title: U0126 + Wortmannin rep2

city: Yokohama

first: Kazuhiro

last: Kajiyama

state: Kanagawa

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

description:
replicate 2
SAMPLE 20

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: MCF7 cells, no drug treatment

label_protocol: Five hundred nanograms of total RNA was subjected and Biotinylated cRNA were prepared with the Illumina ToTalPrep RNA Amplification Kit

growth_protocol: The MCF7 was obtained from the American Type Culture Collection and maintained in DMEM supplemented with 10% FBS.

extract_protocol: RNA was isolated using the miRNeasy Mini kit (QIAGEN) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Medium was switched to DMEM supplemented with 2% FBS and the cultures were maintained overnight, and the drug was added and incubated for 6hr.

value: MCF7 breast cancer

tag: treatment

value: U0126 + Wortmannin


title: U0126 + Wortmannin rep3

status: Public on Jul 10 2013

type: RNA

description:
replicate 3
SAMPLE 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: kidney 130 wks rep 2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: The labeled cDNA was hybridized to the Mouse GeneChip 430 2.0 (Affymetrix, Santa Clara, CA, USA). The GeneChip Hybridization, Wash and Stain Kit (Affymetrix, CA) was used for the hybridizations according to the protocol of the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 HR GeneChip Scanner and GCOS

data_processing: The data were analyzed with the R statistical programming language (http://cran.r-project.org/) and the bioconductor affy package. The raw data were annotated according de Leeuw et al. (2008; BMC Res Notes. 19: 1-66 (hence the odd probeset identifiers)) and normalized using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003; Biostatistics 4: 249-264). Please note that we corrected the data for labelling-batch effects in the paper.

organism: Mus musculus

source_name: kidney 130 wks

label_protocol: In short, biotin-labeled cRNA samples were prepared as described in the Affymetrix expression analysis technical manual (Affymetrix) using 3 μg of purified total RNA as template for the reaction. For this the One-Cycle cDNA Synthesis Kit (Affymetrix) was used.

growth_protocol: Female C57BL6/J mice were marked and randomized at the day of birth in different groups; i.e. longevity cohorts (previously described in Wijnhoven et al. (2005; DNA Repair (Amst) 4: 1314-1324.), or cross-sectional cohorts in which the mice were sacrificed at fixed time points. Cross-sectional cohorts C57BL6/J mice were sacrificed at a fixed age of 13, 26, 52, 78, 104 and 130 weeks. During the entire experiment, animals were kept in the same stringently controlled pathogen free (spf) environment, fed ad libitum and kept under a normal day/night rhythm. The microbiological status of the cohorts was monitored every 3 months.

extract_protocol: Total RNA was isolated from liver, kidney, spleen, lung and brain, using the RNeasy Midi Kit (Qiagen, Valencia, CA, USA;). RNA quality was tested using automated gel electrophoresis (Bioanalyzer 2100; Agilent technologies, Amstelveen, the Netherlands). Only RIN > 7 were processed further.

tag: tissue

value: kidney

tag: strain

tag: age

value: 130 wks


title: kidney 130 wks rep 1


title: Heart_RIIIS/J

city: Los Angeles

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

country: USA

institute: UCLA

data_processing:
GenomeStudio V2010.3 (Gene Expression 1.8.0 module).
Ddata was analyzed using the limma R package.

source_name: Left Ventricle, 10 wks

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

extract_protocol: total RNA was extracted using the Quiagen miRNAeasy 96-well kits using standard protocol.  RNA integrity was determined using an Agilent Bioanalyzer

treatment_protocol: Starting at 8-9 weeks, mice were treated for 3 weeks with 30 ug/g body weight/ day of Isoproterenol or were untreated controls for the same period of time

tag: gender

value: female

value: RIIIS/J

tag: agent

value: untreated

value: Left Ventricle


title: Heart_PL/J ISO

value: PL/J

value: Isoproterenol


title: U0126 + Wortmannin rep1

description:
replicate 1
SAMPLE 19


title: Gefitinib + Wortmannin rep3

description:
replicate 3
SAMPLE 18

value: Gefitinib + Wortmannin


title: kidney 104 wks rep 1

source_name: kidney 104 wks

value: 104 wks


title: Heart_PL/J


title: Gefitinib + Wortmannin rep2

description:
replicate 2
SAMPLE 17


title: kidney 78 wks rep 3

source_name: kidney 78 wks

value: 78 wks


title: Heart_NOD/LtJ

value: NOD/LtJ


title: kidney 78 wks rep 2


title: kidney 78 wks rep 1


title: Gefitinib + Wortmannin rep1

description:
replicate 1
SAMPLE 16


title: kidney 104 wks rep 2


title: Heart_BXD21/TyJ ISO


title: Heart_BXA24/PgnJ ISO


title: Heart_NOD/LtJ ISO


title: kidney 52 wks rep 3

source_name: kidney 52 wks

value: 52 wks


title: Gefitinib + U0126 rep2

description:
replicate 2
SAMPLE 14

value: Gefitinib + U0126


title: Gefitinib + U0126 rep3

description:
replicate 3
SAMPLE 15


title: Heart_BXA24/PgnJ


title: Heart_BXA16/PgnJ ISO


title: Wortmannin rep3

description:
replicate 3
SAMPLE 12

value: Wortmannin


title: Heart_BXD21/TyJ


title: Heart_BXA16/PgnJ


title: rectosigmoid biopsy_Patient ID: 3037

type: genomic

city: San Francisco

first: Ivan

last: Vujkovic-Cvijin

state: California

address: 1001 Potrero Ave, Bldg 3

institute: University of California, San Francisco

description: 16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

hyb_protocol: Hybridization solution contained 100 mM MES (N-morpholinoethanesulfonic acid), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, pH 6.6 (referred to as 1X MES). In addition, the solution contained 0.1 mg of herring sperm DNA (Promega)/ml, 0.5 mg of acetylated bovine serum albumin (BSA; Invitrogen)/ml, and 50 pM control oligonucleotide B2 (Affymetrix). Hybridization was carried out at 45°C for 16 h with mixing on a rotary mixer at 60 rpm. Following hybridization, the sample solution was removed and the array was washed and stained in a GeneChip Fluidics Station (Affymetrix). In brief, to enhance the signals, 10 ug of streptavidin (Vector Laboratories)/ml and 2 mg of BSA/ml in 1X MES were used as the first staining solution. After the streptavidin solution was removed, an antibody mix was added as the second stain, containing 0.1 mg of goat immunoglobulin G (Sigma-Aldrich)/ml, 5 ug of biotinylated anti-streptavidin antibody (Vector Laboratories)/ml, and 2 mg of BSA/ml in 1X MES. Nucleic acid was fluorescently labeled by incubation with 10 ug of streptavidin R-phycoerythrin conjugate (Molecular Probes)/ml and 2 mg of BSA/ml in 1X MES.

scan_protocol: The arrays were scanned at 570 nm with a resolution of 3 um with a GeneChip Scanner 3000 (GCS 3000; Affymetrix).

data_processing: Fluorescence intensities were normalized to spike-in control oligonucleotides provided by SecondGenome, Inc. (San Bruno, CA, USA) using the proprietary PhyCA processing technique, which utilizes aggregate measures of mismatch probe fluorescence intensity as well as distribution of total chip fluorescence (“r scores”). Quartile r score cutoffs were chosen based on r scores retrieved for control probes spiked-in at known concentrations, as recorded from all Phylochip microarrays of the current study, and were as follows: rQ1 > .30, rQ2 > .65, rQ3 > .88.

molecule: genomic DNA

source_name: rectosigmoid biopsy, HIV+ HAART

label_protocol: DNA was resuspended in 96 ul of 30 mM MOPS (morpholinepropanesulfonic acid, pH 7.5), and 4 ul of a 50 mM polyethylene oxide-iodoacetyl biotin (Pierce Chemical) solution was added to introduce the biotin label. The reaction mixture was incubated at 37°C for 1 h, and the labeled DNA was subsequently ethanol precipitated and washed twice with 70% ethanol to remove unreacted biotin compounds.

extract_protocol: Rectosigmoid biopsies were transferred to Lysis Matrix B (MP Biomedicals, OH) tubes containing 600ul RLT buffer (Qiagen, CA). Samples were subjected to 30 seconds of bead beating at 5.5 m/second, followed by centrifugation for one minute at 2000 rpm. Supernatant was transferred to the AllPrep DNA (Qiagen, CA) spin column and nucleic acid purification was carried out according to the manufacturer's instructions. Nucleic acid concentrations were determined using a NanoDrop spectophotometer (Thermo Scientific, MA).

treatment_protocol: Enrolled subjects were given a mild enema prior to colonoscopy, and rectosigmoid biopsies were obtained between 10 and 20 cm from the anus. Extracted biopsies were snap-frozen in liquid N2 for storage at -80°C. Biopsies were re-suspended in RNAlater ICE (Life Technologies, Carlsbad, CA) according to manufacturer's instructions.

