Unaffected site

source_name: Patient 56 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 55, Unaffected site

source_name: Patient 55 gingival tissue sample collected as Unaffected


title: Lung_C57BL_41 days unexposed to P. murina_rep4


title: Lung_C57BL_41 days unexposed to P. murina_rep5


title: Gingival tissue sample 3 from patient 53, Affected site

source_name: Patient 53 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 55, Affected site


title: Gingival tissue sample 2 from patient 53, Affected site


title: IFNB 24 hr B

first: Jim

last: Boonyaratanakornkit

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

description: Replicate B

hyb_protocol: Samples were hybridized at 10 RPM at 65 °C for 18 hours as per the two-color microarray-based gene expression analysis version 5.5 protocol (Agilent Technologies).

scan_protocol: Microarrays were scanned with an Agilent Microarray Scanner (Part Number G2565BA). Agilent Feature Extraction Software 9.5.1 was used for image acquisition. The single pass scan resolution was 5 micrometers, and extended dynamic range was activated.

data_processing: Normalized values were derived from: 1) Averaging on-chip replicates; 2) Cy5/Cy3; 3) per chip normalization to the median

source_name: A549, IFN-beta, 24 hr

label_protocol: Sample labeling with Cy5 and Cy3 from 1 µg total RNA was performed using the Agilent 2-Color Low RNA Input Linear Amp Kit PLUS (Agilent Technologies) as per the manufacturer's protocols (Agilent).

growth_protocol: A549 cells were grown in F12 (Ham) media supplemented with 5% fetal bovine seruma, 4 mM L-glutamine, 0.1 mg/mL gentamicin.  Cells were subcultured 1:3, twice a week

extract_protocol: Cellular homogenization, lysis, and RNA extraction was prepared using the QIAshredder and Qiagen RNeasy mini kits as per the manufacturer's protocols (Qiagen).

treatment_protocol: Sucrose purified wild-type, C(F170S), and P(C-) HPIV1 in Opti-MEM supplemented with 1.2 % Trypsin was inoculated at a multiplicity of infection of 5.  300 pg/mL (60 IU/mL) IFN-beta in Opti-MEM was used to treat A549 cells.

tag: A549 human respiratory epithelial cell line from lung carcinoma derived from 58 year old Caucasian male

source_name: A549, Mock Treatment, 24 hr


title: Gingival tissue sample 1 from patient 56, Affected site


title: Gingival tissue sample 2 from patient 50, Affected site

source_name: Patient 50 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 52, Affected site

source_name: Patient 52 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 52, Affected site


title: Lung_C57BL_41 days unexposed to P. murina_rep2


title: Gingival tissue sample 1 from patient 54, Affected site


title: Lung_C57BL_41 days unexposed to P. murina_rep1


title: IFNB 24 hr C

description: Replicate C


title: Gingival tissue sample 1 from patient 50, Affected site


title: IFNB 6 hr C

description: Replicate C

source_name: A549, IFN-beta, 6 hr

source_name: A549, Mock Treatment, 6 hr


title: IFNB 6 hr B

description: Replicate B


title: Lung_C57BL_41 days unexposed to P. murina_rep3


title: Gingival tissue sample 3 from patient 5, Affected site

source_name: Patient 5 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 5, Affected site


title: IFNB 24 hr A

description: Replicate A


title: Gingival tissue sample 1 from patient 5, Unaffected site

source_name: Patient 5 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 49, Unaffected site

source_name: Patient 49 gingival tissue sample collected as Unaffected


title: Lung_C57BL_14 days exposed to P. murina_rep1


title: expt 19 LEPTIN 1H

source_name: primary trophoblast cells treated for 1 hour with recombinant mouse leptin


