title: fhm_ovary_con_61951

description:
Sample 61951 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

data_processing: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5. The intensity of each spot was summarized by the median pixel intensity. A log10 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: fhm ovary, exposed to control water for 96 h

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

growth_protocol: 25 degrees C.  16:8 light:dark photoperiod.  Fed frozen Artremia twice daily to satiation.

extract_protocol: Total RNA was isolated from fathead minnow ovary samples using RNeasy kits (Qiagen). RNA quality was assessed with a Agilent 2100 Bioanalyzer and quantity was determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Samples for microarray analysis were generated in a 96 h, continuous flow-through experiment. Nominal treatment concentrations for the microarray experiment were 0 and 50 μg haloperidol/L. Chemical (or control water) delivery was initiated 24 h prior to adding fish to the tanks. To start the experiment, fathead minnows (4 males, 4 females per tank) were added to each of three tanks per treatment group. The time of fish addition was staggered by replicate within each treatment such that all samples from a given exposure tank could be collected within 60 min of the intended 96 h exposure duration. After 96 h, fish were anesthetized in buffered MS-222 and weighed. Whole gonads were removed, weighed, and preserved in RNAlater. Samples were stored at -20oC until extracted and analyzed.

value: 6 months

extract_protocol: Total RNA was isolated from tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Control fish

value: Male and female

tag: tissues

value: Gonad, liver, brain


title: HCT-8_indole_4h_rep2

status: Public on Dec 22 2009

type: RNA

city: College Station

first: Tarun

last: Bansal

state: TX

address: 3122 TAMU

department: Chemical Engineering

country: USA

institute: Texas A & M University

description: Cells were grown in RPMI 1640 medium

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 4.1.0.29054

label: biotin, Alexa-647 Streptavidin

molecule: total RNA

organism: Homo sapiens

source_name: HCT-8 cell monolayer treated with indole for 4 hr

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: HCT-8 cells were grown in monolayers till 80% confluence. Indole was added to cells and they were incubated for further 4h or 24 h. RNA was extracted using Qiagen RNeasy Kit.

tag: Human colon-cancer cell line HCT-8


title: Favorable Histology Wilms Tumor (WT00-015)

city: Chicago

first: Elizabeth

middle: J

last: Perlman

state: IL

address: 2373 North Lincoln Avenue, Room A.204

department: Pathology

institute: Children's Memorial Research Center

hyb_protocol: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols.

scan_protocol: The arrays were scanned in an HP GeneArray Scanner.

data_processing: Data were normalized using robust multi-array average (RMA) method. This normalized value of each probeset for each tumor is provided in the file “All Normalized Data.”

label: biotin

source_name: Pretreatment tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).

tag: Pretreatment tumor tissue


title: HCT-8_indole_4h_rep1

description: Cells were grown in RPMI 1640 medium


title: HCT-8_indole_24h_rep1

description: Cells were grown in RPMI 1640 medium

source_name: HCT-8 cell monolayer treated with indole for 24 hr


title: HCT-8_control_rep1

description: Cells were grown in RPMI 1640 medium

source_name: HCT-8 cell monolayer


title: HCT-8_indole_4h_rep3

description: Cells were grown in RPMI 1640 medium


title: Patient 11

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

description: patient 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with IlluminaGUI in R and log2 transformed

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrepTM RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment (Amersam Biosciences) in accordance with the prescribed protocol provided by the manufacturer

tag: disease

value: type 1 diabetes

tag: gender

value: female

tag: cell type

value: endothelial progenitor cell


title: Patient 10

description: patient 10


title: Patient 5

description: patient 5


title: Patient 9

description: patient 9


title: HCT-8_indole_24h_rep2

description: Cells were grown in RPMI 1640 medium


title: Patient 7

description: patient 7

value: male


title: Patient 6

description: patient 6


title: Patient 8

description: patient 8


title: fhm_ovary_con_61965

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
Sample 61965 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

scan_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

tag: age

tag: tissue

value: gonad

tag: sample

source_name: Reference pool


title: fhm_ovary_hal_61972

description:
Sample 61972 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: fhm ovary, exposed to 50 ug haloperidol/L for 96 h


title: fhm_ovary_hal_61953

description:
Sample 61953 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: fhm_ovary_con_61950

description:
Sample 61950 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Patient 3

description: patient 3


title: Patient 4

description: patient 4


title: Patient 1

description: patient 1


title: fhm_ovary_hal_61954

description:
Sample 61954 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Patient 2

description: patient 2


title: fhm_ovary_hal_61963

description:
Sample 61963 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: fhm_ovary_con_61957

description:
Sample 61957 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: savant_rep28

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

hyb_protocol: The two differentially labeled probes (Cy3 vs Cy5) were mixed and dried. 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS), as well as Human COT1-DNA (Life Technologies) and Poly(A)-DNA (Pharmacia) were added. Each sample was hybridized on a TIGR40K cDNA microarray overnight. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using TIGR Spotfinder.

data_processing: The intensity data was normalized and filtered using Lowess normalization and standard deviation regularization within Midas software and analyzed using MeV, which are open-access software programs for DNA microarray analyses.  All analyses were performed with a 70% data filter which means that each gene included in the analyses must have an expression value in 70% of the 116 samples studied. Significant differentially expressed genes were identified using the Significance Analysis of Microarrays (SAM) module within MeV for both 2-class and 4-class analyses, with a maximum false discovery rate (FDR) of 5%.

source_name: LCL derived from autistic – savant

label_protocol: 10 ug of total RNA were primed with 2 ul of Random Hexamer Primers (3 mg/mL) at 70°C for 10 min, then reversed transcribed at 42°C overnight in the presence of 400 U SuperScript II RTase (Invitrogen), and 1.2 ul of 25X aminoallyl-dNTP mix (Ambion). 4.5 ul of the appropriate NHS-ester Cy dye (AmershamPharmacia) in DMSO was added to aa-cDNA.

extract_protocol: Total RNA was isolated from LCL using the TRIzol (Invitrogen) isolation method according to the manufacturer’s protocols.

value: lymphoblastoid

tag: cell line

value: Lymphoblastoid cell line derived from peripheral blood mononuclear cells

tag: sample type

value: test

source_name: Stratagene Universal Human RNA

value: reference


title: savant_rep27


title: HCT-8_control_rep3

description: Cells were grown in RPMI 1640 medium


title: savant_rep29


title: fhm_ovary_hal_61969

description:
Sample 61969 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: savant_rep25


title: savant_rep21


title: savant_rep26


title: savant_rep20


title: savant_rep24


title: savant_rep23


title: fhm_ovary_con_61966

description:
Sample 61966 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: fhm_ovary_con_61958

description:
Sample 61958 - ovary from fathead minnow exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: savant_rep30


title: savant_rep22


title: savant_rep18


title: savant_rep17


title: savant_rep16


title: savant_rep15


title: fhm_ovary_hal_61962

description:
Sample 61962 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: savant_rep19


title: HCT-8_control_rep2

description: Cells were grown in RPMI 1640 medium


title: savant_rep10


title: savant_rep12


title: savant_rep14


title: savant_rep13


title: savant_rep9


title: savant_rep8


title: savant_rep6


title: savant_rep4


title: mild_rep23

source_name: LCL derived from autistic – mild


title: savant_rep7


title: savant_rep1


title: mild_rep21


title: mild_rep26


title: mild_rep24


title: savant_rep3


title: mild_rep20


title: mild_rep25


title: mild_rep19


title: mild_rep17


title: mild_rep18


title: mild_rep22


title: savant_rep2


title: mild_rep16


title: mild_rep14


title: mild_rep15


title: mild_rep11


title: mild_rep8


title: mild_rep12


title: mild_rep7


title: mild_rep13


title: mild_rep9


title: mild_rep6


title: mild_rep3


title: mild_rep4


title: mild_rep2


title: language_rep22

source_name: LCL derived from autistic – severe language impaired


title: language_rep24


title: mild_rep5


title: language_rep21


title: language_rep29


title: language_rep28


title: language_rep27


title: language_rep26


title: language_rep23


title: language_rep20


title: language_rep17


title: language_rep25


title: language_rep18


title: language_rep16


title: language_rep14


title: language_rep13


title: language_rep15


title: savant_rep11


title: language_rep12


title: language_rep19


title: language_rep10


title: language_rep11


title: mild_rep10


title: control_rep28

source_name: LCL derived from nonautistic control


title: language_rep4


title: control_rep27


title: language_rep6


title: language_rep9


title: mild_rep1


title: control_rep26


title: control_rep24


title: Knockout_4h lipopolysaccharide_replicate 2

city: Bethesda

first: Bradley

middle: A

last: Carlson

state: MD

address: 9000 Rockville Pike

institute: National Cancer Institute

description: Biological replicate 2 of 3.

hyb_protocol: Hybridization was done according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed using GCOS 1.3 (Affymetrix).

data_processing: For data processing, data files (in txt format) and cel files were imported into the microarray database (mAdb) and analyzed by software tools provided by the National Cancer Institute, Center for Cancer Research in collaboration with the National Institutes of Health, Center for Information Technology, Bioinformatics and Molecular Analysis Section. All Absent calls were excluded.

organism: Mus musculus

source_name: bone marrow-derived macrophages, trsp knockout, LPS stimulated

label_protocol: GeneChip® IVT Labeling Kit according to manufacturer's instructions.