value: rectosigmoid biopsy

tag: disease status

value: HIV-infected subject undergoing highly active antiretroviral therapy (HAART)


title: Gefitinib + U0126 rep1

description:
replicate 1
SAMPLE 13

value: MCF7 breast cancer


title: Heart_BXA14/PgnJ ISO


title: kidney 52 wks rep 2

value: kidney


title: rectosigmoid biopsy_Patient ID: 1825

source_name: rectosigmoid biopsy, HIV-

value: HIV-uninfected risk-matched control subject


title: Wortmannin rep2

description:
replicate 2
SAMPLE 11


title: rectosigmoid biopsy_Patient ID: 1808


title: Heart_BXA14/PgnJ

value: female


title: kidney 52 wks rep 1


title: kidney 26 wks rep 3

source_name: kidney 26 wks

value: 26 wks


title: Heart_C3H/HeJ

value: untreated

value: Left Ventricle


title: U0126 rep2

description:
replicate 2
SAMPLE 8


title: rectosigmoid biopsy_Patient ID: 1838


title: Wortmannin rep1

description:
replicate 1
SAMPLE 10


title: kidney 26 wks rep 2


title: rectosigmoid biopsy_Patient ID: 3054


title: rectosigmoid biopsy_Patient ID: 1774

source_name: rectosigmoid biopsy, HIV+ VU

value: HIV-infected, Viremic Untreated (VU) subject


title: Heart_C3H/HeJ ISO

value: Isoproterenol


title: kidney 26 wks rep 1


title: U0126 rep1

description:
replicate 1
SAMPLE 7


title: Gefitinib rep3

description:
replicate 3
SAMPLE 6

value: Gefitinib


title: Heart_BXD40/TyJ


title: Gefitinib rep2

description:
replicate 2
SAMPLE 5


title: U0126 rep3

description:
replicate 3
SAMPLE 9


title: Heart_BXD40/TyJ ISO


title: Heart_BXD39/TyJ ISO


title: Heart_BXD39/TyJ


title: kidney 13 wks rep 1

source_name: kidney 13 wks

value: 13 wks


title: Gefitinib rep1

description:
replicate 1
SAMPLE 4


title: NC rep3

description:
replicate 3
SAMPLE 3

value: Control


title: rectosigmoid biopsy_Patient ID: 2433


title: rectosigmoid biopsy_Patient ID: 3022


title: rectosigmoid biopsy_Patient ID: 2408


title: kidney 13 wks rep 2


title: NC rep1

description:
replicate 1
SAMPLE 1


title: NC rep2

description:
replicate 2
SAMPLE 2


title: Hipocampus_WT_rep3

city: Houston

first: Baiping

last: Wang

state: TX

address: One Baylor Plaza

department: HCOA

institute: Baylor College of Medicine

description: Gene expression data from 2 months old hipocampal brain tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array from Affymetrix

scan_protocol: Scanning was done using an Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: normal

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

value: male

tag: genotype

value: wild type

value: 2 months

value: hipocampal brain


title: Hipocampus_WT_rep4


title: Heart_BXD32/TyJ


title: rectosigmoid biopsy_Patient ID: 2273

value: rectosigmoid biopsy

value: HIV-infected subject undergoing highly active antiretroviral therapy (HAART)


title: Hipocampus_N-dCKO_rep4


title: rectosigmoid biopsy_Patient ID: 1386, after 9 months HAART


title: Hipocampus_APPKO_rep4

value: APP-/-


title: rectosigmoid biopsy_Patient ID: 2356


title: rectosigmoid biopsy_Patient ID: 2256


title: Heart_BXD32/TyJ ISO


title: rectosigmoid biopsy_Patient ID: 1805

value: HIV-uninfected risk-matched control subject


title: Heart_DBA/2J ISO

value: female


title: Hipocampus_APPKO_rep3


title: rectosigmoid biopsy_Patient ID: 1726


title: Hipocampus_APLP2KO_rep4


title: Heart_DBA/2J


title: Heart_FVB/NJ ISO

value: FVB/NJ


title: Heart_FVB/NJ

value: untreated


title: Murine Bone Marrow Macrophages: Control vs. RANKL Stimulated

city: Tokyo

first: Hitoshi

last: Kohsaka

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Medicine and Rheumatology

institute: Tokyo Medical and Dental University

description: Sample 1

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min. Slides were hybridized for 12 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried prior to scan.

scan_protocol: Scanned on a GenePix 4000B (Axon Instruments, CA, USA). Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays. We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas. We normalized biases in net intensity between the two fluorescent dye channel in a microarray by locall regression (loess) normalization using its software. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.). Please note that *raw.txt and *raw_13columns.txt contains the same data. *raw.txt is the original raw data file provided by the submitter (2 rows per each feature w/ 9 columns and 4 columns each), which was re-formatted as raw_13columns.txt (1 row per each feature with 13 columns).

label_protocol: Chemically synthesized oligoribonucleotides (Ambion), or purified miRNAs were labeled with the mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer. Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy3 or Cy5 dye (GE Healthcare Bio-Science Corp., Piscataway, NJ, USA). Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure.

growth_protocol: Bone marrow cells from 8 week-old DBA1J male mice were cultured in the presence of 20 ng/ml M-CSF (R&D systems) for 2 days to induce bone marrow macrophages (BMMs)

extract_protocol: Total RNA extracted using ISOGEN (Nippon Gene Co) following manufacturer's instructions. To isolate miRNA fractions from total RNA, total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per  the manufacturer’s recommendation.

treatment_protocol: BMMs were cultured with 20 ng/ml M-CSF in the presence or absence of 50 ng/ml RANKL for 24 hours, and lysed for total RNA isolation.

value: 8-week old

tag: cell type

value: Bone marrow macrophages

tag: cultured with

value: 20 ng/ml M-CSF w/x 50 ng/ml RANKL for 24 hrs

value: 20 ng/ml M-CSF w/ 50 ng/ml RANKL for 24 hrs


title: rectosigmoid biopsy_Patient ID: 2046


title: Hipocampus_N-dCKO_rep3


title: Heart_CBA/J ISO

value: CBA/J

value: Isoproterenol

value: Left Ventricle


title: rectosigmoid biopsy_Patient ID: 1946


title: rectosigmoid biopsy_Patient ID: 1878


title: Hipocampus_APLP2KO_rep2

value: male


title: kidney 104 wks rep 3

value: kidney

value: 104 wks


title: Hipocampus_N-dCKO_rep2

value: 2 months

value: hipocampal brain


title: Hipocampus_APLP2KO_rep3


title: rectosigmoid biopsy_Patient ID: 1602, after 9 months HAART

value: rectosigmoid biopsy

value: HIV-infected subject undergoing highly active antiretroviral therapy (HAART)


title: Heart_C57BL/6J ISO

value: female


title: rectosigmoid biopsy_Patient ID: 1602

value: HIV-infected, Viremic Untreated (VU) subject


title: Heart_CBA/J

value: untreated


title: kidney 13 wks rep 3

value: 13 wks


title: rectosigmoid biopsy_Patient ID: 1386


title: Heart_C57BL/6J


title: Hipocampus_APPKO_rep1

value: APP-/-


title: rectosigmoid biopsy_Patient ID: 1898

value: HIV-uninfected risk-matched control subject


title: Heart_BUB/BnJ ISO

value: BUB/BnJ


title: rectosigmoid biopsy_Patient ID: 1162

source_name: rectosigmoid biopsy, HIV+ LTNP

value: HIV-infected, long-term non-progressor (LTNP), untreated subject


title: rectosigmoid biopsy_Patient ID: 2367


title: DEREG x Ldlr-/- DT P

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

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

scan_protocol: An Affimetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affimetrix AGCC software.

data_processing: Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R.

source_name: mouse intestine, treatment DT

label_protocol: cDNA was labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Chimeric DEREG x Ldlr-/- mice were kept on a high fat diet for 8 weeks

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

treatment_protocol: treated with DT  or PBS  i.p. for 8 weeks.

value: Diphtheria toxin

value: DEREG x Ldlr-/-

value: intestine


title: Heart_AXB18 ISO

value: Isoproterenol

value: Left Ventricle


title: Heart_AXB19/PgnJ ISO


title: Heart_AXB18


title: rectosigmoid biopsy_Patient ID: 2067


title: Heart_AXB8/PgnJ ISO_2


title: rectosigmoid biopsy_Patient ID: 2304


title: Hipocampus_APLP2KO_rep1

value: male

value: 2 months


title: Heart_AXB8/PgnJ


title: carcinoma-asssociated fibroblasts, biological replicate 4

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

description:
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls955

hyb_protocol: cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

scan_protocol: GeneChips were scanned using Affymetrix scanner

data_processing: The data were analyzed with RMA  using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E

source_name: carcinoma-asssociated fibroblasts

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

growth_protocol: LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment

treatment_protocol: LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).

value: lung

value: carcinoma-asssociated fibroblasts


title: Heart_BUB/BnJ

value: female


title: carcinoma-asssociated fibroblasts, biological replicate 3

description:
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls953


title: Hipocampus_N-dCKO_rep1

value: hipocampal brain


title: DEREG x Ldlr-/- DT O


title: carcinoma-asssociated fibroblasts, biological replicate 5

description:
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls990


description:
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls930


title: rectosigmoid biopsy_Patient ID: 2119

value: rectosigmoid biopsy

value: HIV-infected subject undergoing highly active antiretroviral therapy (HAART)


title: lung fibroblasts, biological replicate 5

description:
Gene expression data from lung fibroblasts, biological replicate 1
LFs ls938

source_name: lung fibroblasts

value: normal fibroblasts


title: Hipocampus_WT_rep2

value: wild type


title: DEREG x Ldlr-/- DT L


title: rectosigmoid biopsy_Patient ID: 1921

value: HIV-uninfected risk-matched control subject


title: rectosigmoid biopsy_Patient ID: 1780

value: HIV-infected, Viremic Untreated (VU) subject


title: rectosigmoid biopsy_Patient ID: 2231


title: carcinoma-asssociated fibroblasts, biological replicate 2

description:
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls940


title: Hipocampus_APPKO_rep2

value: APP-/-


title: Heart_AXB19/PgnJ

value: untreated


title: rectosigmoid biopsy_Patient ID: 1950


title: Hipocampus_WT_rep1


title: DEREG x Ldlr-/- DT N

value: Diphtheria toxin

value: DEREG x Ldlr-/-

value: intestine


title: DEREG x Ldlr-/- PBS G

source_name: mouse intestine, control PBS

value: PBS


title: rectosigmoid biopsy_Patient ID: 1415


title: lung fibroblasts, biological replicate 4

description:
Gene expression data from lung fibroblasts, biological replicate 1
LFs ls934


title: DEREG x Ldlr-/- PBS I


title: rectosigmoid biopsy_Patient ID: 4001


title: DEREG x Ldlr-/- DT K


title: DEREG x Ldlr-/- PBS F


title: lung fibroblasts, biological replicate 3

description:
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs686


title: DEREG x Ldlr-/- PBS D


description:
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs561


title: 30 min High 10 2

status: Public on Jul 09 2013

city: Lethbridge

first: Olga

last: Kovalchuk

state: Alberta

address: 4401 University Drive West

department: Biology

country: Canada

institute: University of Lethbridge

description:
replicate 2
SAMPLE 8

data_processing: The data were normalised using average normalisation with Illumina's GenomeStudio.