title: Lung_C57BL_34 days unexposed to P. murina_rep5


title: Gingival tissue sample 2 from patient 49, Affected site

source_name: Patient 49 gingival tissue sample collected as Affected


title: IFNB 6 hr A

description: Replicate A


title: Lung_C57BL_34 days unexposed to P. murina_rep3


title: Lung_C57BL_34 days unexposed to P. murina_rep2


title: Lung_C57BL_34 days unexposed to P. murina_rep4


title: Gingival tissue sample 2 from patient 48, Affected site

source_name: Patient 48 gingival tissue sample collected as Affected


title: Lung_C57BL_34 days unexposed to P. murina_rep1

source_name: Mouse lung homogenate


title: P(C-) 24 hr C

description: Replicate C

source_name: A549, P(C-) infection, 24 hr

source_name: A549, Mock Infection, 24 hr


title: P(C-) 6 hr C

description: Replicate C

source_name: A549, P(C-) infection, 6 hr

source_name: A549, Mock Infection, 6 hr


title: Gingival tissue sample 2 from patient 47, Affected site

source_name: Patient 47 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 48, Affected site


title: P(C-) 12 hr C

description: Replicate C

source_name: A549, P(C-) infection, 12 hr

source_name: A549, Mock Infection, 12 hr


title: Gingival tissue sample 3 from patient 48, Unaffected site

source_name: Patient 48 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 47, Unaffected site

source_name: Patient 47 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 46, Unaffected site

source_name: Patient 46 gingival tissue sample collected as Unaffected


title: F170S 48 hr C

description: Replicate C

source_name: A549, C(F170S) infection, 48 hr

source_name: A549, Mock Infection, 48 hr


title: Gingival tissue sample 1 from patient 47, Affected site


title: Gingival tissue sample 1 from patient 49, Affected site


title: Lung_C57BL_41 days exposed to P. murina_rep10


title: Lung_C57BL_41 days exposed to P. murina_rep8


title: P(C-) 48 hr C

description: Replicate C

source_name: A549, P(C-) infection, 48 hr


title: Gingival tissue sample 2 from patient 46, Affected site

source_name: Patient 46 gingival tissue sample collected as Affected


title: Lung_C57BL_41 days exposed to P. murina_rep5


title: F170S 24 hr C

description: Replicate C

source_name: A549, C(F170S) infection, 24 hr


title: Lung_C57BL_41 days exposed to P. murina_rep9


title: Gingival tissue sample 3 from patient 45, Unaffected site

source_name: Patient 45 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 45, Affected site

source_name: Patient 45 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 46, Affected site


title: F170S 12 hr C

description: Replicate C

source_name: A549, C(F170S) infection, 12 hr


title: Gingival tissue sample 2 from patient 43, Affected site

source_name: Patient 43 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 43, Unaffected site

source_name: Patient 43 gingival tissue sample collected as Unaffected


title: WT 48 hr C

description: Replicate C

source_name: A549, WT infection, 48 hr


title: Gingival tissue sample 2 from patient 44, Affected site

source_name: Patient 44 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 44, Affected site


title: Gingival tissue sample 2 from patient 45, Affected site


title: Lung_C57BL_41 days exposed to P. murina_rep7

source_name: Mouse lung homogenate


title: Lung_C57BL_41 days exposed to P. murina_rep6


title: Lung_C57BL_41 days exposed to P. murina_rep4


title: Gingival tissue sample 3 from patient 42, Unaffected site

source_name: Patient 42 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 42, Affected site

source_name: Patient 42 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 42, Affected site


title: Lung_C57BL_41 days exposed to P. murina_rep2


title: Lung_C57BL_41 days exposed to P. murina_rep3


title: Lung_C57BL_34 days exposed to P. murina_rep10


title: WT 6 hr C

description: Replicate C

source_name: A549, WT infection, 6 hr

source_name: A549, Mock Infection, 6 hr


title: WT 24 hr C

description: Replicate C

source_name: A549, WT infection, 24 hr

source_name: A549, Mock Infection, 24 hr


title: P(C-) 48 hr B

description: Replicate B

source_name: A549, P(C-) infection, 48 hr

source_name: A549, Mock Infection, 48 hr


title: Lung_C57BL_41 days exposed to P. murina_rep1


title: Gingival tissue sample 1 from patient 40, Affected site

source_name: Patient 40 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 41, Affected site