growth_protocol: Bone marrow cells were differentiated for 7 days in the presence of M-CSF.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: BMDM were treated with or without LPS for 4h, cells washed with PBS and cells harvested.

tag: strain

tag: genotype

value: Trspfl/fl-LysM-Cre+/-

tag: treatment

value: LPS


title: language_rep3


title: control_rep23


title: Knockout_4h lipopolysaccharide_replicate 3

description: Biological replicate 3 of 3.


title: savant_rep5


title: language_rep1


title: language_rep2


title: control_rep29


title: Knockout_4h lipopolysaccharide_replicate 1

description: Biological replicate 1 of 3.


title: control_rep21


title: control_rep20


title: language_rep7


title: language_rep5


title: control_rep25


title: language_rep8


title: language_rep30


title: control_rep19


title: Control_4h lipopolysaccharide_replicate 3

description: Biological replicate 3 of 3.

source_name: bone marrow-derived macrophages, control, LPS stimulated

value: Trspfl/fl-LysM-Cre-/-


title: control_rep18


title: control_rep12


title: control_rep14


title: control_rep13


title: control_rep16


title: control_rep17


title: control_rep3


title: control_rep15


title: control_rep4


title: control_rep2


title: Control_untreated_replicate 3

description: Biological replicate 3 of 3.

source_name: bone marrow-derived macrophages, control, untreated


title: Knockout_untreated_replicate 1

description: Biological replicate 1 of 3.

source_name: bone marrow-derived macrophages, trsp knockout, untreated


title: Control_4h lipopolysaccharide_replicate 2

description: Biological replicate 2 of 3.


title: Knockout_untreated_replicate 2

description: Biological replicate 2 of 3.


title: control_rep22


title: control_rep10


title: control_rep11


title: control_rep5


title: control_rep7


title: Knockout_untreated_replicate 3

description: Biological replicate 3 of 3.


title: Control_untreated_replicate 2

description: Biological replicate 2 of 3.


title: Control_4h lipopolysaccharide_replicate 1

description: Biological replicate 1 of 3.


title: control_rep8


title: Control_untreated_replicate 1

description: Biological replicate 1 of 3.


title: language_rep31


title: C3H sick 2

status: Public on Dec 21 2009

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

country: Canada

institute: McGill University

description: Gene expression data from C3H/HeJ strain treated with 18Gy thoracic irardiation

hyb_protocol: The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99C, incubated for 5 minutes at 45C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in 13 hybridization buffer for 10-20 minutes at 45C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 458C overnight (16-20 hours).

scan_protocol: GeneChips were scanned using a GeneArray Scanner (Agilent technologies)

data_processing: data was analyzed using the MAS5.0 algorithm.

source_name: C3H/HeJ strain lung RNA, treated

label_protocol: After second-strand synthesis, the probe cDNA was purified by phenol chloroform extraction with Phase-Lock tubes (Eppendorf) and redissolved in 20 ml DEPC water. Biotinylated probe was prepared from the entire cDNA reaction mixture with the ENZO bioarray high-yield RNA transcript labeling kit (ENZO diagnostics). The probe synthesis reaction was performed at 378C for 5 hours with occasional agitation. The biotinylated probe was purified by using an RNAeasy spin column (Qiagen), eluted in 80 ml of DEPC water, quantified by spectrophotometry, and analyzed on a nondenaturing gel. The average probe length was reduced by incubating the purified probe in 13 fragmentation buffer for 35 minutes at 958C.

extract_protocol: Following sacrifice, the right lung was immediately homogenized in 2 mL of Trizol reagent and placed in dry ice. The homogenates were stored at -85 degrees C until RNA isolation. Total lung RNA was extracted according to the manufacturer’s (Sigma) instructions. To define the set of expressed genes the RNA from three post treatment moribund mice, and three samples from control mice, was evaluated for each strain.  RNA quality was assessed and confirmed using the Agilent Bioanalyzer (Agilent Technologies, Palo Alto, California).

treatment_protocol: Mice were treated at 8 weeks of age. Lung damage was elicited by whole thorax radiation exposure (18 Gy) using a Gamma cell Cesium-137 unit. The rest of the body was shielded with 3 cm of lead, to reduce the beam strength to 3% in this area.  The mice were weighed weekly from eight weeks after radiation and sacrificed when moribund which was defined as loss of > 20% body weight, exhibition of distress through ruffled fur, accelerated breathing and hunched posture.

value: lung

value: 20-22 weeks

value: 18Gy thoracic irradiation


title: C3H control 3

description: Gene expression data from untreated C3H/HeJ strain

source_name: C3H/HeJ strain lung RNA, control

value: 15-26 weeks

value: untreated


title: control_rep9


title: control_rep6


title: control_rep1


title: mesocarp_36h_1-MCP_17b

status: Public on Apr 01 2010

city: Padova

first: Livio

last: Trainotti

address: Via Ugo Bassi 58/B

department: Biology

country: Italy

institute: University of Padova

description:
The fine tuning of the excitation/emission settings has been possible due to the presence of control probes on the platform.
Technical replicate of "mesocarp_36h_1-MCP_17a"

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm. Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 90-100 pmol of Cy3- and Cy5-labelled target cDNAs. The hybridisation solution was kept in place by means of a microarray gene frame (ABgene, UK), while the glass slides were placed in a hybridisation chamber (HybChamber, by Genomic Solutions, USA) kept on a rotary oven for at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing:
Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data.
Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones.
The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”, keeping as reference the Cy3 channel. The “IA” and “IB” values have been used to determine log2(IB/IA) reported in the “VALUE” column.
Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses. Since each comparison (air vs 1-MCP and 1-MCP vs air –“dye-swap”-) was repeated twice, and a “percentage cutoff filter”, set to 75%, was used to eliminate those gene with less than 3 data points, there were at least 3 values for each gene to be used in the SAM analysis. Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of about 5%.

organism: Prunus persica

label_protocol: Total RNA (15 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dye: the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) stored in air and used as control.

extract_protocol: Total RNA was extracted following the protocol described by Chang et al. (1993). RNA yield and purity were checked by means of UV absorption spectra, whereas RNA integrity was ascertained by electrophoresis in agarose gel followed by ethidium bromide staining.

treatment_protocol: One hundred fruit, homogeneous for size and position on the plant, were placed in a sealed 30-L plastic jars (50 fruit each) for 12 h at 25 °C without 1-MCP (air controls). At the end of treatment, temperature, ethylene and CO2 concentration within the jar were determined. Fruit were then transferred in a growth chamber at 25°C for 24 hours.For molecular analyses, mesocarp from a pool of 10 fruit per class was frozen in liquid nitrogen and stored at -80°C until use.

tag: experimental protocol

value: mesocarp

label_protocol: Total RNA (15 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dye: the red-fluorescent cyanine5 (Cy5) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) treated with 1-methylcyclopropene (1-MCP).

extract_protocol: As in channel 1

treatment_protocol:
channel 2 protocol
One hundred fruit, homogeneous for size and position on the plant, were placed in a sealed 30-L plastic jars (50 fruit each). SmartFreshTM (AgroFresh Inc., Philadelphia, PA, USA), a commercial powder containing 0.14% (w/w) 1-MCP a.i., was prepared as a 10-fold concentrated stock solution following the technical bulletin of the company, and injected as 10 mL of air (final concentration 1 µL/L equivalent to 1 ppm). At the end of treatment, temperature, ethylene and CO2 concentration within the jars were determined. Fruit were then transferred in a growth chamber at 25°C for 24 hours.For molecular analyses, mesocarp from a pool of 10 fruit per class was frozen in liquid nitrogen and stored at -80°C until use.


title: C3H control 1


title: B6 control 2

description: Gene expression data from untreated C57BL6/J strain

source_name: C57BL6/J strain lung RNA, control


title: C3H control 2


title: B6 control 3


title: B6 sick 2

description: Gene expression data from C57BL6/J strain treated with 18Gy thoracic irardiation

source_name: C57BL6/J strain lung RNA, treated

value: 28-30 weeks


title: AJ control 2

description: Gene expression data from untreated A/J strain

source_name: A/J strain lung RNA, control

value: A/J


title: MEF2-LPS

city: Ube

first: Akira

last: Nakai

state: Yamaguchi Prefecture

address: Minami-Kogushi 1-1-1

department: Graduate School of Medicine

country: Japan

institute: Yamaguchi University

description: Gene expression data from cells treated with LPS (1 μg/ml) for 4 hours

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Mouse embryo fibroblasts #2

label_protocol: Biotinylated cRNA were prepared from 1 μg total RNA with a One-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: Cells were maintained at 37˚C in 5% CO2 in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum.