source_name: full thickness artificial human skin tissues model

label_protocol: Biotinylated cRNA were prepared with the Ambion's Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays.

extract_protocol: RNA was extracted with Illustra RNAspin mini kit (GE Healthcare Life Sciences). Quality control was performed with Agilent Bioanalyser.

tag: name of tissue

value: EpiDermFT

tag: company

value: MatTek

value: artificial human skin tissue

value: high THz


title: 30 min Low 10 3

description:
replicate 3
SAMPLE 12

value: low THz


title: 30 min UV 1

description:
replicate 1
SAMPLE 4

value: UV


title: DEREG x Ldlr-/- PBS E


title: Control 30 min 2

description:
replicate 2
SAMPLE 2

value: control


title: 30 min UV 3

description:
replicate 3
SAMPLE 6


title: Furfural shock_Time_120_rep2

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

description: Furfural shock_Time_120

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

source_name: Furfural

growth_protocol: Batch fermentations were conducted in approximately 4 L of MTC medium in 7.5 L BioFlo110 biopreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH and temperature probes and controls as described previously (Yang et al., 2008).

extract_protocol: Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Clostridium thermocellum was grown in batch fermentation to an OD600 of approximately 0.5 before treatment with either 3.95 g.L-1 ethanol, 3 g.L-1 furfural or the elevated temperature of 68°C. Total RNA was recovered at 10, 30, 60, and 120 min post-treatment for comparison with untreated controls.

tag: time

value: Furfural


title: 30 min Low 10 1

description:
replicate 1
SAMPLE 10


title: 30 min High 10 1

description:
replicate 1
SAMPLE 7


title: Furfural shock_Time_30_rep2

description: Furfural shock_Time_30

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: PVEC_EUGR_rep1

city: Hangzhou

first: Liyan

last: Zhang

state: Zhejiang

address: #57 Zhugan Lane

department: the children's Hospital

country: China

institute: Zhejiang university school of medicine

hyb_protocol: The labeled DNA samples were combined and hybridized to RAT Rat 3x720K Multiplex CpG Island Plus RefSeq Promoter Array (Nimblegen). After washing, the arrays were scanned using a MS200 scanner (Nimblegen). Data were extracted and exported to excel using NimbleScan.

scan_protocol: Raw excel data files obtained from tiling array experiments were analyzed using NimbleScan™2.3 software.

data_processing:
The ratios of Cy5 to Cy3 signals were calculated for all high-quality hybridization dots, normalized, and transformed to Log2Ratio. One-side Kolmogorov-Smirnov (KS) test was conducted to obtain p value and P value (-Log10 p value) of each probe, according to Log2Ratio of ambient probes within 750bp sliding window width. Peak score was generated by interval analysis with a cutoff value of 2, maximum gap at 500bp, and a minimum run with at least two consecutive probes.
The regions with peak scores were defined as methylated, and the level of methylation was a positive correlation with peak scores. If the methylation frequency of a region in EUGR was significantly higher than that control PVECs, we defined the region as a hypermethylation region. On the contrary, we defined it as a hypomethylation region. GFF files of Log2Ratio, P value, Peak score, and Rat 3x 720K Multiplex CpG Island Plus RefSeq Promoter Array Annotation data were exported to Signalmap 1.0 software for visual analysis and review.

organism: Rattus norvegicus

source_name: PVEC Input DNA from PVEC in EUGR_CY3

label_protocol: After heat-denaturation, individual DNA samples were probed with 1 μg of mouse anti-5-methylcytidine monoclonal antibody (Abcam，Ab10805) in IP buffer (0.5% NP40, 1.1% Triton X-100, 1.5 mM EDTA, 50 mMTris-HCl, and 150 mMNaCl) with gentle rotation at 4°C overnight.Subsequently, the mixture of DNA and anti-5-methylcytidine was reacted with Dynabeads@M-280 sheep anti-mouse IgG (Dynal，112-01D) at 4°C for 2 h. After washing, the beads were re-suspended and the bound proteins were digested with 70 μg of proteinase-K in digestion buffer (50 mMTris, pH 8.0, 10 mM EDTA, 0.5% SDS) at 55°C overnight. The remaining DNA was extracted with phenol- chloroform and precipitated with ethanol. 10ng IP DNA and 10ng input genomic DNA were amplified with the Sigma WGA2 Kit (Sigma Aldrich, WGA2-50RXN). The immunoprecipitated methylated DNA was labeled with Cy5 fluorophore and the input genomic DNA was labeled with Cy3 fluorophore.

growth_protocol: Following natural birth, pups were weighed and randomly assigned to a large litter consisting of 20 pups. A EUGR rat model was induced by postnatal nutritional restriction that we adjust litter size (for pups in a large litter).  In large litters, less milk has been shown to be available per pup than in control litters, resulting in undernutrition. And then pulmonary vascular endothelial cells (PVEC) from the above animals were isolated by magnetic-activated cell sorting (MACS).

extract_protocol: Genomic DNA of pulmonary vascular endothelial cells were extracted with promega kit（Wizard® Genomic DNA Purification Kit，A1620 ),digested overnight into 200-1000 bp of random fragments with Mse I（NEB，R0525S）and purified with QIAquick  PCR  Purification  Kit（Qiagen，28104). Review agarose gels for sample degradation and analyze the samples using spectrophotometry.

value: male

value: SD

tag: developmental stage

value: 9 weeks

value: pulmonary vascular endothelial cells were MACs sorted from lung tissue

source_name: PVEC MeDIP DNA from PVEC in EUGR_CY5


title: PVEC_EUGR_rep2


title: Control 30 min 3

description:
replicate 3
SAMPLE 3


title: 30 min Low 10 2

description:
replicate 2
SAMPLE 11


title: Control 30 min 1

description:
replicate 1
SAMPLE 1


title: 30 min High 10 3

description:
replicate 3
SAMPLE 9


title: 30 min UV 2

description:
replicate 2
SAMPLE 5


title: Furfural shock_Time_60_rep2

description: Furfural shock_Time_60

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: Furfural shock_Time_10_rep2

description: Furfural shock_Time_10


title: Control_Tme_30_rep5

source_name: Control

value: Control


title: Furfural shock_Time_30_rep1

description: Furfural shock_Time_30


title: Furfural shock_Time_60_rep1

description: Furfural shock_Time_60


title: Furfural shock_Time_10_rep1

description: Furfural shock_Time_10


title: P0 Lower Incisor Ameloblast

city: Iowa City

first: Brad

last: Amendt

state: Iowa

address: 100 Bowen Science Building

department: Anatomy and Cell Biology

institute: University of Iowa

description: Lower incisors of 3-5 P0 WT

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Lower Incisor (tooth)

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

extract_protocol: For miRNA comparison between the labial CL cells and pre-ameloblast and ameloblast cells, these two regions from the P0 mouse lower incisors were manually dissected under dissection microscopy. Total RNA including miRNA from these tissues was prepared using the miRNeasy Mini Kit (Qiagen)

value: ameloblast

value: wild type

tag: genetic background

value: mixed


title: rectosigmoid biopsy_Patient ID: 3010

value: rectosigmoid biopsy

value: HIV-infected subject undergoing highly active antiretroviral therapy (HAART)


title: P0 Lower Incisor Cervical loop

description: Lower incisors of 3-5 P0 WT

value: cervical loop cells


title: Control_Tme_10_rep3


title: Control_Tme_60_rep3


title: Furfural shock_Time_120_rep1

description: Furfural shock_Time_120


title: PVEC_EUGR_rep3


title: PVEC_CONTROL_rep3

source_name: PVEC Input DNA from PVEC in CONTROL_CY3

growth_protocol: a control litter, consisting of 10 pups

source_name: PVEC MeDIP DNA from PVEC in CONTROL_CY5


title: Heat shock_Tme_60_rep1

description: Heat shock_Tme_60

source_name: Heat

value: Heat


title: sd37 seedling, biological rep1

city: Beijing

first: zhang

last: jie

address: Datun Road

institute: BVRC

description: Gene expression data from rice seedling

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

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

data_processing: The data were analyzed with GCOS1.4

organism: Oryza sativa Indica Group

source_name: sd37 mutant seedling grown in phytotron

growth_protocol: To examine rice young seedling growth, rice seeds were germinated in sterilized water and then grown on MS pots in a phytotron with a 16 h light (26°C) and 8 h dark (18°C) photoperiod

extract_protocol: RNeasy mini kit, QIAGEN, P/N 74104

treatment_protocol: rice seeds were dechorionated with 50% bleach, then germinated in sterilized water and then grown on MS pots in a phytotron

tag: cultivar

value: seedling


title: Heat shock_Tme_120_rep4

description: Heat shock_Tme_120

tag: treatment


title: Heat shock_Tme_120_rep1

description: Heat shock_Tme_120


title: Heat shock_Tme_120_rep3

description: Heat shock_Tme_120


title: Heat shock_Tme_60_rep2

description: Heat shock_Tme_60


title: Heat shock_Tme_120_rep2

description: Heat shock_Tme_120


title: sd37 seedling, biological rep2

description: Gene expression data from rice seedling


title: sd37 seedling, biological rep3

description: Gene expression data from rice seedling


title: Control_Tme_120_rep4


title: 3037 seedling, biological rep3

description: Gene expression data from rice seedling

source_name: 3037 seedling grown in phytotron


title: 3037 seedling, biological rep2

description: Gene expression data from rice seedling


title: PVEC_CONTROL_rep1


title: 3037 seedling, biological rep1

description: Gene expression data from rice seedling


title: Ethanol shock_Tme_120_rep3

description: Ethanol shock_Tme_120

source_name: Ethanol

value: Ethanol


title: Heat shock_Tme_30_rep1

description: Heat shock_Tme_30


title: Heat shock_Tme_30_rep2

description: Heat shock_Tme_30


title: Ethanol shock_Tme_30_rep3

description: Ethanol shock_Tme_30


title: Heat shock_Tme_10_rep2

description: Heat shock_Tme_10


title: Biofilms, glass 2 rep

city: Boston

first: Geoffrey

last: Gonzalez

address: 55 Fruit St

department: Infectious Diseases

institute: Massachusetts General Hospital

description: This sample is from planktonic growth of S. Typhimurium in the flow through system, is the first of two biological replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.  The array used was S. Typhimurium LT2  TI99287 (NC_003197, NC_003277)See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. typhimurium biofilm cells on glass