source_name: Patient 41 gingival tissue sample collected as Affected


title: F170S 6 hr C

description: Replicate C

source_name: A549, C(F170S) infection, 6 hr


title: P(C-) 6 hr B

description: Replicate B

source_name: A549, P(C-) infection, 6 hr


title: Gingival tissue sample 2 from patient 40, Affected site


title: WT 12 hr C

description: Replicate C

source_name: A549, WT infection, 12 hr

source_name: A549, Mock Infection, 12 hr


title: Gingival tissue sample 2 from patient 4, Affected site

source_name: Patient 4 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 4, Affected site


title: Gingival tissue sample 2 from patient 41, Affected site


title: P(C-) 24 hr B

description: Replicate B

source_name: A549, P(C-) infection, 24 hr


title: Gingival tissue sample 3 from patient 4, Unaffected site

source_name: Patient 4 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 39, Affected site

source_name: Patient 39 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 38, Unaffected site

source_name: Patient 38 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 39, Affected site


title: Lung_C57BL_34 days exposed to P. murina_rep8

source_name: Mouse lung homogenate


title: Gingival tissue sample 3 from patient 39, Unaffected site

source_name: Patient 39 gingival tissue sample collected as Unaffected


title: P(C-) 12 hr B

description: Replicate B

source_name: A549, P(C-) infection, 12 hr


title: Gingival tissue sample 2 from patient 38, Affected site

source_name: Patient 38 gingival tissue sample collected as Affected


title: Lung_C57BL_34 days exposed to P. murina_rep9


title: Lung_C57BL_34 days exposed to P. murina_rep6


title: Lung_C57BL_34 days exposed to P. murina_rep7


title: F170S 48 hr B

description: Replicate B

source_name: A549, C(F170S) infection, 48 hr


title: Gingival tissue sample 3 from patient 37, Unaffected site

source_name: Patient 37 gingival tissue sample collected as Unaffected


title: F170S 24 hr B

description: Replicate B

source_name: A549, C(F170S) infection, 24 hr

source_name: A549, Mock Infection, 24 hr


title: Gingival tissue sample 1 from patient 38, Affected site


title: F170S 12 hr B

description: Replicate B

source_name: A549, C(F170S) infection, 12 hr


title: Gingival tissue sample 3 from patient 36, Unaffected site

source_name: Patient 36 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 37, Affected site

source_name: Patient 37 gingival tissue sample collected as Affected


title: Lung_C57BL_34 days exposed to P. murina_rep4


title: WT 48 hr B

description: Replicate B

source_name: A549, WT infection, 48 hr

source_name: A549, Mock Infection, 48 hr


title: Lung_C57BL_34 days exposed to P. murina_rep5


title: Lung_C57BL_34 days exposed to P. murina_rep3


title: Gingival tissue sample 2 from patient 36, Affected site

source_name: Patient 36 gingival tissue sample collected as Affected


title: Lung_C57BL_34 days exposed to P. murina_rep2


title: F170S 6 hr B

description: Replicate B

source_name: A549, C(F170S) infection, 6 hr

source_name: A549, Mock Infection, 6 hr


title: Lung_C57BL_32 days unexposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 35, Affected site

source_name: Patient 35 gingival tissue sample collected as Affected


title: WT 24 hr B

description: Replicate B

source_name: A549, WT infection, 24 hr


title: WT 12 hr B

description: Replicate B

source_name: A549, WT infection, 12 hr

source_name: A549, Mock Infection, 12 hr


title: Gingival tissue sample 1 from patient 36, Affected site


title: Gingival tissue sample 3 from patient 34, Unaffected site

source_name: Patient 34 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 33, Affected site

source_name: Patient 33 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 32, Unaffected site

source_name: Patient 32 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 34, Affected site

source_name: Patient 34 gingival tissue sample collected as Affected


title: P(C-) 24 hr A

description: Replicate A

source_name: A549, P(C-) infection, 24 hr

source_name: A549, Mock Infection, 24 hr


title: Gingival tissue sample 2 from patient 34, Affected site


title: WT 6 hr B

description: Replicate B

source_name: A549, WT infection, 6 hr


title: Gingival tissue sample 2 from patient 37, Affected site

source_name: Patient 37 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 35, Affected site