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

treatment_protocol: Cells were maintained at 37˚C (Control), treated with lipopolysaccharide (LPS, E. coli 0127:B8, Sigma, 1 μg/ml) for 4 hours, or treated with LPS for 4 hours after the pretreatment of heat shock at 42˚C for 1 hour.

value: ICR

value: Embryo

tag: developmental stage

value: Embryonic day 15.5

tag: agent

value: LPS (1 μg/ml) for 4 hours


title: AJ control 3


title: AJ sick 2

description: Gene expression data from A/J strain treated with 18Gy thoracic irardiation

source_name: A/J strain lung RNA, treated

value: 30-32 weeks


title: MEF2-Control

description: Gene expression data from untreated cells


title: AJ control 1


title: B6 sick 1


title: MEF1-LPS

source_name: Mouse embryo fibroblasts #1


title: B6 control 1


title: MEF1-Control


title: AJ sick 1


title: wt_4

city: Memphis

first: Darryl

last: Quarles

state: TN

address: 920 Madison Ave

institute: University of Tennessee Health Science Center (UTHSC)

description: We isolated total RNAs from long bones of both WT and Hyp mice at 12 days of age. Since the RNA yields from the long bones are very low, we combined 2 bone samples with same genotype (WT or Hyp) for one RNA extraction. We will compare the difference of the gene expressions between Hyp and WT. We will use 4 samples in each animal condition.

hyb_protocol: 200ul hybridization solution per GeneChip. Hybridization Solution Contents: Final Concentrations 0.05ug per ul fragmented cRNA , 50pM control oligo B2 , spike hybridization controls[1.5 pM bioB , 5 pM bioC , 25 pM bioD , 100 pM cre] , 0.1mg per ml Herring Sperm DNA , 0.5mg per ml Acetylated Bovine Serum Albumin, 10% DMSO (3 prime Amplification labeling kit only) , 1x Hybridization buffer, H2O to a final volume of 300ul. Hybridization Description: 45C , 16hr , 60 rpm rotation in GeneChip hybridization trays using GeneChip Hybridization oven 640. Washing Protocol: EukGE-WS2v5_450

scan_protocol: single scan

data_processing: Microarray data were analyzed using GeneSpring GX 9 (Silicon Genetics). The Robust Multichip Averaging (RMA) probe summarization algorithm was used to perform background correction, normalization and probe summarization. The baseline transformation to median of all samples was applied.

source_name: long bones of WT mice

label_protocol: Invitro Transcription using the GeneChip Expression 3prime-Amplification Labeling kit.

growth_protocol: Hyp mice were purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained in the vivarium at University of Kansas Medical Center under standard diet purchased from Harlan Talked (Madison, WI), which contains 0.6% Ca, 0.54% Pi and 2200 IU vitamin D. All the mice were utilized in accordance with the recommendations in the “Guide for Care and Use of Laboratory Animals” and the guidelines established by the University of Kansas Medical Center Institutional Animal Care and Committee.

extract_protocol: We extract total RNA with TRI REAGENT from Molecular Research Center, Inc.

tag: Strain

value: wild type

tag: Age

value: 12 days

tag: Gender

value: male

tag: Tissue

value: long bone (tibia and femur)


title: C3H sick 3

value: lung


title: C3H sick 1

value: 20-22 weeks


title: B6 sick 3

value: 18Gy thoracic irradiation


title: NCC2913 7 min HS (2913-7HS-3)

city: Lausanne 26

first: Bernard

last: Berger

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

description: biological replicate  HS39

hyb_protocol: The hybridization conditions and the washing of the slide were performed as follows. To the 20 l of cDNA (obtained with the Genisphere kit), 25 ul of control target Agilent, 60 l of H2O and 105 ul of Agilent buffer were added. After 10 minutes of incubation at 80°C and 15 minutes at 65°C, the reaction was loaded on a pre-warmed slide in the hybridization chamber and incubated for 16 hours at 65°C, at four rpm in an Agilent oven. The cDNA hybridization was washed 10 min at 42°C in 6x SSC, 0.005% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100. The 3DNA hybridization was carried out as described in the Genisphere protocol except for the hybridization volume which was increased to 204 l and the washing modified as follows : 10 min at 65°C in 2x SSC, 0.0016% Triton x-100, 5 min at RT in 2x SSC, 0.0016% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100.

scan_protocol: The slides were scanned at 10 m with a Scanarray 4000 (Packard Biochip Technologies, Billerica, MA, USA)

data_processing: Data were extracted with Imagene 5.6 (Biodiscovery, El Segundo, CA, USA). Data were treated with homemade scripts in Python language (www.python.org) and a local installation of the ArrayPipe web server (15). Probes showing a signal smaller than twice the standard deviation of the local background were considered without signal. Probes showing no signal or saturated signals in both channels were discarded from the analysis. Assuming an intensity-dependent variation in dye signal, (limma) loess global normalization was applied on signal ratios.

organism: Bifidobacterium longum

source_name: NCC2913 7 min HS

label_protocol: RNA labelling and cDNA synthesis were carried out using the 3DNA Array 900 MPX Genisphere kit (Genisphere Inc., Hatfield, PA, USA) combined with the In situ Hybridization Kit Plus.

growth_protocol: in MRS cystein medium

extract_protocol: Total RNA extraction as described in Parche et al. 2006. J.Bacteriol. 188:1260-1265.

tag: 7 min HS

source_name: NCC2705 7 min HS


title: NCC2913 before HS (2913-bHS-4)

description: biological replicate  HS38

source_name: NCC2913 before HS

tag: before HS

source_name: NCC2705 before HS


title: NCC2913 stationary phase (2913-stat-1)

description: biological replicate  HS45

source_name: NCC2913 stationary phase

tag: stationary phase

source_name: NCC2705 stationary phase


title: wt_1


title: NCC2913 stationary phase (2913-stat-2)

description: biological replicate  HS45


title: NCC2913 stationary phase (2913-stat-4)

description: biological replicate  HS50


title: NCC2913 7 min HS (2913-7HS-1)

description: biological replicate  HS22


title: NCC2913 stationary phase (2913-stat-3)

description: biological replicate  HS50


title: wt_2


title: NCC2913 before HS (2913-bHS-3)

description: biological replicate  HS38


title: NCC2912 stationary phase (2912-stat-4)

description: biological replicate  HS50

source_name: NCC2912 stationary phase


title: wt_3


title: AJ sick 3

tag: tissue

tag: age


title: NCC2913 before HS (2913-bHS-2)

description: biological replicate  HS20


title: NCC2913 7 min HS (2913-7HS-4)

description: biological replicate  HS39


title: Lung ECS-PEITC-I3C

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

institute: University of Genoa

hyb_protocol: Microarray were hybridized in 6X SSPE/30% formamide at 25°C for 18h, washed in 0,75XTNT buffer at 37 for 40 min, and processed using direct detection of the biotin-containing transcript by streptavidin-Alexa647 conjugate.

scan_protocol: The processed slides were scanned by using an Axon 4000B microarray Scanner, with the laser set at 635 nm and Power 80% and the photomultiplier set at 70 with a scan resolution of 10 µm

data_processing: Local background was subtracted from raw data, which were then log transformed, normalized, and analyzed by GeneSpring software version 7.2 (Agilent Technologies, Santa Clara, CA).  Expression data were median centered by using the Gene-Spring normalization option, which normalizes both per gene and per array.  Quadruplicate data generated for each miRNA were compared among the various experimental groups by volcano-plot analysis, which evaluates both fold variations and statistical significance of differences by ANOVA and Bonferroni multiple testing correction.  Global miRNA expression profiles of the various experimental groups were compared by hierarchical cluster analysis and by bidimensional principal component analysis (PCA).

organism: Rattus norvegicus

source_name: Lung

label_protocol: Five µg of total RNA was reverse-transcribed using a reaction mix containing 1µg of (3'(N)8-(A)12-biotin-(A)12-biotin 5') oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. Four µl of 5X first-strand buffer, 2 volumes of DTT 0,1M, 1µl of 10 mM dNTPs mix and 1µl Superscript II RNaseH reverse transcriptase (200 U/µl) were added. The samples were incubated for 90 min at 37°C. To denature the RNA/DNA hybrids and degrade RNA templates a mixture of  3,5 µl of 0,5M NaOH/ 50mM EDTA were added to 20 µl of first reaction mix. Five µl of 1M Tris-HCl pH7,6 were added to neutralize the reaction mix, and the labeled targets were stored at -80°C until hybridization.

growth_protocol: Half of 16 groups of adult male Sprague-Dawley rats, were exposed to ECS for 28 days, while the remaining (sham exposed) were kept for the same period of time in filtered air

extract_protocol: The lungs were collected, immersed in an RNA stabilizing buffer and frozen at -80°C

treatment_protocol: 14 of 16 groups were treated with chemopreventive agents starting 3 days before exposure to ECS. NAC were given with the drinking water, wile all other agents were supplemented to the diet.

value: Sprague-Dawley

value: environmental cigarette smoke and phenethyl isothiocyanate and indole-3-carbinol


title: PT2-LLNLe_48h

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

institute: IRCCS AOU San Martino – IST, Genova

description: Gene expression data from GBM TICs were treated with the gamma secretase inhibitor z-Leu-leu-Nle-CHO (LLNle) for 48 hours.

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Human Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were subsequently scanned using a confocal laser GeneChip Scanner 3000 7G and GeneChip Command Console (Affymetrix).

data_processing: Affymetrix raw data files (CEL files) are used as input files in expression console environment (Affymetrix, Inc., Santa Clara, CA). Briefly, Cel files were processed using Robust Multi-Array Analysis procedure (Irizarry et al., 2003). The RMA method was used, first, to convert the intensities from the multiple probes in a probeset into a single expression value with greater precision and reduced background noise, relying on the perfect match probes only (ignoring the mismatch probes) and, after, to normalize by sketch quantile normalization. Also quality assessement were performed in expression console environment.

source_name: Human glioblastoma (GBM) tumor initiating cells (TICs).