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Salmonella Typhimurium 14028s was grown until mid-log phase in LB medium supplemented with 3% bile and inoculated into glass chambers (Stovall Life Science Inc, IA) coated or not with cholesterol (Sigma). Bacteria were allowed to adhere for 2 hours before starting the flow with LB bile (3%) at 270 ul/min for 24 hours.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by Nanodrop.

tag: mode of gowth

value: Biofilm

value: Wild-type

tag: phenotype

value: normal

tag: accession


title: Heat shock_Tme_10_rep1

description: Heat shock_Tme_10

tag: strain


title: Ethanol shock_Tme_10_rep2

description: Ethanol shock_Tme_10


title: Ethanol shock_Tme_60_rep1

description: Ethanol shock_Tme_60


title: Ethanol shock_Tme_60_rep2

description: Ethanol shock_Tme_60


title: lung fibroblasts, biological replicate 2

description:
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs585

tag: tissue

value: lung

value: normal fibroblasts


title: Ethanol shock_Tme_120_rep1

description: Ethanol shock_Tme_120


title: PVEC_CONTROL_rep2

tag: gender

value: male

value: SD

value: 9 weeks


title: Ethanol shock_Tme_30_rep1

description: Ethanol shock_Tme_30


title: Biofilms, glass 1 rep


title: Biofilms, cholesterol 2 rep

source_name: S. typhimurium biofilm cells on cholesterol


title: Biofilms, cholesterol 1 rep


title: Control_Tme_120_rep1

value: Control


title: Control_Tme_120_rep3


title: Ethanol shock_Tme_10_rep1

description: Ethanol shock_Tme_10


title: Ethanol shock_Tme_120_rep2

description: Ethanol shock_Tme_120


title: Ethanol shock_Tme_30_rep2

description: Ethanol shock_Tme_30


title: Planktonic, cholesterol 2 rep

source_name: S. typhimurium planktonic cells on cholesterol surfaces

value: Planktonic


title: Planktonic, cholesterol 1 rep


title: Control_Tme_60_rep1


title: Planktonic, glass 2 rep

source_name: S. typhimurium planktonic cells on glass


title: Control_Tme_120_rep2


title: Control_Tme_30_rep3


title: Control_Tme_30_rep4


title: Planktonic, glass 1 rep


title: Control_Tme_10_rep2


title: cDC from spleen of BTV infected sheep 1 day 6

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

description: Sp cDC Inf-1

hyb_protocol: cRNA (600 ng) was fragmented and used for hybridization on custom designed Agilent ovine arrays (ID 29915)

scan_protocol: Standard Agilent protocol.

data_processing: A median normalization was operated for each micro-array using Limma R package. Duplicated probes signal has been averaged.

organism: Ovis aries

source_name: cDC from spleen of BTV infected sheep

label_protocol: Each RNA sample (25 to 50 ng) was amplified and cyanin 3 (Cy3) labeled,using the one-color Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: Sorting of pDC and cDC from different lymphoid organs

extract_protocol: Total RNA was extracted using the Arcturus PicoPure RNA Isolation kit

treatment_protocol: Sheep were infected intravenously (5ml) and subcutaneouly (1ml) with BTV8 that titrated 8.1 10(6) BTV8 RNA copies/ml. pDC and cDC were sorted from lymph node, spleen and blood cells at day 6 post infection.

value: Spleen

value: cDC

tag: infection

value: BTV


title: pDC from blood of BTV infected sheep 1 day 6

description: Bl pDC Inf-1

source_name: pDC from blood of BTV infected sheep

value: Blood

value: pDC


title: Control_Tme_60_rep2


title: pDC from blood of BTV infected sheep 2 day 6

description: Bl pDC Inf-2


title: P0 Dicer1 cKO 2

description: Lower incisors of 3-5 P0 Pitx-Cre;Dicer1 cKO

hyb_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from Codelink Expression Analysis Version 5.0

label_protocol: Codelink Gene Expression System: Manual Labelled cRNA Target Preparation according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/iexpress2006_web.pdf

extract_protocol: Total RNA were extracted from P0 mouse lower incisor with miRNeasy kit from Qiagen

tag: genotype

value: Dicer KO

value: lower incisor

value: mixed


title: cDC from spleen of control sheep 1

description: Sp cDC Ctr-1

source_name: cDC from spleen of control sheep

tag: cell type

value: control


title: Control_Tme_30_rep2


title: Control_Tme_30_rep1


title: Control_Tme_10_rep1


title: cDC from spleen of BTV infected sheep 2 day 6

description: Sp cDC Inf-2


title: pDC from blood of control sheep 1

description: Bl pDC Ctr-1

source_name: pDC from blood of control sheep


title: cDC from spleen of control sheep 2

description: Sp cDC Ctr-2


title: cDC from spleen of control sheep 3

description: Sp cDC Ctr-3


title: DLBCL cell line RL versus male control DNA (part c)

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

description: RL vs maleControlDNA

hyb_protocol: NimbleGen Hybridization Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/hybridization/index.html)

scan_protocol: NimbleGen Scan Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/software/nimblescan/index.html)

data_processing: The unspecific binding intensity was estimated using the random control probes and subtracted. Outlier probes and probes with too low signal were detected and removed (set to NaN).

source_name: DLBCL cell line RL [EXP]

label_protocol: NimbleGen Labeling Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/labeling/index.html)

extract_protocol: Genomic DNA from DLBCL cell lines was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's recommendations.

tag: cell line

value: DLBCL cell line RL

source_name: male control DNA [REF]


title: DLBCL cell line DB versus male control DNA (part c)

description: DB vs maleControlDNA

source_name: DLBCL cell line DB [EXP]

value: DLBCL cell line DB


title: pDC from lymph node of BTV infected sheep 3 day 6

description: LN pDC Inf-3

value: Lymph node


title: pDC from lymph node of BTV infected sheep 2 day 6

description: LN pDC Inf-2


title: pDC from lymph node of BTV infected sheep 1 day 6

description: LN pDC Inf-1


title: pDC from blood of control sheep 3

description: Bl pDC Ctr-3


title: pDC from lymph node of control sheep 3

description: LN pDC Ctr-3

source_name: pDC from lymph node of control sheep


title: P0 Wild Type 2

description: Lower incisors of 3-5 P0 WT

source_name: Lower Incisor (tooth)

value: wild type


title: P0 Dicer1 cKO 1


title: S5-22528

city: Newcastle upon Tyne

middle: Stewart

last: Jackson

address: Central Parkway

department: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

description: Tumour which developed in MYC predisposition background, no transposition

hyb_protocol: Approximately 750ng of each cRNA was hybridised using the standard Illumina hybridization protocol

data_processing: Standard Illumina processing followed by RMA quantile normalisation.

source_name: Medulloblastoma, MYC model

label_protocol: Approximately 200ng of each RNA was amplified and Biotinylated using the Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA. USA), with the size distribution of cRNA being assessed using the Agilent Bioanalyser.

extract_protocol: RNA was extracted using the Qiagen RNeasy Lipid Tissue mini kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.Quality control was performed using an Agilent 2100 Bioanalyser.

value: GTML

tag: age(weeks)

tag: organ

value: Brain, Cerebellum

tag: disease state

value: Tumour

tag: insert in network gene

tag: insert in nfia


title: cDC from lymph node of BTV infected sheep 3 day 6

description: LN cDC Inf-3


title: S4-21541


title: P0 Wild Type 1

description: Lower incisors of 3-5 P0 WT

tag: developmental stage

tag: genetic background


title: cDC from lymph node of BTV infected sheep 1 day 6

description: LN cDC Inf-1


title: S6-22737


title: cDC from lymph node of control sheep 2

description: LN cDC Ctr-2

source_name: cDC from lymph node of control sheep


title: pDC from lymph node of control sheep 1

description: LN pDC Ctr-1


title: cDC from lymph node of control sheep 3

description: LN cDC Ctr-3


title: B5-300

description: Control Group 2 - Tumour which developed in Ptch+/- predisposition background with no transposition

source_name: Medulloblastoma, Ptch+/- model

value: CBA/J


title: S3-11185


title: cDC from lymph node of BTV infected sheep 2 day 6

description: LN cDC Inf-2


title: B4-159


title: B6-483


title: B3-105


title: S2-10519


title: pDC from lymph node of control sheep 2

description: LN pDC Ctr-2


title: B2-104


title: P4

city: Chapel Hill

first: Daria

middle: Y

last: Alakhova

state: NC

address: 120 Mason Farm rd GMB 1098

department: MOPH

institute: UNC

description:
Methyl-sensitive cut counting high-throughput sequencing data from murine leukemia cells
Library strategy: MRE-Seq
Instrument model: Illumina HiSeq 2000

data_processing:
18-bp sequence tags are aligned with the mouse genome (mm9) using the short read sequence aligner Bowtie
The library is then matched to all possible unique tags (courtesy of Madeleine Ball, Harvard University, Boston, Massachusetts, USA), and the appropriate gene using perl scripts developed by the UNO/UNMC Genetic Sequence Analysis Facility and Microsoft Access and Excel. Counts of each sequence tag that represented a unique unmethylated HpaII site were determined.
Counts of each sequence tag representing a unique unmethylated HpaII site are determined. A change in tag count between control and treatment group indicates a corresponding change in the methylation status of each HpaII CpG.
To determine HpaII sites that have a statistically significant change in methylation, comparisons are analyzed using edgeR (a bioconductor package for R programming language), which uses the Bayesian estimation and exact tests based on the negative binomial distribution to make pair wise comparisons between groups
The false discovery rate (FDR) is then determined based on the Benjamini Hochberg method, and an FDR of up to 5% will be considered significant.
Genome build: mm9
Processed data file format and content: File methylation_tag_counts.rtf reports counts of each sequence tag that represented a unique unmethylated HpaII site (linked as supplementary file on the Series record).
Processed data file format and content: File Kabanov_chr1_X_Promoter_Meth_Average_Change_compared_to_Saline.txt reports fold changes and comparisons based on counts data from methylation_tag_counts.rtf.