title: Lung_C57BL_32 days unexposed to P. murina_rep1

source_name: Mouse lung homogenate


title: Lung_CD40L-KO_32 days unexposed to P. murina_rep3


title: P(C-) 48 hr A

description: Replicate A

source_name: A549, P(C-) infection, 48 hr

source_name: A549, Mock Infection, 48 hr


title: Gingival tissue sample 1 from patient 33, Affected site


title: Gingival tissue sample 1 from patient 32, Affected site

source_name: Patient 32 gingival tissue sample collected as Affected


title: P(C-) 12 hr A

description: Replicate A

source_name: A549, P(C-) infection, 12 hr


title: Lung_CD40L-KO_32 days unexposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 32, Affected site


title: Gingival tissue sample 3 from patient 31, Unaffected site

source_name: Patient 31 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 31, Affected site

source_name: Patient 31 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 31, Affected site


title: P(C-) 6 hr A

description: Replicate A

source_name: A549, P(C-) infection, 6 hr

source_name: A549, Mock Infection, 6 hr


title: Gingival tissue sample 2 from patient 3, Affected site

source_name: Patient 3 gingival tissue sample collected as Affected


title: Gingival tissue sample 3 from patient 3, Unaffected site

source_name: Patient 3 gingival tissue sample collected as Unaffected


title: F170S 48 hr A

description: Replicate A

source_name: A549, C(F170S) infection, 48 hr


title: Lung_CD40L-KO_32 days unexposed to P. murina_rep1


title: Gingival tissue sample 1 from patient 30, Affected site

source_name: Patient 30 gingival tissue sample collected as Affected


title: Lung_C57BL_75 days exposed to P. murina_rep2


title: Lung_C57BL_75 days exposed to P. murina_rep3


title: F170S 24 hr A

description: Replicate A

source_name: A549, C(F170S) infection, 24 hr


title: F170S 12 hr A

description: Replicate A

source_name: A549, C(F170S) infection, 12 hr

source_name: A549, Mock Infection, 12 hr


title: Gingival tissue sample 3 from patient 29, Unaffected site

source_name: Patient 29 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 3, Affected site


title: F170S 6 hr A

description: Replicate A

source_name: A549, C(F170S) infection, 6 hr


title: Gingival tissue sample 1 from patient 29, Affected site

source_name: Patient 29 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 30, Affected site


title: Lung_CD40L-KO_75 days exposed to P. murina_rep3

source_name: Mouse lung homogenate


title: Gingival tissue sample 2 from patient 28, Affected site

source_name: Patient 28 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 29, Affected site


title: WT 12 hr A

description: Replicate A

source_name: A549, WT infection, 12 hr


title: Lung_CD40L-KO_75 days exposed to P. murina_rep2


title: Gingival tissue sample 1 from patient 28, Unaffected site

source_name: Patient 28 gingival tissue sample collected as Unaffected


title: WT 48 hr A

description: Replicate A

source_name: A549, WT infection, 48 hr

source_name: A549, Mock Infection, 48 hr


title: WT 24 hr A

description: Replicate A

source_name: A549, WT infection, 24 hr

source_name: A549, Mock Infection, 24 hr


title: Gingival tissue sample 3 from patient 27, Unaffected site

source_name: Patient 27 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 4 from patient 26, Unaffected site

source_name: Patient 26 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 1 from patient 27, Affected site

source_name: Patient 27 gingival tissue sample collected as Affected


title: Internal Control repl 4

city: Cincinnati

first: Lee

last: Denson

state: OH

address: 3333 Burnet Avenue

institute: CCHMC

description: gene expression data from human colon

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the human HG-U133 Plus 2.0 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8) , then normalized to the internal control for each batch and the mean of the healthy control reference samples.