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes.

growth_protocol:
Proliferation medium was DMEM-F12/Neurobasal additioned with 1% v/v B27 supplement, (Gibco Ltd, Paisley, Scotland), 2 mM L-glutamine (Gibco Ltd), recombinant human fibroblast growth factor (FGF-2, 10 ng/ml Peprotech, London, UK), recombinant human epidermal growth factor (EGF, 20 ng/ml Peprotech). The medium was changed twice a week. Under these conditions, TICs were grown as a monolayer in flasks coated with Matrigel (BD Biosciences, San Jose, CA) express stem cell markers, maintained intact self-renewal capacity, partial multilineage differentiation ability and gave rise to tumor when injected orthotopically in nude mice (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity.
Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).

extract_protocol:
miRNeasy Mini Kit (Qiagen) with DNase treatment.
RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor z-Leu-leu-Nle-CHO (LLNle) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

tag: GBM TICs were obtained from tumor samples of patients subjected to surgery at Neurosurgery Department of the San Martino Hospital in Genova. An informed consent was obtained from all patients before surgery as required by the Ethic Board.

tag: Cells isolation was described in detail elsewhere (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity.


title: hyp_3

description:
Hyp mice have a 3' deletion of the Phex gene on a C57BL/6 genetic background.
We isolated total RNAs from long bones of both WT and Hyp mice at 12 days of age. Since the RNA yields from the long bones are very low, we combined 2 bone samples with same genotype (WT or Hyp) for one RNA extraction. We will compare the difference of the gene expressions between Hyp and WT. We will use 4 samples in each animal condition.

source_name: long bones of Hyp mice


title: NCC2913 before HS (2913-bHS-1)

description: biological replicate  HS20


title: hyp_2


title: hyp_4


title: PT3-LLNLe_48h

tag: Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).


title: hyp_1


title: PT3-DAPT_48h

description: Gene expression data from GBM TICs were treated the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) for 48 hours.

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: PT1-LLNLe_48h


title: NCC2913 7 min HS (2913-7HS-2)

description: biological replicate  HS22


title: PT3-DMSO_48h

description: Gene expression data from GBM TICs were treated with vehicle alone (DMSO 0.1%) for 48 hours.

treatment_protocol: GBM TICs were treated with vehicle alone (DMSO 0.1%) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: NCC2912 stationary phase (2912-stat-3)

description: biological replicate  HS50


title: NCC2912 7 min HS (2912-7HS-3)

description: biological replicate  HS39

source_name: NCC2912 7 min HS


title: NCC2912 7 min HS (2912-7HS-4)

description: biological replicate  HS39


title: NCC2912 stationary phase (2912-stat-2)

description: biological replicate  HS45


title: Lung PEITC-I3C

tag: strain

value: phenethyl isothiocyanate and indole-3-carbinol


title: Lung OPZ-NAC

value: oltipraz and N-acetylcysteine


title: NCC2912 stationary phase (2912-stat-1)

description: biological replicate  HS45


title: NCC2912 7 min HS (2912-7HS-1)

description: biological replicate  HS22


title: NCC2912 before HS (2912-bHS-4)

description: biological replicate  HS38

source_name: NCC2912 before HS


title: PT2-DMSO_48h


title: NCC2912 7 min HS (2912-7HS-2)

description: biological replicate  HS22


title: NCC2912 before HS (2912-bHS-1)

description: biological replicate  HS20


title: PT3-DAPT_24h

description: Gene expression data from GBM TICs were treated the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) for 24 hours.

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT)  and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).


title: PT3-DMSO_24h

description: Gene expression data from GBM TICs were treated with vehicle alone (DMSO 0.1%) for 24 hours.

treatment_protocol: GBM TICs were treated with vehicle alone (DMSO 0.1%) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).


title: B.subtilis strain PB565 L2(20); time 395_rep2 biological

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

institute: TNO

description: This sample is collected from cells growing in the presence of light at 395 minutes after inoculation. It is the second of two biological replicates used in this experiment (replicate from sample 14).

hyb_protocol: The NimbleGen hybridization system was used to hybridize the probes to the oligos on the array. First, 4 µl of yeast tRNA was supplemented to each sample prior to the drying step. Dried nucleotides were suspended in 11.5 µl DIG Easyhyb hybridization buffer (Roche) and 0.5 µl of the 50 mM C3-CPK6-48mer suspension (NimbleGen). The mixture was incubated for 5 min at 95°C and transferred to a 42°C block and hybridized on 60-mer B. subtilis subsp. subtilis strain NC_000964 microarray slides (Roche NimbleGen, Inc.). Hybridization was performed overnight at 42ºC in a Nimblegen hybridization system 4 (Roche NimbleGen, Inc.) according to the manufacturer's protocol. Microarray slides were washed for 10 sec in 1x SSC/0.2% SDS at 37 ºC, 10 sec in 0.5x SSC at 37 ºC, and twice for 10 min in 0.2x SSC at room temperature. Slides were dried by the use of a nitrogen flow and scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

scan_protocol: Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences).

data_processing: The TIFF-images were quantified with the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).The raw data (.pair file) were 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 (Roche NimbleGen, Inc.).

organism: Bacillus subtilis

label_protocol: From the isolated RNA 1 μg was vacuum dried and cDNA was synthesized by the use of random hexamer pd(N)6-primers (Roche, Mannheim, Germany), Superscript II reverse transcriptase (Life Technologies) and 2 mM dATP, 2 mM dGTP, 2 mM dCTP, 1.2 mM dTTP (Roche) and 0.8 mM aa-dUTP (Sigma). Subsequently, RNA was hydrolyzed in the presence of NaOH and  the cDNA solution was purified using QIAquick®Spin colomns (QIAGen). The cDNA was eluted from the column with 30 μl milliQ water and vacuum dried. For coupling of the Cy3 dye ester DNA samples were suspended in 0.1 M Na3CO3 buffer pH 9.0, at room temperature. The Cy3 ester was added in a final concentration of 0.1 mM (Amersham Pharmacia) and incubated for 1 hour at RT in the dark and purified using G50 Autoseq columns (GE Healthcare). Quality and incorporation of the Cy3 dye was checked with the NanoDrop® ND-1000 UV Spectrophotometer.

growth_protocol: The medium used for these experiments was TSB (tryptic soy broth, 30 g/L), supplemented with 0.5% glucose, 5 μg/mL chloramphenicol, 1 μg/mL erythromycin and 10 μg/mL kanamycin, where applicable. Overnight cultures of strain PB565/pYtvA and PB565 were grown in this medium in the dark, starting from a single colony of a fresh plate of the same medium. The overnight cultures were diluted and allowed to grow in the dark until they had reached the exponential growth phase again, re-diluted in an end-volume of 10 ml, and distributed over different 100-ml Erlenmeyer flasks to initiate an experiment. The Erlenmeyer flasks were placed in a shaking water bath at 37 °C and 250 rpm in the light or in the dark.

extract_protocol: Cells were disrupted in a 2-ml screw-cap tube in the presence of 100-μm zirconium beads and SDS/phenol for 60 seconds in the Minibeadbeater 8™ (Biospec Products). After chloroform extraction, nucleic acids were precipitated, vacuum-dried, and further purified with the ChargeSwitch total RNA cell kit (Invitrogen) according to manufacturer’s instructions. RNA purity was verified by its absorption characteristics in the UV region using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). RNA MW profiles were verified with the 2100 Electrophoresis Bioanalyzer (Agilent Technologies). The RNA 6000 ladder (Ambion Inc, Austin TX, USA) consisting of 6 transcripts at a concentration of 20 ng/μl, and ranging from 0.2 to 6.0 kb in length was used as a marker. In addition, a fast migrating reference marker compound was added to all samples for software alignment of the electropherograms within one LabChip run (Agilent Technologies).

treatment_protocol:
For the YtvA-dependent experiment, strain PB565/pYtvA was grown in TSB (tryptic soy broth, 30 g/L), supplemented with 0.5% glucose, 5 μg/mL chloramphenicol, 10 μg/mL kanamycin. IPTG 1mM final concentration was added to cells grown exponentially in the dark and in the presence of light when the OD was 0.6. Samples (dark, light, and their replicas) were taken before and 118 min after addition of IPTG and immediately flash frozen in liquid nitrogen and storage at -80.
For the YtvA-independent experiment, strain PB565 was grown in TSB (tryptic soy broth, 30 g/L), supplemented with 0.5% glucose, 5 μg/mL chloramphenicol, 0.5 μg/mL erythromicinthe presence and in absence of light, until cells were at the beginning of stationary phase (~OD 4, 285 minutes after inoculation). Samples were taken at 285 minutes and 390 minutes after inoculation (~100 minutes after cells enter stationary phase) and immediately flash frozen in liquid nitrogen and storage at -80. For both experiments, white light was used (see below) and two cultures (coming from two independent colonies) were grown in parallel as biological replicas.

tag: condition

value: light

tag: time

value: 395 min

tag: replicate

value: biological


title: B.subtilis strain PB565 L1(19); time 395_rep1 technical+biological

description: This sample is collected from cells growing in the presence of light at 395 minutes after inoculation. It is the first of two technical and biological replicates used in this experiment (technical replicate from sample 15, biological replicate from sample 16).