source_name: Murine leukemia ascitic cells from Polymers alone-treated mice with P388 ascitic tumors, Passage 4

growth_protocol: P388 parental cells were maintained in RPMI media, supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco) at 37°C and 5% CO2.

extract_protocol:
genomic DNA was isolated using DNeasy blood & tissue DNA isolation kit from Qiagen following manufacturer's protocol (cat. No 69504)
Sample libraries were developed by the University of Nebraska Epigenomics Core facility. Briefly, 2 μg genomic DNA was digested with 20 U of the restriction enzyme HpaII (NEB), and an adapter containing a recognition site for the restriction enzyme MmeI is ligated to digested DNA fragments using T4 DNA ligase (NEB). DNA is ethanol precipitated and nick repaired using 8 U Bst DNA polymerase (NEB). The DNA is then digested with 2 U MmeI to capture the 18 bases adjacent to HpaII sites, and the fragments are then ligated to a second adapter to allow for PCR amplification and final high-throughput sequencing. After appropriate tag size purification using a 10% PAGE gel, the DNA is PCR amplified using BioRad iProof high-fidelity polymerase and quantitative PCR procedures to avoid over-amplification and skewing the production of final tags. Final tags are checked for proper size and concentration using a Bioanalyzer High Sensitivity DNA chip (Agilent) and Qubit Fluorometer (Invitrogen). High-throughput sequencing of library tags was performed by the UNMC Sequencing Core Facility using an Illumina HiSeq 2000 Genome Analyzer.

treatment_protocol: in vivo cell transplantation: P388 parental cells (0.5x106/100 μl saline/mouse) were inoculated intraperitoneally (i.p.) to the 6-week-old female BDF1 mice. The mice received three injections i.v. of 1) saline, 2) polymers alone, 3) Dox (2.5 mg/kg) or 4) SP1049C (2.5 mg/kg Dox, 2.25 mg/kg or 0.225 mg/kg polymer mixture) (100μl/mouse) on days 1, 4 and 7 (Passage 1). (This drug dosing regiment is typical for mouse studies, which commonly report injections of 2.5 mg/kg to 5 mg/kg for Dox every 3rd day [28,29]). On day 10 the ascitic cells (0.5 mL) were collected with syringe in 5 mL ACK lysis buffer to remove red blood cells, washed twice with PBS and resuspended in serum-free RPMI-1640 media, and used for future analysis. The isolated cells were also used for transplantation to new host animals for the next passage (up to 7 passages, 0.5x106/100 μl saline/mouse i.p.).

tag: passage

value: leukemia ascitic cells

tag: cells isolated from


title: S1-10087


title: cDC from lymph node of control sheep 1

description: LN cDC Ctr-1

value: cDC


title: D4

source_name: Murine leukemia ascitic cells from Doxorubicin-treated mice with P388 ascitic tumors, Passage 4


title: SP4

source_name: Murine leukemia ascitic cells from SP1049C-treated mice with P388 ascitic tumors, Passage 4


title: S4

source_name: Murine leukemia ascitic cells from Saline-treated mice with P388 ascitic tumors, Passage 4


title: B1-19


title: SP1

source_name: Murine leukemia ascitic cells from SP1049C-treated mice with P388 ascitic tumors, Passage 1


title: top ABC DLBCL reference sample from GSE4475 (part a)

description:
reference array
Re-analysis of GSM100583

hyb_protocol: Affymetrix Hybridization Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=131467&categoryId=35807#1_1)

scan_protocol: Affymetrix Scan Protocol (Proprietary protocol information available at http://www.affymetrix.com/Auth/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf)

data_processing: Raw CEL data were RMA background corrected and then quantile-normalized. Probes were aggregated to Entrez Gene probesets as defined by the custom CDF [1] as described in [2] via median polish.  [1]http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.download/HuEx10stv2_Hs_ENTREZG_14.1.0.zip  [2]M. Dai, F. Meng et al. (2005) Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of GeneChip Data. Nucleic Acid Research 33 (20), e175.

source_name: morphological DLBCL

label_protocol: Affymetrix Labeling Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=prod110002&categoryId=35699#1_1)

growth_protocol: tumor sample biopsy

extract_protocol: total RNA was extracted by RNeasy Mini Kit (Quiagen) according to manufacturers protocol

treatment_protocol: fresh frozen tumor samples

tag: sample type

value: reference DLBCL

tag: subtype

value: ABC


title: Euploid DS2U neurons biological replicate 3

city: Madsion

first: Anita

last: Bhattacharyya

state: WI

address: 1500 Highland Avenue

department: Waisman Center

institute: University of Wisconsin

description: DS2U day 30 neurons C

hyb_protocol: Following Affymetrix recommended protocols and procedures, biotin-labeled cRNA or end-terminus biotin labeled DNA was hybridized to the appropriate GeneChip® overnight in the AFX HybOven480, post processed on the automated Fluidics450 Station.

scan_protocol: Scanned on the GC 3000 G7 Scanner.

data_processing: Data was extracted from the scanned image using AFX Expression Console software. t tests were performed using Genesifter software (Geospiza).  lists (Datasets S1–S4). Subsequent analyses used one-way  ANOVA followed by Tukey honestly significant difference  (HSD) posthoc tests.

source_name: Euploid DS2U neurons

label_protocol: Performed using  Ambion's MessageAmp™ II aRNA Amplification and Labeling Kit

growth_protocol: iPSCs were grown on mouse embryo fibroblasts in human embryonic stem cell media and passaged with collagenase. Neurons were differentiated from human iPSCs (grown on MEFs) following previously published protocols (Hu BY, et al. (2010) Proc Natl Acad Sci USA 107(9):4335–4340; Hu BY, Zhang SC (2010) Methods Mol Biol 636(2010):123–137; Zhang SC (2006) Brain Pathol 16(2):132–142; Zhang SC, Wernig M, Duncan ID, Brüstle O, Thomson JA (2001) Nat Biotechnol 19(12):1129–1133).

extract_protocol: Extraction of total RNA was performed according using EZRNA to the manufacturer's instructions (Omega Bio-Tek).

tag: condition

value: neurons differentiated from human induced pluripotent stem cells

tag: time

value: day 30


title: Euploid DS2U neurons biological replicate 1

description: DS2U day 30 neurons A


title: primary DLBCL sample 114 (part a)

description: primary DLBCL sample

value: primary DLBCL

value: GCB


title: primary DLBCL sample 104 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 107 (part a)

description: primary DLBCL sample

value: UC


title: Euploid DS2U neurons biological replicate 2

description: DS2U day 30 neurons B


title: primary DLBCL sample 090 (part a)

description: primary DLBCL sample


title: D1

source_name: Murine leukemia ascitic cells from Doxorubicin -treated mice with P388 ascitic tumors, Passage 1

tag: strain


title: primary DLBCL sample 111 (part a)

description: primary DLBCL sample


title: top GCB DLBCL reference sample from GSE4475 (part a)

description:
reference array
Re-analysis of GSM100651


title: C3-1012

description: Control Group 1 - Normal Cerebellum

scan_protocol: Standard Illumina scanning protocol

source_name: Normal Cerebellum, No predisposition control

tag: genotype

value: Strain CBA/J,T2Onc+/-;SB11+/-

value: Normal


title: C5-1020

description: Control Group 1 - Normal Cerebellum


title: T cells JPH203

city: Tochigi

first: Keitaro

last: Hayashi

address: 880 Kitakobayashi, Mibu, Shimotsuga

institute: Dokkyo Medical University

description: SAMPLE 3

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions.   On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Scaled signal intensity was adjusted the average intensity value to 2500.
The ratio data generated by JPH203 sample data divided by control sample data is provided in the 'ratio_data.txt' as a Series supplementary file.

source_name: CD4+ T cells_JPH203

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human CD4+ T cells from freshly drawn peripheral blood from healthy volunteer were purified by FACS. Cells were activated with anti-CD3 and anti-CD28 in the presence of 1uM JPH203 for 3days.

extract_protocol: Total RNA from cultured CD4+ T cells was extracted by RNAiso Plus (TAKARA) according to the manufacturer's instructions.