source_name: human colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Plus Mini kit (QIAGEN, Hilden, Germany)

tag: Internal Control replicate sample

tag: batch 1


title: Gingival tissue sample 2 from patient 27, Affected site


title: Gingival tissue sample 2 from patient 26, Affected site

source_name: Patient 26 gingival tissue sample collected as Affected


title: Lung_CD40L-KO_75 days exposed to P. murina_rep1


title: Gingival tissue sample 3 from patient 28, Affected site


title: Lung_CD40L-KO_39 days exposed to P. murina_rep2


title: Lung_C57BL_32 days exposed to P. murina_rep3


title: Lung_CD40L-KO_39 days exposed to P. murina_rep1


title: Gingival tissue sample 2 from patient 25, Affected site

source_name: Patient 25 gingival tissue sample collected as Affected


title: Lung_C57BL_32 days exposed to P. murina_rep1


title: Gingival tissue sample 1 from patient 26, Affected site


title: WT 6 hr A

description: Replicate A

source_name: A549, WT infection, 6 hr

source_name: A549, Mock Infection, 6 hr


title: Gingival tissue sample 1 from patient 25, Affected site


title: Gingival tissue sample 4 from patient 23, Unaffected site

source_name: Patient 23 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 23, Affected site

source_name: Patient 23 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 24, Affected site

source_name: Patient 24 gingival tissue sample collected as Affected


title: Internal Control repl 3

description: gene expression data from human colon

tag: batch 4


title: Gingival tissue sample 1 from patient 23, Affected site


title: Internal Control repl 2

description: gene expression data from human colon

tag: batch 2


title: Gingival tissue sample 2 from patient 22, Affected site

source_name: Patient 22 gingival tissue sample collected as Affected

tag: Gingival tissue phenotype


title: Internal Control repl 1

description: gene expression data from human colon

tag: batch 5


title: Gingival tissue sample 1 from patient 22, Affected site


title: Lung_C57BL_32 days exposed to P. murina_rep2

source_name: Mouse lung homogenate


title: Lung_CD40L-KO_32 days exposed to P. murina_rep3


title: Gingival tissue sample 4 from patient 35, Unaffected site

source_name: Patient 35 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 21, Unaffected site

source_name: Patient 21 gingival tissue sample collected as Unaffected


title: UC colon repl 8

description: gene expression data from human colon

tag: UC replicate sample


title: Lung_C57BL_75 days exposed to P. murina_rep1


title: Gingival tissue sample 1 from patient 21, Affected site

source_name: Patient 21 gingival tissue sample collected as Affected


title: UC colon repl 7

description: gene expression data from human colon


title: UC colon repl 6

description: gene expression data from human colon


title: Lung_CD40L-KO_32 days exposed to P. murina_rep2


title: Gingival tissue sample 2 from patient 21, Affected site


title: Lung_CD40L-KO_32 days exposed to P. murina_rep1


title: Gingival tissue sample 1 from patient 20, Unaffected site

source_name: Patient 20 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 3 from patient 20, Affected site

source_name: Patient 20 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 2, Unaffected site

source_name: Patient 2 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 20, Affected site


title: UC colon repl 4

description: gene expression data from human colon


title: UC colon repl 5

description: gene expression data from human colon


title: Gingival tissue sample 1 from patient 2, Affected site

source_name: Patient 2 gingival tissue sample collected as Affected


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 4b

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

description: The labelling procedure uses equal quantities of RNA from adequate CO-RM and control cultures.

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample, vacuum-dried and re-suspended in 120 µl salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 2× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 1500 × g for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner.  The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5).

data_processing: Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

organism: Escherichia coli

source_name: Anaerobic E. coli not exposed to CO-RMs for 15 minutes (control cells)

label_protocol: Approximately 9 µg RNA was annealed to 4.5 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC and cooling on ice for 2 min. This was supplemented with 6 µl of 5× First-strand buffer (Invitrogen), 2.5 µl dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 3 µl 0.1 M DTT, 2 µl 1 mM Cy3 (Perkin Elmer) and 1.5 µl Superscript III reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 3 hours.  The reaction was terminated by the addition of NaOH (7.5 µl of 1M) and HCl (7.5 µl of 1M) before the addition of TE buffer (300 µl).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).