value: technical+biological


title: PT1-DAPT_48h

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT)  and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: Lung ECS-PEITC

tag: agent

value: environmental cigarette smoke and phenethyl isothiocyanate


title: NCC2912 before HS (2912-bHS-3)

description: biological replicate  HS38


title: Lung ECS-NAC

value: environmental cigarette smoke and N-acetylcysteine


title: B.subtilis strain PB565 D1(22); time 395_rep2 technical

description: This sample is collected from cells growing in the dark a at 395 minutes after inoculation. It is the second of two technical replicates used in this experiment (replicate from sample 11).

value: dark

value: technical


title: Lung ECS-OPZ

value: environmental cigarette smoke and oltipraz


title: PT3-LLNLe_24h

tag: Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6)


title: B.subtilis strain PB565 D1(22); time 395_rerp1 technical+biological

description: This sample is collected from cells growing in the dark a at 395 minutes after inoculation. It is the first of two technical and biological replicates used in this experiment (technical replicate from sample 13, biological replicate from sample 12).


title: Lung ECS-BF

value: environmental cigarette smoke and 5,6-benzoflavone


title: NCC2912 before HS (2912-bHS-2)

description: biological replicate  HS20


title: B.subtilis strain PB565 D2 (23); time 395_rep2 biological

description: This sample is collected from cells growing in the dark a at 395 minutes after inoculation. It is the second of two biological replicates used in this experiment (replicate from sample 11).


title: Lung ECS-I3C

value: environmental cigarette smoke and indole-3-carbinol


title: B.subtilis strain PB565 D3(12); time 290_rep2 biological

description: This sample is collected from cells growing in the dark a at 290 minutes after inoculation. It is the second of two biological replicates used in this experiment.

value: 290 min


title: PT2-DMSO_24h


title: Lung OPZ

value: oltipraz


title: B.subtilis strain PB565 D1(10); time 290_rep1 biological

description: This sample is collected from cells growing in the dark a at 290 minutes after inoculation. It is the first of two biological replicates used in this experiment.


title: B.subtilis strain PB565/pYtvA dark 1(20): time after IPTG 118 min_rep1 biological

description: This sample is collected from cells growing in the dark and 118 min after adding IPTG. It is the first of two biological replicates used in this experiment.

tag: protocol

value: after IPTG

value: 118  min


title: PT1-DMSO_48h


title: PT2-DAPT_24h


title: PT2-LLNLe_24h

description: Gene expression data from GBM TICs were treated with the gamma secretase inhibitor z-Leu-leu-Nle-CHO (LLNle) for 24 hours.

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor z-Leu-leu-Nle-CHO (LLNle) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).


title: Lung BF

value: Sprague-Dawley


title: B.subtilis strain PB565/pYtvA dark 2(22): time after IPTG 118min_rep2 biological

description: This sample is collected from cells growing in the dark and 118 min after adding IPTG. It is the second of two biological replicates used in this experiment.


title: B.subtilis strain PB565/pYtvA dark 1(2):  time before IPTG adition_rep1 biological

description: This sample is collected from cells growing in the dark and before adding IPTG. It is the first of two biological replicates used in this experiment.

value: before IPTG

value: control


title: B.subtilis strain PB565/pYtvA light 2(21); time after IPTG 118 min_rep2 biological

description: This sample is collected from cells growing in the presence of light and 118 min after adding IPTG. It is thesecond of two biological replicates used in this experiment.

value: light


title: Lung PEITC

value: phenethyl isothiocyanate


title: Lung NAC

value: N-acetylcysteine


title: B.subtilis strain PB565/pYtvA dark 2(4):  time before IPTG adition_rep2 biological

description: This sample is collected from cells growing in the dark and before adding IPTG. It is the second of two biological replicates used in this experiment.

value: biological


title: Lung ECS

value: environmental cigarette smoke


title: PT1-LLNLe_24h


title: B.subtilis strain PB565/pYtvA light 1(19); time after IPTG 118 min_rep1 biological

description: This sample is collected from cells growing in the presence of light and 118 min after adding IPTG. It is the first of two biological replicates used in this experiment.


title: PT1-DAPT_24h

description: Gene expression data from GBM TICs were treated with the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) for 24 hours.

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes

treatment_protocol: GBM TICs were treated with the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).


title: B.subtilis strain PB565/pYtvA light 1(1): time before IPTG adition_rep1 biological

description: This sample is collected from cells growing in the presence of light and before adding IPTG. It is the first of two biological replicates used in this experiment.


title: B.subtilis strain PB565/pYtvA light 2(3): time before IPTG adition_rep2 biological

description: This sample is collected from cells growing in the presence of light and before adding IPTG.It is the second of two biological replicates used in this experiment.


title: Lung Control


title: PT1-DMSO_24h

description: Gene expression data from GBM TICs were treated with vehicle alone (DMSO 0.1%) for 24 hours.


title: Calu-3-H3N2-06h-3

status: Public on Dec 19 2009

city: Newcastle

first: Alan

middle: Chen-Yu

last: Hsu

state: NSW

address: Lvl 3 HMRI, John Hunter Hospital, Lookout Rd, New Lambton Height

department: Respiratory Medicine

country: Australia

institute: University of Newcastle

description:
H3N2-06-3
4569624067_F

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Data was imported into BeadStudio 3.0 (Illumina) and normalized to the median hybridization intensity of all genes on the beadchip, and exported to GeneSpring GX 10 (Agilent Technologies) for further analysis. Data were first normalized to the uninfected medium control, and a one-way analysis of variance (ANOVA) was used with Benjamini-Hochberg correction to identify genes that were differentially expressed in H3N2 and H11N9 infection. A p value ≤ 0.05 was considered to be significant and a fold change ≥ 2 in expression was defined as the cut-off for significant change in expression. Hierarchical clustering was performed using centroid linkage clustering with Euclidean Distance.

Non-normalized data is available in the 'GSE19580.non-normalized.txt' file, which is linked to the Series GSE19580 record as a supplementary file.

source_name: Calu-3, infected with H3N2, RNA collected at 6hr

label_protocol: Streptavidin-Cy3 (2ul of 1mg.mL stock per chip) was added to block E1 buffer (2ml per chip). The mix was then added to the beadchip, and incubated in dark at room temp for 10 min.

growth_protocol: Calu-3 cells were maintained in MEM/10% Fetal bovine serum until the day of infection. After infection, the cells were cultured in serum-free MEM.

extract_protocol: Total RNA extraction was performed by adding RLT buffer to the cells and incubated for 15min at room temp. Harvested RNA in RLT buffer was then extracted using Rneasy Mini kit (Qiagen).

treatment_protocol: Cells were infected with human influenza H3N2 and a low pathogenic avian influenza H11N9.

tag: cell line

tag: cell type

value: bronchial epithelial cells

tag: virus infection

tag: time of harvest


title: TFIIB_ChIP-chip_LCL721_Px7

type: genomic

city: Muenster

first: Thomas

middle: Karl

last: Albert

address: Robert-Koch-Strasse 43

department: IMTB - Institute of Molecular Tumor Biology

country: Germany

institute: University Muenster

hyb_protocol: Hybridization was performed by NimbleGen (Reykjavik, Iceland)

scan_protocol: Slides were scanned by NimbleScan (Reykjavik, Iceland)

data_processing: Data were processed by NimbleGen according to standard procedures (see http://www.nimblegen.com). Each of the 24,134 human promoter regions is represented by a probe set consisting of 15x 50-mer individual oligonucleotide probes on the array. The median of the scaled log2 ChIP/input ratio of each probe set provides a measure for promoter occupancy. For each feature a log2 ratio of the hybridization intensities of the cohybridized ChIP-enriched sample (Cy5 channel) and non-enriched input sample (Cy3 channel) was determined. These ratios were scaled to center the data around zero by robust statistics. Specifically, scaling was performed by subtracting Tukey's bi-weight mean for the log2 ratios of all array features from each individual log2 ratio.

molecule: genomic DNA

source_name: Input DNA_Px7 cells

label_protocol: Probe labeling was performed by NimbleGen (Reykjavik, Iceland)

growth_protocol: LCL 721 cells were cultured for seven passages (Px7) in RPMI 1640 medium at 37°C and 5% CO2 in a humidified incubator. Medium was supplemented with 10% heat-inactivated foetal bovine serum, 5 mM L-glutamine and 100 units/ml penicillin-streptomycin.