tag: tissue

value: peripheral blood

tag: cell type

value: CD4+ T cells

tag: treated with

value: 1uM JPH203 for 3days


title: primary DLBCL sample 099 (part a)

description: primary DLBCL sample


title: Ts21 DS4 neurons biological replicate 1

description: DS4 day 30 neurons A

source_name: Ts21 DS4 neurons


title: Ts21 DS4 neurons biological replicate 2

description: DS4 day 30 neurons B


title: T cells control

description: SAMPLE 2

source_name: CD4+ T cells_control


title: primary DLBCL sample 092 (part a)

description: primary DLBCL sample


title: C4-1018

description: Control Group 1 - Normal Cerebellum

tag: age(weeks)

tag: organ

value: Brain, Cerebellum


title: C6-1014

description: Control Group 1 - Normal Cerebellum

tag: disease state

tag: insert in network gene


title: S1

source_name: Murine leukemia ascitic cells from Saline-treated mice with P388 ascitic tumors, Passage 1


title: P1

source_name: Murine leukemia ascitic cells from Polymers alone-treated mice with P388 ascitic tumors, Passage 1


title: primary DLBCL sample 085 (part a)

description: primary DLBCL sample


title: P388

source_name: P388 parental cell line

value: P388 parental cells (untreated)


title: C2-910

description: Control Group 1 - Normal Cerebellum

value: CBA/J

tag: insert in nfia


title: Ts21 DS4 neurons biological replicate 3

description: DS4 day 30 neurons C


title: Ts21 DS1 neurons biological replicate 3

description: DS1 day 30 neurons C

source_name: Ts21 DS1 neurons


title: C1-909

description: Control Group 1 - Normal Cerebellum


title: primary DLBCL sample 076 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 079 (part a)

description: primary DLBCL sample


title: MB41-280

description: Tumour which developed in Ptch+/- predisposition background, with SB transposition

source_name: Medulloblastoma, Ptch+/- model, SB induced

value: Tumour

value: Y


title: Ts21 DS1 neurons biological replicate 1

description: DS1 day 30 neurons A


title: primary DLBCL sample 073 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 081 (part a)

description: primary DLBCL sample


title: MB37-366

value: N


title: primary DLBCL sample 069 (part a)

description: primary DLBCL sample

value: ABC


title: MB35-849


title: Euploid iPSC DS2U biological replicate 2

description: DS2U p47

source_name: Euploid iPSC DS2U

value: induced pluripotent stem cells


title: Ts21 iPSC DS4 biological replicate 3

description: DS4 p34

source_name: Ts21 iPSC DS4


title: primary DLBCL sample 063 (part a)

description: primary DLBCL sample


title: MB34-619


title: MB38-731


title: MB39-68


title: Euploid iPSC DS2U biological replicate 3

description: DS2U p48


title: primary DLBCL sample 071 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 061 (part a)

description: primary DLBCL sample


title: Ts21 DS1 neurons biological replicate 2

description: DS1 day 30 neurons B

value: neurons differentiated from human induced pluripotent stem cells

value: day 30


title: Euploid iPSC DS2U biological replicate 1

description: DS2U p46


title: Ts21 iPSC DS1 biological replicate 3

description: DS1 p31

source_name: Ts21 iPSC DS1


title: Ts21 iPSC DS4 biological replicate 2

description: DS4 p29


title: MB40-565


title: primary DLBCL sample 057 (part a)

description: primary DLBCL sample

value: primary DLBCL


title: MB32-116


title: Ts21 iPSC DS1 biological replicate 2

description: DS1 p25


title: Ts21 iPSC DS4 biological replicate 1

description: DS4 p28


title: primary DLBCL sample 059 (part a)

description: primary DLBCL sample

value: GCB


title: HT empty vector 24h R2 (part b)

hyb_protocol: hybridization was performed with HumanHT-12 v4 Expression Bead Chip kit (Illumina) according to manufacturers protocol

scan_protocol: scan was performed according to manufacturers protocol

data_processing: Data were imported on raw bead level (see supplementary data linked below) and subsequently a bead level spotfilter was applied for each microarray based on the fitted density mode for the background intensities. Afterwards bead intensities of all measured microarrays were quantile-normalized and beads were grouped by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations.

source_name: DLBCL cellline HT

label_protocol: RNA was transcribed and labeld by Illumina TotalPrep RNA Amplification kit according to manufacturers protocol

growth_protocol: cell line HT was maintained in RPMI medium with 10%FBS at 37°C with 5% CO2

extract_protocol: total RNA was extractet with NucleoSpin RNAII kit (illumina) according to manufacturers protocol

treatment_protocol: cell line HT was retroviral transduced with PTEN cDNA or empty vector, transduced cells were selected by tetracycline, PTEN cDNA expression was induced by doxycyline

tag: cell line

value: DLBCL cellline HT

tag: treatment

value: empty vector

tag: duration in hours

tag: replicate


title: primary DLBCL sample 058 (part a)

description: primary DLBCL sample

tag: sample type

tag: subtype


title: Ts21 iPSC DS1 biological replicate 1

description: DS1 p24

tag: condition

tag: passage


title: MB29-260

tag: strain

tag: genotype


title: MB27-833


title: primary DLBCL sample 042 (part a)

description: primary DLBCL sample

value: UC


title: MB28-457


title: primary DLBCL sample 054 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 040 (part a)

description: primary DLBCL sample


title: primary DLBCL sample 050 (part a)

description: primary DLBCL sample


title: HT empty vector 24h R1 (part b)


title: MB25-540


title: primary DLBCL sample 041 (part a)

description: primary DLBCL sample


title: MB18-751


title: MB31-835


title: primary DLBCL sample 028 (part a)

description: primary DLBCL sample


title: MB23-793


title: HT empty vector 12h R2 (part b)


title: MB20-146


title: HT empty vector 18h R1 (part b)


title: MB15-791


title: PC13: SSA/P1

city: Cleveland

first: Rish

last: Pai

state: Ohio

address: 9500 Euclid Avenue, L25

department: PLMI

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were processed with force positive, log2 transformation, and quantile normalization for further analysis in R (v.2.14.2).

label: Biotin

source_name: serrated adenomas/polyps

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

extract_protocol: RNA was extracted with a High Pure RNA Paraffin Kit , followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel analysis.

tag: age

tag: gender

value: female

tag: tissue

value: human colon

tag: location

value: proximal colon

tag: tissue subtype

value: precancerous SSA/Ps


title: primary DLBCL sample 021 (part a)

description: primary DLBCL sample

source_name: morphological DLBCL


title: MB21-48

value: CBA/J

tag: age(weeks)

tag: organ

value: Brain, Cerebellum

tag: disease state

tag: insert in network gene


title: primary DLBCL sample 025 (part a)

description: primary DLBCL sample


title: PC17: SSA/P5


title: primary DLBCL sample 037 (part a)

description: primary DLBCL sample


title: PC14: SSA/P2

value: male


title: MB17-786

value: Tumour

value: Y

tag: insert in nfia


title: primary DLBCL sample 034 (part a)

description: primary DLBCL sample


title: PC18: SSA/P6


title: PC15: SSA/P3


title: HT empty vector 18h R2 (part b)

tag: cell line

tag: treatment

tag: duration in hours

tag: replicate


title: primary DLBCL sample 017 (part a)

description: primary DLBCL sample

tag: sample type

tag: subtype

value: ABC


title: MB12-224

tag: strain

tag: genotype

value: N


title: HT PTEN 24h R2 (part b)

value: PTEN cDNA


title: PC8: MVHP2

source_name: microvesicular hyperplastic polyps

tag: age

tag: gender

value: rectosigmoid colon

value: benign MVHPs


title: HT empty vector 12h R1 (part b)

value: DLBCL cellline HT


title: HT empty vector 6h R1 (part b)

value: empty vector


title: MB16-421


title: primary DLBCL sample 019 (part a)

description: primary DLBCL sample

value: primary DLBCL


title: primary DLBCL sample 013 (part a)

description: primary DLBCL sample

value: UC


title: PC16: SSA/P4

tag: tissue

value: human colon

tag: location


title: HT empty vector 6h R2 (part b)


title: MB14-756

tag: age(weeks)


title: PC11: MVHP5

tag: tissue subtype


title: primary DLBCL sample 016 (part a)

description: primary DLBCL sample

value: GCB


title: MB11-8

tag: organ

tag: disease state


title: PC12: MVHP6


title: HT PTEN 24h R1 (part b)


title: PC9: MVHP3


title: PC7: MVHP1

value: female


title: MB9-580

value: CBA/J

tag: insert in network gene

tag: insert in nfia


title: HT PTEN 18h R1 (part b)

tag: cell line

tag: treatment


title: MB4-730

value: Brain, Cerebellum


title: HT PTEN 12h R1 (part b)

tag: duration in hours

tag: replicate


title: HT PTEN 6h R2 (part b)


title: MB3-754


title: HT PTEN 12h R2 (part b)


title: HT PTEN 18h R2 (part b)


title: PC4: Normal colon4

source_name: normal colon control

value: normal colon


title: MB7-286

value: Tumour


title: PC5: Normal colon5


title: PC3: Normal colon3

value: male

value: proximal colon


title: HT PTEN 6h R1 (part b)


title: MB2-349

value: Y


title: non-TPC Cells_rep5

status: Public on Jul 08 2013

city: Stanford

first: Yanyan

last: Zheng

institute: Stanford University

description: Gene expression in non-TPC lung tumor cells with KrasG12D, Trp53fl/fl genotype

hyb_protocol: The Cy-5 labeled test sample was pooled with a Cy-3 labeled Universal Mouse Reference RNA (Agilent Technologies, Palo Alto, CA) and hybridized onto Agilent Whole Mouse Genome 4x44K arrays as described in manufacturer’s protocol

scan_protocol: Arrays were washed, dried and scanned using an Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction software 9.5 was used to analyze acquired array images and obtain individual log2 ratios of background-subtracted signal intensities.

source_name: freshly FACS-sorted mouse non-TPC cells

label_protocol: IVT reaction was performed using the Agilent Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA) to label cDNAs with Cy-5.