extract_protocol: Samples (30 ml) were harvested directly into cold phenol ethanol (187 µl phenol, 3.56 ml ethanol) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by suppliers. RNA was quantified using a BioPhotometer (Eppendorf).

tag: Anaerobic MG1655 not exposed to CO-RMs for 15 minutes (control cells)

source_name: Anaerobic E. coli were exposed to CO-RMs for 15 minutes

label_protocol: Approximately 9 µg RNA was annealed to 4.5 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC and cooling on ice for 2 min. This was supplemented with 6 µl of 5× First-strand buffer (Invitrogen), 2.5 µl dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 3 µl 0.1 M DTT, 2 µl 1 mM Cy5 (Perkin Elmer) and 1.5 µl Superscript III reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 3 hours.  The reaction was terminated by the addition of NaOH (7.5 µl of 1M) and HCl (7.5 µl of 1M) before the addition of TE buffer (300 µl).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).

tag: Anaerobic MG1655 were exposed to CO-RMs for 15 minutes


title: Gingival tissue sample 4 from patient 18, Unaffected site

source_name: Patient 18 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 2, Affected site


title: UC colon repl 3

description: gene expression data from human colon

source_name: human colon


title: Gingival tissue sample 3 from patient 18, Affected site

source_name: Patient 18 gingival tissue sample collected as Affected


title: Gingival tissue sample 2 from patient 18, Affected site


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 4a

source_name: Anaerobic E. coli exposed to CO-RMs for 15 minutes

tag: Anaerobic MG1655 exposed to CO-RMs for 15 minutes


title: UC colon repl 2

description: gene expression data from human colon


title: Gingival tissue sample 2 from patient 24, Affected site


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 3b


title: Gingival tissue sample 4 from patient 17, Unaffected site

source_name: Patient 17 gingival tissue sample collected as Unaffected


title: UC colon repl 1

description: gene expression data from human colon


title: Gingival tissue sample 2 from patient 16, Affected site

source_name: Patient 16 gingival tissue sample collected as Affected


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 3a


title: Gingival tissue sample 2 from patient 17, Affected site

source_name: Patient 17 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 17, Affected site


title: REF colon repl 10

description: gene expression data from human colon

tag: healthy control reference sample


title: Gingival tissue sample 1 from patient 18, Affected site


title: Lung_C57BL_34 days exposed to P. murina_rep1

source_name: Mouse lung homogenate


title: Gingival tissue sample 1 from patient 16, Affected site


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 2a


title: REF colon repl 9

description: gene expression data from human colon


title: Gingival tissue sample 3 from patient 14, Unaffected site

source_name: Patient 14 gingival tissue sample collected as Unaffected


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 1b


title: Gingival tissue sample 1 from patient 15, Affected site

source_name: Patient 15 gingival tissue sample collected as Affected


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 2b


title: REF colon repl 11

description: gene expression data from human colon


title: Gingival tissue sample 2 from patient 15, Affected site


title: REF colon repl 8

description: gene expression data from human colon


title: REF colon repl 7

description: gene expression data from human colon


title: Gingival tissue sample 3 from patient 13, Unaffected site

source_name: Patient 13 gingival tissue sample collected as Unaffected


title: Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 1a


title: Gingival tissue sample 1 from patient 14, Affected site

source_name: Patient 14 gingival tissue sample collected as Affected


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 3b

source_name: Aerobic E. coli exposed to CO-RMs for 15 minutes

tag: Aerobic MG1655 exposed to CO-RMs for 15 minutes

source_name: Aerobic E. coli not exposed to CO-RMs for 15 minutes (control cells)

tag: Aerobic MG1655 not exposed to CO-RMs for 15 minutes (control cells)


title: REF colon repl 6

description: gene expression data from human colon


title: REF colon repl 5

description: gene expression data from human colon


title: Gingival tissue sample 2 from patient 14, Affected site

tag: Tissue


title: Gingival tissue sample 4 from patient 12, Unaffected site

source_name: Patient 12 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 13, Affected site