extract_protocol: 1x10E8 cells (cell density 0.4x10E6 cells/ml) were pelleted by centrifugation (1200 rpm, 5 min), washed with PBS, and the pellet was resuspended in 36 ml of PBS (all steps at room temperature). Cells were fixed by adding 4 ml of a freshly prepared 10% formaldehyde solution (10% formaldehyde, 140 mM NaCl,  1 mM EDTA, 0.5 mM EGTA, 50 mM Hepes-KOH pH 8.0). Cross-linking was done for 9 min at room temperature, followed by quenching with 125 mM glycine, with immediate transfer of the cell suspension to and 5 min incubation on ice. Cells were washed twice with ice-cold PBS and sequentially lysed by resuspending the cell pellet in 5 ml of ice-cold ChIP lysis buffer 1 (50 mM Hepes-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100, freshly added 1x protease inhibitor cocktail) and 10 min rotation at 4°C. Cells were collected by centrifugation (4000 rpm, 10 min, 4°C), followed by resuspension in 5 ml of ice-cold ChIP lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, freshly added 1x protease inhibitor cocktail) and 10 min rotation at 4°C. After centrifugation (4000 rpm, 10 min, 4°C), the pellet was resuspended in 3 ml of ice-cold ChIP lysis buffer 3 (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, freshly added 0.5% N-lauryl sarcosine, 0.1% sodium deoxycholate and 1x protease inhibitor cocktail). Acid-washed glass beads (212-300 microns) were added, and the crosslinked chromatin was sheared to an average size of 300 bp by 6 min sonication (40% power output, with pulses set to 30 sec ON / 10 sec OFF) in an ice-water bath using a Branson 250-D sonicator and a microtip. After sonication, Triton X-100 was added to 0.5% final concentration, and the lysate was centrifuged (5500 rpm, 5 min, 4°C) to remove cell debris. The chromatin extract was pre-cleared with 100 µl blocked (pre-absorbed with PBS/0.5% BSA) protein A/G sepharose beads for 2 h at 4°C, quantified in a UV spectrophotometer and diluted to 1 mg/ml and 0.25% N-lauryl sarcosine. 500 µl of the chromatin extract were used per single ChIP reaction in lubricated tubes in a total volume of 1000 µl. The extract was incubated overnight at 4°C with 50 µl blocked protein A/G sepharose beads which had been pre-adsorbed with 10 µg of antibody. Immune complexes were collected by centrifugation (3000 rpm, 1 min, 4°C) and washed six times with 1 ml of ice-cold ChIP wash buffer (50 mM Hepes-KOH pH 7.4, 500 mM LiCl, 1 mM EDTA, 1% NP40, 0.7% sodium deoxycholate, freshly added 0.5x protease inhibitor cocktail) and one time with 1x TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA) containing 50 mM NaCl. The protein-DNA complexes were eluted from the beads by adding 200 µl ChIP elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and incubation at 65°C under constant agitation for 10 min. After removal of beads by centrifugation (6000 rpm, 5 min, room temperature), the supernatant was incubated at 65°C overnight to revert the cross-links. Then, the sample was diluted to 400 µl with 1x TE. 8 µg of RNAse A were added and the sample was incubated for 1 hour at 37°C, followed by addition of proteinase K to 250 µg/ml and digestion for 2 hours at 55°C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1% of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: standard growth conditions, no treatment

value: Epstein-Barr-Virus (EBV)-transformed human lymphoblastoid B cell line LCL 721

tag: antibody

source_name: TFIIB ChIP DNA Px7cells

value: anti-TFIIB polyclonal rabbitt IgG antibody (sc-225)


title: Calu-3-H3N2-06h-2

description:
H3N2-06-2
4569624067_E


title: Calu-3-H11N9-06h-1

description:
H11N9-06-1
4569624059_C

source_name: Calu-3, infected with H11N9, RNA collected at 6hr


title: Calu-3-H3N2-24h-2

description:
H3N2-24-2
4569624067_G

source_name: Calu-3, infected with H3N2, RNA collected at 24hr


title: TFIIB_ChIP-chip_LCL721_Px5

source_name: Input DNA_Px5 cells

growth_protocol: LCL 721 cells were cultured for five passages (Px5) in RPMI 1640 medium at 37°C and 5% CO2 in a humidified incubator. Medium was supplemented with 10% heat-inactivated foetal bovine serum, 5 mM L-glutamine and 100 units/ml penicillin-streptomycin.

source_name: TFIIB ChIP DNA Px5


title: Calu-3-H3N2-06h-1

description:
H3N2-06-1
4569624067_D


title: Calu-3-H11N9-24h-3

description:
H11N9-24-3
4569624059_H

source_name: Calu-3, infected with H11N9, RNA collected at 24hr


title: NC2_ChIP-chip_LCL721_Px5

source_name: NC2 ChIP DNA Px5 cells

value: anti-NC2 alpha monoclonal rat IgG antibody (4G7)


title: Calu-3-H3N2-24h-3

description:
H3N2-24-3
4569624067_H


title: Calu-3-H3N2-02h-1

description:
H3N2-02-1
4569624067_C

source_name: Calu-3, infected with H3N2, RNA collected at 2hr


title: Calu-3-H11N9-02h-1

description:
H11N9-02-1
4569624059_B

source_name: Calu-3, infected with H11N9, RNA collected at 2hr


title: Calu-3-H11N9-24h-1

description:
H11N9-24-1
4569624059_F


title: Calu-3-H11N9-06h-3

description:
H11N9-06-3
4569624059_E


title: PT2-DAPT_48h

description: Gene expression data from GBM TICs were treated the gamma secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) for 48 hours.


title: Calu-3-Media-24h-1

description:
Med-24-1
4569624067_B

source_name: Calu-3, uninfected medium control, 24hr

value: uninfected control


title: Calu-3-H11N9-24h-2

description:
H11N9-24-2
4569624059_G


title: Calu-3-H11N9-06h-2

description:
H11N9-06-2
4569624059_D


title: xen10_2

city: New York

first: Ann

last: Foley

state: NY

address: 510 E70th Street

institute: Weill Cornell Medical College

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol (58 degrees for 16-20 hours).

data_processing: The data was normalized using LumiExpresso_(_) function of the lumi Bioconductor package in R (www.bioconductor.org).

source_name: cell line

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Thermo Scientific nanodrop 1000.

value: ICR

value: blastocyst derived cells


title: xen10_1

description: replicate 1


title: Calu-3-H3N2-24h-1

description:
H3N2-24-1
4569624059_A


title: Lung ECS-OPZ NAC

source_name: Lung

value: environmental cigarette smoke and oltipraz and N-acetylcysteine


title: end2_3

description: replicate 3

value: embryonal carcinoma cell line


title: Calu-3-Media-24h-2

description:
Med-24-2
4569624067_A


title: pys2_1

description: replicate 1

value: tumor cells


title: end2_2

description: replicate 2


title: pys2_2

description: replicate 2


title: xen10_3

description: replicate 3


title: end2_1

description: replicate 1


title: bmPMN-B2

city: Princeton

first: Troels

middle: Torben

last: Marstrand

state: NJ

address: Lewis-Sigler Institute Princeton University

institute: Princeton University

hyb_protocol: Hybridization was according to manufacturer's recommendations

scan_protocol: MicroArray Suite 5

data_processing: Fluorescence signals were normalized using dChip version 1.3, expression values were calculated using the perfect match/mismatch difference model by Li and Wong

source_name: bone marrow neutrophils

label_protocol: Total RNA was biotinylated according to manufacturer's recommendations

extract_protocol: Total RNA extracted using Trizol according to manufacturer's recommendations

value: bone marrow neutrophils


title: PM-A2

source_name: promyelocytes

value: promyelocytes


title: pbPMN-A2

source_name: peripheral blood neutrophils

value: peripheral blood neutrophils


title: bmPMN-B3


title: PM-B1


title: PM-B2


title: PM-A3


title: PM-A1


title: PM-B3


title: bmPMN-B1


title: pbPMN-B2


title: MY-A2

source_name: myeloblasts

value: myeloblasts


title: MY-A1


title: MY-A3


title: pbPMN-B1


title: pbPMN-B3


title: MY-B2


title: K562 DMSO sample 12

city: Duesseldorf

first: Daniela

last: Bruennert

address: Universitaetsstr. 1

department: Clinic for Hematology, Oncology and clin. Immunology

institute: University Clinic Duesseldorf

description: K562 cells (CML cell line) treated with DMSO as control for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG U133 A2.0. GeneChips were washed and stained in the Gene Chips® Fluidics Station; Affymetrix.

scan_protocol: GeneChips were scanned using the GenArray® 2500 scanner (Agilent).

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. Scaling factor was 500.

source_name: K562 cell line

label_protocol: Biotin Label Protocol GeneChip Expression 3’-Amplification One-Cycle-Target, 10 ug cRNA were used.

growth_protocol: RPMI, 10% FBS, 2 mM L-Gluthamine, 100 U/ml Penicillin, 100 µg/ml Streptomycin, 37°C humified incubator

extract_protocol: Qiagen RNeasy mini kit (Qiagen; 74106)

treatment_protocol: K562 cells were treated with 0.5 µM Imatinib (STI571), 0.05 µM Nilotinib (AMN107) (IC50 concentration) or DMSO as control for 24 hours.

tag: treatment

value: DMSO (control)


title: MY-B1


title: Interstitial leukocytes from Rag1 KO, NK-depleted mice exposed to silica, replicate 2

city: Missoula

first: Corbin

last: Schwanke

state: MT

department: Biomedical and Pharmaceutical Sciences

institute: University of Montana

description:
Biological replicate 2 of 2, RagKO silica.
RagKO-si-2

hyb_protocol: Agilent Gene Expression Hybridization Kit.

scan_protocol: Axon GenePix 4000B scanner, Axon GenePix Pro 5.0 software.

data_processing: Axon GenePix Pro 5.0, normalization using a LOWESS R script written by Terry Speed, Microsoft Excel. Matrix data was filtered to include only non-control genes and genes present above background in at least 2 of 4 replicates for wild-type or RagKO data.

source_name: RagKO, NK-deficient lung interstitial leukocytes

label_protocol: Agilent Quick-Amp Labeling Kit, Dual Color.