extract_protocol: RNA were extracted by using RNAeasy microKit (Qiagen) following the manufacturer's recommendations, Ten to fifty nanograms of total RNA were amplified by two rounds of cDNA synthesis using Message Amp II aRNA Amplification kit (Applied Biosystems, Foster City, CA).

treatment_protocol: Primary mouse lung adenocarcinoma cells were FACS-sorted into TPC(CD24+ITGB4+Notch(hi)) and non-TPC(remainder of tumor cells) populations.Cells pellets were kept in RNAlater and stored at -80C

value: lung adenocarcinoma

tag: cell type

value: non-TPC

value: KrasG12D, Trp53fl/fl


title: PC6: Normal colon6

value: rectosigmoid colon


title: non-TPC Cells_rep4


title: non-TPC Cells_rep1


title: primary DLBCL sample 006 (part a)

description: primary DLBCL sample

tag: sample type

tag: subtype


title: non-TPC Cells_rep3

tag: genotype


title: TPC Cells_rep6

description: Gene expression in lung TPC cells with KrasG12D, Trp53fl/fl genotype

source_name: freshly FACS-sorted mouse TPC cells

value: TPC


title: non-TPC Cells_rep2


title: TPC Cells_rep3


title: TPC Cells_rep4


title: TPC Cells_rep5


title: PC2: Normal colon2

tag: age

tag: gender


title: TPC Cells_rep1

tag: tissue


title: PC1: Normal colon1

tag: location


title: CD24 negative cells _rep005

description: Gene expression in lung CD24- tumor cells with  KrasG12D genotype

source_name: freshly FACS-sorted mouse CD24- tumor cells

treatment_protocol: Primary mouse lung adenocarcinoma cells were FACS-sorted into CD24+ and CD24- populations.Cells pellets were kept in RNAlater and stored at -80C


title: CD24 positive cells _rep004

source_name: freshly FACS-sorted mouse CD24+ tumor cells


title: CD24 negative cells _rep006


title: TPC Cells_rep2


title: CD24 positive cells _rep006


title: CD24 negative cells _rep003


title: MB6-16

tag: strain

tag: age(weeks)

value: N


title: CD24 positive cells _rep001


title: CD24 negative cells _rep004


title: CD24 positive cells _rep005


title: CD24 positive cells _rep003


title: CD24 negative cells _rep001


title: White warm rep3

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

hyb_protocol: Standard Illumina hybridisation protocol

data_processing: All data was processed using Genespring GX ver 10 (Agilent Technologies)

source_name: Mouse white adipose tissue

label_protocol: RNA samples were labeled and amplified using the Illumina RNA amplification kit as per mnufacturer's instructions

growth_protocol: Mice were housed individually in cages measuring 48x14x13 cm, 16 hour light 8 hour dark cycle, access to to beeding material, standard mouse chow diet.

extract_protocol: RNA was extracted using Tri Reagent (Sigma)

treatment_protocol: Warm group treated at 22 C for 72 hours. Cold group treated at 22 C for 48 hours then 8 C for 24 hours.

value: 22 C, 72 hours

value: White Adipose

tag: Sex

value: Female


title: White Cold rep2

value: 22 C, 48 hours + 8 C, 24 hours


title: CD24 negative cells _rep002


title: Brown Cold rep3

source_name: Mouse brown adipose tissue

value: Brown Adipose


title: Liver Cold rep2

source_name: Mouse liver tissue

value: Liver


title: Liver Cold rep1


title: Brown Warm rep3


title: Brown Cold rep2


title: CD24 positive cells _rep002


title: Brown Cold rep1


title: White Cold rep3


title: Liver Warm rep2


title: White Cold rep1


title: White Warm rep1


title: White Warm rep2


title: MB10-386

value: CBA/J

tag: organ

value: Brain, Cerebellum

tag: disease state

tag: insert in network gene


title: PC10: MVHP4

value: male

value: human colon

tag: tissue subtype

value: benign MVHPs


title: Brown Warm rep2

tag: treatment


title: Liver Warm rep1


title: Brown Warm rep1


title: HBEC30KT cells, 24h treatment with Z-isomer of JIB-04

city: Dallas

first: Elisabeth

last: Martinez

address: 6000 Harry Hines Blvd

department: Department of Pharmacology

institute: UT Southwestern Medical Center

description: Gene expression profiling of HBEC30KT cells treated with Z-isomer of JIB-04 for 24h

hyb_protocol: Standard Illumina procedure.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Log2-transformed quantile normalized
P-value computed from the background model characterizing the chance that the target sequence signal was distinguishable from the negative controls

label_protocol: Standard Illumina procedure.

growth_protocol: H358 and HCC4017 cells were maintained in 5% FBS RPMI media and HBEC30KT cells (immortalized with cdk4 and h telomerase) were maintained in KSFM media supplemented with pituitary extract and EGF. Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol: RNA was extracted with RNeasy technology from Qiagen.

treatment_protocol: Exponentially growing cells were treated for 4 or 24 h with DMSO, JIB-04 E-isomer or Z-isomer.

tag: cell line

value: 500 nM Z-isomer JIB-04

tag: treatment time


title: HCC4017 cells, 4h treatment with Z-isomer of JIB-04

description: Gene expression profiling of HCC4017 cells treated with Z-isomer of JIB-04 for 4h


title: HCC4017 cells, 24h treatment with DMSO

description: Gene expression profiling of HCC4017 cells treated with DMSO for 24h

source_name: HCC4017 cells treated with DMSO for 24h

value: DMSO


title: HCC4017 cells, 24h treatment with E-isomer of JIB-04

description: Gene expression profiling of HCC4017 cells treated with E-isomer of JIB-04 for 24h

value: 500 nM E-isomer JIB-04


title: HBEC30KT cells, 4h treatment with E-isomer of JIB-04

description: Gene expression profiling of HBEC30KT cells treated with E-isomer of JIB-04 for 4h


title: HCC4017 cells, 4h treatment with DMSO

description: Gene expression profiling of HCC4017 cells treated with DMSO for 4h

source_name: HCC4017 cells treated with DMSO for 4h


title: HBEC30KT cells, 4h treatment with DMSO

description: Gene expression profiling of HBEC30KT cells treated with DMSO for 4h

source_name: HBEC30KT cells treated with DMSO for 4h


title: HCC4017 cells, 24h treatment with Z-isomer of JIB-04

description: Gene expression profiling of HCC4017 cells treated with Z-isomer of JIB-04 for 24h


title: TNBS colitis day 28_mouse#5

city: Leiden

first: Rob

last: Mariman

address: Vestwal 5

institute: TNO

description: replicate _5

data_processing: Image Analysis and extraction of raw and background subsracted expression data were preformed with Genome Studio software. GeneSpring GX 11.0 was used for quantile normalization and converting expression levels to a log2 scale

source_name: distal colon

label_protocol: Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification   Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification  Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification

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

value: BALB/c

tag: disease status

value: TNBS colitis

tag: time

value: day 28

tag: animal


title: TNBS colitis day 16_mouse#5

description: replicate _5

value: day 16


title: HBEC30KT cells, 24h treatment with E-isomer of JIB-04

description: Gene expression profiling of HBEC30KT cells treated with E-isomer of JIB-04 for 24h


title: HBEC30KT cells, 24h treatment with DMSO

description: Gene expression profiling of HBEC30KT cells treated with DMSO for 24h


title: TNBS colitis day 28_mouse#4

description: replicate _4


title: HBEC30KT cells, 4h treatment with Z-isomer of JIB-04

description: Gene expression profiling of HBEC30KT cells treated with Z-isomer of JIB-04 for 4h


title: TNBS colitis day 9_mouse#5

description: replicate _5

value: day 9


title: H358 cells, 24h treatment with Z-isomer of JIB-04

description: Gene expression profiling of H358 cells treated with Z-isomer of JIB-04 for 24h


title: H358 cells, 24h treatment with E-isomer of JIB-04

description: Gene expression profiling of H358 cells treated with E-isomer of JIB-04 for 24h


title: H358 cells, 4h treatment with Z-isomer of JIB-04

description: Gene expression profiling of H358 cells treated with Z-isomer of JIB-04 for 4h


title: HCC4017 cells, 4h treatment with E-isomer of JIB-04

description: Gene expression profiling of HCC4017 cells treated with E-isomer of JIB-04 for 4h


title: TNBS colitis day 14_mouse#5

description: replicate _5

value: day 14


title: H358 cells, 4h treatment with E-isomer of JIB-04

description: Gene expression profiling of H358 cells treated with E-isomer of JIB-04 for 4h


title: TNBS colitis day 23_mouse#5

description: replicate _5

value: day 23


title: TNBS colitis day 9_mouse#4

description: replicate _4


title: TNBS colitis day 14_mouse#3

description: replicate _3


title: TNBS colitis day 16_mouse#4

description: replicate _4


title: TNBS colitis day 9_mouse#3

description: replicate _3


title: TNBS colitis day 21_mouse#5

description: replicate _5

value: day 21


title: Healthy Control _mouse#4

description: replicate _4

value: Healthy Control


title: TNBS colitis day 14_mouse#4

description: replicate _4


title: Healthy Control _mouse#3

description: replicate _3


title: Lung at at TIMM 4903, biological rep1

city: Yokohama,

first: Yoichiro

last: Okubo

address: 2-3-2, Nakao, Asahi-Ku

department: Pathology

institute: Kanagawa Cancer Center

description:
Gene expression data from the lung of mice infected with C. gattii TIMM4903
TIMM 4903 infected mouse

hyb_protocol: Following fragmentation, 12.5 μg of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix). The array was incubated for 16 hr at 45°C, then automatically washed and stained with GeneChip(R) Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix GeneChip® Command Console AGCC Software.

source_name: Lung tissue specimens from  C. gattii TIMM4903 infected mouse

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

growth_protocol: All strains were pre-incubated with Yeast Peptone Dextrose (YPD) Broth at 30°C for 48 hours

extract_protocol: RNA targets preparation were performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix).