source_name: Patient 13 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 12, Affected site

source_name: Patient 12 gingival tissue sample collected as Affected


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 1a


title: Gingival tissue sample 1 from patient 13, Affected site


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 2a


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 1b


title: Gingival tissue sample 2 from patient 11, Affected site

source_name: Patient 11 gingival tissue sample collected as Affected


title: Gingival tissue sample 1 from patient 11, Affected site


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 2b


title: Gingival tissue sample 2 from patient 12, Affected site


title: REF colon repl 2

description: gene expression data from human colon

source_name: human colon


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 3a


title: Gingival tissue sample 4 from patient 10, Unaffected site

source_name: Patient 10 gingival tissue sample collected as Unaffected


title: Gingival tissue sample 2 from patient 10, Affected site

source_name: Patient 10 gingival tissue sample collected as Affected


title: REF colon repl 4

description: gene expression data from human colon


title: REF colon repl 3

description: gene expression data from human colon


title: Gingival tissue sample 2 from patient 1, Affected site

source_name: Patient 1 gingival tissue sample collected as Affected


title: Gingival tissue sample 4 from patient 1, Unaffected site

source_name: Patient 1 gingival tissue sample collected as Unaffected


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 4a

label: Cy 3


title: Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 4b

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample, vacuum-dried and re-suspended in 120 ul salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 2× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 1500 × g for 2 min before scanning.


title: Gingival tissue sample 1 from patient 10, Affected site


title: REF colon repl 1

description: gene expression data from human colon


title: Polysome RHA downregulation Rep 2

status: Public on Dec 20 2008

city: Columbus

first: Kathleen

last: Boris-Lawrie

address: 1925 Coffey Rd

department: Department of Veterinary Biosciences

institute: The Ohio State University

description: RNAs in the polysome fraction under decreased levels of RHA

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the Rhesus Macaque Genome Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

organism: Chlorocebus aethiops

source_name: Polysome fraction from lysates treated with RHA targeted siRNAs

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Seven 100 mm plates seeded with 1 x 106 cells were transfected with siRNAs targeting RHA or scrambled control siRNA. Incubation for 4 hours at 37°C in medium without serum was followed by a 24 hour incubation in 10% FBS medium. Cells were split and 24 hours later transfected again with siRNAs as above and incubated at 37°C for 24 hours.

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

treatment_protocol: For RHA downregulation , COS cells were transfected with siRNAs (Dharmacon) targeted to the coding region (nucleotides 2701-2721 and 2784-2803) of human RHA (NCBI accession code NM_001357), or scrambled RHA siRNAs to a final concentration of 0.5 nM.

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-46

tag: Size fractionated RNA


title: FLAG-RHA IP_062207

description: RNAs that associate with RHA

source_name: RNAs co-immunoprecipitated with FLAG-RHA

growth_protocol: Ten replicate 100 mm plates seeded with 1 x 106 COS cells were transfected with pcDNA-FLAG-RHA. After 48 hours, the cells were harvested and a 200 ul cytoplasmic lysate was made.

treatment_protocol: The immunoprecipitation utilized anti-FLAG M2 monoclonal antibody-conjugated agarose beads (Sigma). Cytoplasmic lysates were incubated with the beads overnight at 4°C. RHA mRNP complexes were eluted with 2 ml 100 ng/ul of 3X FLAG peptide solution (Sigma) according to manufacturer’s instructions.