growth_protocol: Rag1-/- mice were injected i.p. with 300 μg of anti-NK1.1 mAb on days -6, -3, and -1 prior to the first i.n. instillation (day 0).  NK cell depletion was maintained via weekly injections of 300 μg of anti-NK1.1 mAb throughout the course of the study, which was administered two days prior to particle exposure.

extract_protocol: The lungs were asceptically removed, cut away from the heart, and placed in ice cold sterile phosphate-buffered saline (PBS, pH 7.4).  Thereafter, the lungs were minced into small pieces and incubated in complete RPMI 1640 culture medium supplemented with 10% FCS, antibiotic/antimycotic solution, β-mercaptoethanol, and sodium pyruvate containing 1 mg/ml collagenase IA with 1 µl DNAase I during 2 hours at 37oC. Digested lungs were further disrupted by gently pushing the tissue through a 70 μm cell strainer. Enzymatic action was terminated by adding excess RPMI medium and pelleting by centrifugation at 1500 rpm for 5 minutes at 4oC. Leukocytes were isolated by centrifugation over a 40-70% Percol gradient.  Total RNA was isolated using Trizol according to manufacturer's protocol, followed by Qiagen RNeasy RNA cleanup with DNase digest.

treatment_protocol: For “chronic” exposure studies, Rag1-/- NK-depleted and C57Bl/6 wild-type mice were anesthetized with ketamine (80 mg/kg) and instilled i.n. with either 25 μl of sterile saline, 1 mg crystalline silica (SiO2) or 0.5 mg titanium dioxide (TiO2) suspended in 25 μl of sterile saline once a week for four weeks.

tag: genotype

tag: tissue

value: lung

value: interstitial leukocytes

tag: age

value: 6-8 weeks

value: silica

source_name: Universal Mouse Reference RNA

tag: supplier

value: Stratagene


title: Interstitial leukocytes from Rag1 KO, NK-depleted mice exposed to saline, replicate 2

description:
Biological replicate 2 of 2, RagKO saline.
RagKO-sal-2

value: saline


title: K562 DMSO sample 11


title: K562 DMSO sample 10


title: K562 STI sample 5

description: K562 cells (CML cell line) treated with IC50 concentration of STI571 (Imatinib) (0.5 µM) for 24 hours

value: STI (Imatinib)


title: K562 STI sample 7


title: B.subtilis strain PB565 L1(19); time 395_rep2 technical

description: This sample is collected from cells growing in the presence of light at 395 minutes after inoculation. It is the second of two technical replicates used in this experiment (technical replicate from sample 14).

tag: strain

value: light

value: 395 min

value: technical


title: K562 STI sample 6


title: K562 DMSO sample 9


title: K562 STI sample 8


title: PC3 Histone 3 Lysine 27 Trimethylation ChIP

city: Rehovot

first: Gilad

last: Landan

address: PO Box 26

department: Applied Math & Computer Science, Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Nimblegen Inc.

scan_protocol: Nimblegen Inc.

data_processing: Array data were normalized by estimating the curve of log channels intensity ratio [log(cy5/cy3)] as a function of the control channel [usually log(cy3)]. This curve was subtracted from the observed log intensity ratio and used in subsequent analysis. Duplicates were averaged, as were all 20 normal prostate cDNA samples.

label_protocol: Nimblegen standard protocol

extract_protocol: Twenty fresh frozen radical prostatectomy (RP) samples were derived from an institutional review board-approved study cohort at Dana-Farber Cancer Institute (DFCI). Patients underwent RP between 2001 and 2005. Five-micron sections of each RP specimen were reviewed by a pathologist to confirm the diagnoses of prostatic adenocarcinoma. Areas of tumor were selected where >60% of cells consisted of tumor cells. Areas of benign tissue were selected where >50% of cells consisted of non-neoplastic epithelium and were at least 5 mm away from any area of tumor focus. From these areas, two 2 mm punch biopsy cores of frozen tissue were processed for DNA and RNA extraction using a modified Qiagen Allprep DNA/RNA protocol. Double-stranded cDNA synthesis from RNA was performed using the Promega ImProm-II kit. Resulting cDNA from benign RP tissue and corresponding genomic DNA were hybridized to the tiling array described above.    About 100 µg total RNA was extracted from each cell line (LNCaP, PC3, HCT116, and MCF7) using Aurum Total RNA Kit (Bio-Rad). Ribosomal RNA (rRNA) was depleted using RiboMinus Transcriptome Isolation Kit (Invitrogen) according to manufacturer's protocol. About 5 µg double strand cDNA was made from recovered RNA after rRNA depletion using Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen), and then submitted to NimbleGen, Inc. along with 5 µg sonicated genomic DNA (size between 500–2000 bp) from each cell line as a reference.     LNCaP and PC3 cells were maintained in RPMI 1640 supplemented with 5% (v/v) fetal bovine serum (FBS). HCT 116 and COLO 205 cells were cultured in McCoy's 5A with 10% FBS, and MCF7 cells were cultured in DMEM with 10% FBS. All cell lines were obtained from the American Type Culture Collection (ATCC; Manassas, VA), except PC3 cells, originally from ATCC, which were derived by us as strongly AR-transcriptionally competent, although not expressing functional AR.    Cells were cross-linked by adding formaldehyde (1%) directly to the culture medium, and incubated at room temperature for 10 min. The dishes were rinsed twice with ice-cold PBS, and the cells were scraped into PBS containing protease inhibitors (Sigma) and centrifuged for 3 min at 2000 rpm. The cell pellets were resuspended in 0.35 ml lysis buffer [1% SDS, 10 nm EDTA, 50 nm Tris-HCl (pH 8.0), 2× protease inhibitors] and incubated for 10 min on ice. The resulting cell lysates were sonicated in 1.5 ml microfuge tubes for 5 s, followed by a 1-min incubation on ice for a total of four cycles using setting 10 of a Fisher Sonic Dismembrator Model 60 (Tustin, CA). Cell debris was removed by centrifugation for 10 min at 14,000 rpm in a microfuge. The soluble chromatin (100 μl per immunoprecipitation of the supernatant) was transferred to a new microfuge tube and diluted 10-fold in dilution buffer [0.01% SDS, 1.1% Triton X-100, 1.2 mm EDTA, 16.7 mm Tris-HCl (pH 8.0), 167 mm NaCl, protease inhibitors]. The diluted suspension (1 ml) was precleared by incubating with 2 μl sheared salmon sperm DNA (1 μg/μl) (Life Technologies) and 45 μl protein G-Sepharose bead suspension (Amersham Pharmacia Biotech, Piscataway, NJ) [50% slurry in 10 mm Tris-HCl (pH 8.0), 1 mm EDTA] for 1 h at 4°C with rotation. The supernatant was immunoprecipitated by incubating overnight at 4°C with the indicated specific antibodies. The next morning, 2 μl sheared salmon sperm DNA and 45 μl protein G-Sepharose were added for 1 h at 4°C with rotation. The Sepharose-bound immune complexes were sequentially washed for 10 min each in a low salt wash buffer [0.1% SDS, 1% Triton X-100, 2 mm EDTA, 20 mm Tris-HCl (pH 8.0), 150 mm NaCl], a high salt wash buffer [0.1% SDS, 1% Triton X-100, 2 mm EDTA, 20 mm Tris-HCl (pH 8.0), 500 mm NaCl], and a LiCl wash buffer [0.25 M LiCl, 1% IGEPAL CA-630, 1% deoxycholate, 1 mm EDTA, 10 mm Tris-HCl (pH 8.0)] with rotation. The Sepharose-bound immune complexes were further washed twice with TE buffer [10 nm Tris-HCl, 1 mm EDTA (pH 8.0)]. The immune complexes were recovered from the beads with an elution buffer (1% SDS and 0.1 M NaHCO3). Eluates were heated at 65°C for 4 h to reverse the formaldehyde cross-links. DNA was purified by phenol/chloroform extraction and ethanol precipitation. The DNA pellets were finally resuspended in 100 μl H2O ready for real-time PCR analysis (see below). Ten percent input samples were treated in the same way except that no immunoprecipitation steps were performed.