treatment_protocol: The mice were infected by an intratracheal administration of C. gattii TIMM 4097 or 4903. 15 days after infection, the lung of mice were removed and prepared for the analysis

value: lung

tag: age

value: Five-weeks-old

tag: agent

value: C. gattii TIMM 4903


title: H358 cells, 24h treatment with DMSO

description: Gene expression profiling of H358 cells treated with DMSO for 24h

source_name: H358 cells treated with DMSO for 24h


title: Bsub_168_410min_rep3

city: Gdansk

first: Adam

last: Iwanicki

address: Debinki 1

department: Department of Medical Biotechnlogy

country: Poland

institute: Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk

description: This sample is of wild-type Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen 4x72k B. subtilis subsp. subtilis strain NC_000964 microarray slides following operating protocol (Roche NimbleGen Inc.).

scan_protocol: Scaning was performed using Roche MS 200 Microarray Scanner following operating protocol (Roche).

organism: Bacillus subtilis subsp. subtilis str. 168

label_protocol: Extracted total RNA was used for synthesis of double-stranded cDNA using Roche cDNA Synthesis System kit (Roche). cDNA was labeled using Roche Dual-Color DNA Labeling kit (Roche), 168 strain – Cy5, delta-prpE – Cy3)

growth_protocol: Bacteria were inoculated into sporulation medium (Sterlini, J.M. and Mandelstam, J. 1969 Biochem. J. 113:29-37) and grown with shaking at 37°C to an optical density at 570 nm (OD570) of 1. Cells were harvested by centrifugation and resuspended in the starvation sporulation medium (Sterlini and Mandelstam 1969), and incubation was continued with shaking at 37°C. Samples of 10 OD570 units were collected at 60, 130, 200, 270, 340 and 410 min upon resuspension in starvation medium (initiation of sporulation).

extract_protocol: Total RNA was extracted using the Universal RNA Purification Kit (Eurx Ltd, Gdańsk, Poland) and DNA was removed by on-column DNase digestion with the RNase-Free DNase (Fermentas, Lithuania). RNA concentration and purity was determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA).

treatment_protocol: not applicable

tag: genotype

value: wild-type

tag: accession

tag: collection time


title: Bsub_168_410min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis subsp. subtilis str. 168


title: Bsub_prpE_410min_rep3

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis subsp. subtilis str. 168 delta-prpE

value: mutant delta-prpE


title: Bsub_prpE_410min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: TNBS colitis day 23_mouse#4

description: replicate _4

tag: strain


title: Lung at at TIMM 4097, biological rep1

description:
Gene expression data from the lung of mice infected with C. gattii TIMM4097
TIMM 4097 infected mouse

source_name: Lung tissue specimens from  C. gattii TIMM4097 infected mouse

tag: tissue

tag: gender

value: male

value: C. gattii TIMM 4097


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. 5 µM LY-317615 treatment for 8h. [Inflame Ly3x]

city: Heidelberg

first: Tobias

middle: Volker

last: Lanz

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology

institute: German Cancer Research Center (DKFZ)

description:
repetition ov Inflamed LY-treated sample
Inflame Ly3x

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: primary cultured mouse brain microvascular endothelial cells (MBMEC) have been prepared from new-born mice and cultured for one week.

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

treatment_protocol: MBMEC were stimulated 8h with 5 µM LY317615. Two samples had been treated for ghe last 24h with 500 µM TNF-alpha and 500 µM IFN-gamma (inflamed) whereas two samples had been left untreated (naive).


title: Bsub_prpE_410min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.

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


title: Bsub_168_410min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 410 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: H358 cells, 4h treatment with DMSO

description: Gene expression profiling of H358 cells treated with DMSO for 4h

source_name: H358 cells treated with DMSO for 4h

value: DMSO


title: TNBS colitis day 28_mouse#3

description: replicate _3

value: BALB/c


title: Bsub_168_340min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_340min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Lung at at control, biological rep1

description:
Gene expression data from the lung of control mice
Control mouse

source_name: Lung tissue specimens from normal control mouse

value: control


title: Healthy Control _mouse#2

description: replicate _2


title: TNBS colitis day 21_mouse#4

description: replicate _4

value: TNBS colitis


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. 5 µM LY-317615 treatment for 8h. [Inflame Ly 1x]

description:
repetition ov Inflamed LY-treated sample
Inflame Ly 1x

source_name: primary cultured mouse brain microvascular endothelial cells (MBMEC)


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. No LY-317615 treatment. [Inflame ctrl 3]

description:
repetition ov Inflamed ctrl sample
Inflame ctrl 3


title: Bsub_prpE_340min_rep3

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Healthy Control _mouse#1

description: replicate _1


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. 5 µM LY-317615 treatment for 8h. [Inflame Ly3]

description:
repetition ov Inflamed LY-treated sample
Inflame Ly3


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. No LY-317615 treatment. [Inflame ctrl 3x]

description:
repetition ov Inflamed ctrl sample
Inflame ctrl 3x


title: Bsub_prpE_340min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_340min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: MBMEC, treated for 24h with 500 µM TNF-alpha and 500 µM IFN-gamma. No LY-317615 treatment. [Inflame ctrl 2x]

description:
repetition ov Inflamed ctrl sample
Inflame ctrl 2x


title: TNBS colitis day 23_mouse#3

description: replicate _3


title: Bsub_prpE_270min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: TNBS colitis day 28_mouse#2

description: replicate _2

value: day 28


title: Bsub_168_270min_rep3

description: This sample is of wild-type Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_270min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_270min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_270min_rep3

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: MBMEC, 5 µM LY-317615 treatmen for 8h. [Naive Ly3x]

description:
repetition ov Naive LY-treated sample
Naive Ly3x


title: Bsub_prpE_200min_rep3

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_200min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_270min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 270 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_200min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_200min_rep3

description: This sample is of wild-type Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: MBMEC, 5 µM LY-317615 treatmen for 8h. [Naive Ly1x]

description:
repetition ov Naive LY-treated sample
Naive Ly1x


title: Bsub_168_200min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: TNBS colitis day 23_mouse#2

description: replicate _2


title: TNBS colitis day 14_mouse#2

description: replicate _2


title: MBMEC, no LY-317615 treatment. [Naive ctrl 3]

description:
repetition ov Naive ctrl sample
Naive ctrl 3


title: TNBS colitis day 16_mouse#3

description: replicate _3

value: day 16


title: TNBS colitis day 14_mouse#1

description: replicate _1

value: day 14


title: MBMEC, no LY-317615 treatment. [Naive ctrl 3x]

description:
repetition ov Naive ctrl sample
Naive ctrl 3x


title: GMP_988_fl/p30, rep3

city: Copenhagen N

first: Anne-Katrine

last: Frank

address: Ole Maaløesvej 5

department: Porse Group

country: Denmark

institute: Finsenlaboratoriet

description: Sorted myeloid progenitor from bone marrow samples, 3w post-conditional gene knockout.

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturer's specifications.

scan_protocol: Cell intensity files (CEL files) were generated in the GeneChip Command Console Software (AGCC) (Affymetrix, Santa Clara, CA, USA).

data_processing: The data were processed using the Bioconductor affy package. Values are log2 transformed post-RMA processing.

source_name: bone marrow cells, GMPs, cebpa fl/p30; Mx1Cre

label_protocol: 2.5ug of amplified cDNA was fragmented and labeled using Encore Biotin Module V2 according to manufacturer's instructions (www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/).

growth_protocol: Murine bone marrow cells were enriched for cKit+ and hematopoietic progenitor cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene) according to manufacturer's instructions (www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/).

treatment_protocol: Female mice were sacrificed and bones were dissected, bone marrow cells were isolated by crushing and the preGM and GMP populations were sorted by FACS. Immunophenotypes: PreGM: Lin- Sca1- cKit+ CD150- CD41- FcgRII- Endoglin-; GMP: Lin- Sca1- cKit+ CD150- CD41- FcgRII+.

tag: genotype/variation

value: cebpa fl/p30; Mx1Cre

value: bone marrow

tag: cell population

value: GMP:Lin-, Sca1-, cKit+, CD150-, CD41-, FcgRII+

value: female


title: Bsub_prpE_200min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 200 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_130min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 130 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: TNBS colitis day 9_mouse#2

description: replicate _2

value: day 9


title: Bsub_168_130min_rep3

description: This sample is of wild-type Bacillus subtilis 168 collected 130 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_130min_rep3

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: MBMEC, no LY-317615 treatment. [Naive ctrl 1x]

description:
repetition ov Naive ctrl sample
Naive ctrl 1x


title: TNBS colitis day 16_mouse#2

description: replicate _2


title: TNBS colitis day 21_mouse#3

description: replicate _3

value: day 21


title: Bsub_168_130min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 130 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.

value: wild-type


title: GMP_986_fl/p30, rep2


title: Bsub_prpE_130min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 130 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.

value: mutant delta-prpE


title: TNBS colitis day 9_mouse#1

description: replicate _1


title: Bsub_168_60min_rep2

description: This sample is of wild-type Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the second of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_60min_rep3

description: This sample is of wild-type Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: TNBS colitis day 21_mouse#2

description: replicate _2


title: Bsub_168_60min_rep1

description: This sample is of wild-type Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the first of three wild-type strain biological replicates used in this experiment, each from separate cultures.


title: Bsub_prpE_130min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 130 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: GMP_61_fl/BRM2, rep1

source_name: bone marrow cells, GMPs, cebpa fl/BRM2; Mx1Cre

value: cebpa fl/BRM2; Mx1Cre


title: GMP_168_fl/p30, rep1


title: GMP_1257_fl/+, rep3

source_name: bone marrow cells, GMPs, cebpa fl/+; Mx1Cre

value: cebpa fl/+; Mx1Cre