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-40

tag: co-IP RNA


title: FLAG-RHA Total_051707

description: Steady state RNA profile in cells expressing FLAG-RHA

source_name: Steady state RNA levels

tag: Total RNA


title: Cytoplasmic Control Rep 2

description: Cytoplasmic RNA profile under normal levels of RHA

source_name: Cytoplasmic fraction from lysates treated with control siRNAs

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-45

tag: Total cytoplasmic RNA


title: FLAG-RHA IP_051707

description: RNAs that associate with RHA


title: Cytoplasmic RHA downregulation Rep 2

description: Cytoplasmic RNA profile under decreased levels of RHA

source_name: Cytoplasmic fraction from lysates treated with RHA targeted siRNAs

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-47


title: Polysome Control Rep 2

description: RNAs in the polysome fraction under normal levels of RHA

source_name: Polysome fraction from lysates treated with control siRNAs

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-44


title: Cytoplasmic RHA downregulation Rep 1

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-43


title: Polysome RHA downregulation Rep 1

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-42


title: Gingival tissue sample 1 from patient 1, Affected site

tag: Gingival tissue phenotype


title: H1L ESC

status: Public on Dec 21 2008

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Human Embryonic Stem Cell line

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an   AFX GC3000 G7 scanner.

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

source_name: Human Embryonic Stem Cells

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the   MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s   instructions.

growth_protocol: iPS cells were maintained on irradiated   mouse embryonic fibroblasts (MEF) as previously described.  Fibroblast cells   (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium   (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum   (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit   (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: Lentiviral transduction of fibroblast cells was performed as   previously described.

tag: H1 passage 42 Human Embryonic Stem Cells


title: Polysome Control Rep 1


title: XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Crick strand; polyA RNA)

status: Public on Dec 18 2008

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

hyb_protocol: Hybridization was handled by the PAN facility at Stanford University according to Affymetrix protocols.

scan_protocol: Scanning was handled by the PAN facility at Stanford University according to Affymetrix protocols.

data_processing: Output files were generated post hybridization and scanning by Affymetrix software and the resulting files can be viewed using the Affymetrix Genome Browser software.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae experimental RNA

label_protocol: Total RNA samples were prepared following the protocol exactly as described in David et al. PNAS 103(14):5320-5 (2006).  PolyA RNA samples were prepared as follows.  500ug of total RNA were polyA purified using Qiagen Oligotex suspension to produce approximately 10ug of polyA RNA as determined by OD260/280.  2ug of the polyA purified RNA were then used in the generation of cDNA as per Affymetrix First Strand and Second Strand Synthesis protocols utilizing a T7-Oligo(dT) as the primer for the First Strand, followed by in vitro transcription to generate biotin labeled cRNA, as outlined by Affymetrix protocols.  The cRNA was fragmented as described by Affymetrix, and then sent for hybridization and scanning by the PAN facility at Stanford University.

growth_protocol: Our unpublished studies suggested that among two dozen or so different conditions that we assayed, exposure to high salt (0.8M NaCl) results in the expression of the greatest fraction of known and novel transcripts, and thus was chosen as the experimental condition to use to find previously unannotated and low abundance transcripts.  Cells were grown at 30 degrees C in YPD to approximately 1x10^7 cells/ml as determined by a Beckman Coulter Z2 Particle Count and Size Analyzer.  1.6M NaCl (in YPD) was added in an equal volume of YPD prewarmed to 30 degrees C (final concentration 0.8M).  Cells were harvested after 30 minutes by filtration, frozen in liquid nitrogen, and kept at minus 80 degrees C until RNA extraction and purification.

extract_protocol: RNA was extracted from the cells using a slightly modified version of the traditional hot phenol protocol (Schmitt et al. 1990) followed by ethanol precipitation and washing.  Briefly, 5ml of lysis buffer (10mM EDTA ph 8.0, 0.5% SDS, 10mM Tris-HCl pH 7.5) and 5ml of acid phenol were added to frozen cells and incubated at 60 degrees C for 1 hour with occasional vortexing, then placed on ice.  The aqueous phase was extracted after centrifugation and additional phenol extraction steps were performed as needed, followed by a chloroform extraction.  Total RNA was precipitated from the final aqueous solution with 10% volume 3M sodium acetate pH 5.2 and ethanol, and resuspended in nuclease-free water.

tag: Strain Background is FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers

value: his3-delta200, leu2-delta1, trp1-delta63, ura3-52.  The XRLP mutant contains deletions in the genes XRN1, RRP6, LSM1, and PAT1.


title: XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Crick strand; Total RNA)