tag: sample type

value: ChIP DNA

value: ChIP input DNA


title: Interstitial leukocytes from Rag1 KO, NK-depleted mice exposed to saline, replicate 1

description:
Biological replicate 1 of 2, RagKO saline.
RagKO-sal-1


title: Interstitial leukocytes from Rag1 KO, NK-depleted mice exposed to silica, replicate 1

description:
Biological replicate 1 of 2, RagKO silica.
RagKO-si-1


title: Interstitial leukocytes from WT C57Bl6 mice exposed to silica, replicate 2

description:
Biological replicate 2 of 2, WT silica.
WT-si-2

source_name: WT C57 lung interstitial leukocytes

value: wild-type


title: PC3 Histone 3 Lysine 4 Trimethylation ChIP


title: K562 AMN107 sample 4

description: K562 cells (CML cell line) treated with IC50 concentration of AMN107 (Nilotinib) (0.05 µM) for 24 hours

value: AMN107 (Nilotinib)


title: PC3 Histone 3 Lysine 4 Monomethylation ChIP


title: PC3 Histone 3 Lysine 36 Trimethylation ChIP


title: Interstitial leukocytes from WT C57Bl6 mice exposed to silica, replicate 1

description:
Biological replicate 1 of 2, WT silica.
WT-si-1


title: PC3 RNA Polymerase II ChIP

description: PC3 RNA Polymerase II ChIP


title: Interstitial leukocytes from WT C57Bl6 mice exposed to saline, replicate 2

description:
Biological replicate 2 of 2, WT saline.
WT-sal-2


title: LNCaP Histone 3 Lysine 4 Trimethylation ChIP

value: LNCaP


title: K562 AMN107 sample 3


title: K562 AMN107 sample 2


title: LNCaP Androgen Receptor ChIP

description: LNCaP Androgen Receptor ChIP


title: K562 AMN107 sample 1


title: LNCaP Histone 3 Lysine 36 Trimethylation ChIP


title: LNCaP Histone 3 Lysine 4 Monomethylation ChIP


title: PC3 ChIP Acetylation Histone 3 ChIP

description: PC3 ChIP Acetylation Histone 3 ChIP


title: LNCaP RNA Polymerase II ChIP

description: LNCaP RNA Polymerase II ChIP


title: Interstitial leukocytes from WT C57Bl6 mice exposed to saline, replicate 1

description:
Biological replicate 1 of 2, WT saline.
WT-sal-1


title: pys2_3

description: replicate 3

value: tumor cells


title: LNCaP Histone 3 Lysine 27 Trimethylation ChIP


title: 17 days, ipsilateral group, biological replicate 1

status: Public on Dec 18 2009

city: Lonndon

first: David

last: Vega-Avelaira

address: Gower street

country: United Kingdom

institute: University College of London

description: The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group

hyb_protocol: For the mRNA high-throughput screening we used the GeneChip ® Rat expression  230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).

scan_protocol: We used GeneChip Scanner 3000 (Affymetrix®).

data_processing: The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.

source_name: L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery

label_protocol: cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA.  Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water.  Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation

growth_protocol: After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.

extract_protocol: Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).

treatment_protocol: Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.

value: Sprague-Dawley

value: Dorsal root ganglia

tag: postnatal age

value: 17 days

tag: surgery type

value: Spare nerve injury

tag: experimetal group

value: Young Ipsilateral


title: 17 days, sham group, biological replicate 2

description: The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery

source_name: L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after sham surgery

value: Sham

value: Young Sham


title: 17 days, sham group, biological replicate 1


title: 17 days, contralateral group, biological replicate 1

description: The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group

value: Young Contralateral


title: 17 days, contralateral group, biological replicate 2


title: MCF7 Acetylation Histone 3 ChIP

description: MCF7 Acetylation Histone 3 ChIP


title: LNCaP Acetylation Histone 3 ChIP

description: LNCaP Acetylation Histone 3 ChIP


title: HCT116 Acetylation Histone 3 ChIP

description: HCT116 Acetylation Histone 3 ChIP


title: 2 months, contralateral group, biological replicate 2

source_name: L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery

value: 2 months

value: Adult Contralateral


title: 2 months, ipsilateral group, biological replicate 2

value: Adult Ipsilateral


title: 2 months, sham group, biological replicate 1

source_name: L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after sham surgery

value: Adult Sham


title: 2 months, ipsilateral group, biological replicate 3


title: 2 months, ipsilateral group, biological replicate 1


title: Healthy control 11

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

institute: Health e-genomics

description: healthy control 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with IlluminaGUI in R and log2 transformed

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrepTM RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment (Amersam Biosciences) in accordance with the prescribed protocol provided by the manufacturer

tag: disease

value: healthy

tag: gender

value: female

value: endothelial progenitor cell


title: 17 days, ipsilateral group, biological replicate 2


title: 2 months, contralateral group, biological replicate 1


title: 2 months, sham group, biological replicate 3


title: 2 months, sham group, biological replicate 2


title: MCF7 cDNA

type: mixed

description: MCF7 cDNA

tag: cell line

value: cDNA

value: genomic DNA


title: HCT116 cDNA

description: HCT116 cDNA


title: LNCaP cDNA

description: LNCaP cDNA

value: LNCaP


title: PC3 cDNA

description: PC3 cDNA


title: 2 months, contralateral group, biological replicate 3

value: Sprague-Dawley

value: Dorsal root ganglia


title: Healthy control 9

description: healthy control 9

tag: cell type


title: Healthy control 5

description: healthy control 5


title: Patient 10 after folic acid

description: patient 10 after folic acid

value: type 1 diabetes


title: Healthy control 6

description: healthy control 6


title: Patient 9 after folic acid

description: patient 9 after folic acid


title: Healthy control 3

description: healthy control 3

value: male


title: 20 Normal Prostates cDNA

description: Normal Prostate cDNA

tag: ancestry

value: European American

value: prostate


title: Patient 5 after folic acid

description: patient 5 after folic acid


title: Healthy control 1

description: healthy control 1


title: Healthy control 2

description: healthy control 2


title: Patient 4 after folic acid

description: patient 4 after folic acid


title: Patient 8 after folic acid

description: patient 8 after folic acid


title: Patient 7 after folic acid

description: patient 7 after folic acid


title: Patient 1 after folic acid

description: patient 1 after folic acid


title: Patient 6 after folic acid

description: patient 6 after folic acid


title: MY-B3

value: myeloblasts


title: Patient 2 after folic acid

description: patient 2 after folic acid


title: Brain_PostNatalDay22_rep6

city: Lausanne

first: Peter

middle: I

last: Duncan

address: Vers-chez-les-Blanc

description: replicate 6

data_processing: Quality control of the data was performed on all samples with a Pearson correlation matrix and a Principal Component Analysis. The data were normalised using quantile normalisation with IlluminaGUI

source_name: brain, right hemisphere, day 22

label_protocol: Biotinylated cRNA was synthesized, labelled and purified according to the Illumina TotalPrep RNA amplification protocol.

extract_protocol: Total RNA was extracted and purified with the RNAdvance tissue kit (Agencourt) extraction. RNA was quantified with the RiboGreen RNA Quantification Kit (Molecular Probes) and monitored for quality on an Agilent 2100 Bioanalyser.

treatment_protocol: tissue was snap frozen in liquid nitrogen and stored at -80°C.

value: Sprague Dawley

value: postnatal day 22

value: brain, right hemisphere


title: Patient 3 after folic acid

description: patient 3 after folic acid


title: Brain_PostNatalDay15_rep5

description: replicate 5

source_name: brain, right hemisphere, day 15

value: postnatal day 15


title: Brain_PostNatalDay15_rep2

description: replicate 2


title: Brain_PostNatalDay10_rep5

description: replicate 5

source_name: brain, right hemisphere, day 10

value: postnatal day 10


title: Brain_PostNatalDay15_rep1

description: replicate 1


title: Brain_PostNatalDay10_rep4

description: replicate 4


title: Brain_PostNatalDay22_rep2

description: replicate 2


title: Brain_PostNatalDay10_rep6

description: replicate 6


title: Brain_PostNatalDay22_rep1

description: replicate 1


title: Brain_PostNatalDay22_rep3

description: replicate 3


title: Brain_PostNatalDay22_rep4

description: replicate 4


title: Brain_PostNatalDay15_rep3

description: replicate 3


title: Brain_PostNatalDay22_rep5

description: replicate 5


title: Brain_PostNatalDay15_rep6

description: replicate 6


title: Brain_PostNatalDay10_rep3

description: replicate 3


title: Brain_PostNatalDay7_rep5

description: replicate 5

source_name: brain, right hemisphere, day 7

value: postnatal day 7


title: Brain_PostNatalDay7_rep6

description: replicate 6


title: Brain_PostNatalDay7_rep4

description: replicate 4


title: Brain_PostNatalDay7_rep3

description: replicate 3


title: Brain_PostNatalDay10_rep2

description: replicate 2


title: Brain_PostNatalDay5_rep6

description: replicate 6

source_name: brain, right hemisphere, day 5

value: postnatal day 5


title: Brain_PostNatalDay10_rep1

description: replicate 1


title: Brain_PostNatalDay7_rep1

description: replicate 1


title: 17 days, sham group, biological replicate 3

value: 17 days

value: Sham

value: Young Sham


title: Brain_PostNatalDay7_rep2

description: replicate 2


title: Brain_PostNatalDay5_rep5

description: replicate 5


title: Healthy control 10

description: healthy control 10

value: healthy

value: female

value: endothelial progenitor cell


title: Brain_PostNatalDay3_rep6

description: replicate 6

source_name: brain, right hemisphere, day 3

value: postnatal day 3


title: Brain_PostNatalDay5_rep2

description: replicate 2


title: Brain_PostNatalDay5_rep3

description: replicate 3


title: Brain_PostNatalDay2_rep6

description: replicate 6

source_name: brain, right hemisphere, day 2

value: postnatal day 2


title: Brain_PostNatalDay2_rep5

description: replicate 5


title: Brain_PostNatalDay2_rep2

description: replicate 2


title: Brain_PostNatalDay2_rep3

description: replicate 3


title: Brain_PostNatalDay5_rep4

description: replicate 4


title: Brain_PostNatalDay5_rep1

description: replicate 1


title: Brain_PostNatalDay3_rep3

description: replicate 3


title: Brain_PostNatalDay3_rep4

description: replicate 4


title: Healthy control 4

description: healthy control 4

value: male


title: Brain_PostNatalDay3_rep1

description: replicate 1


title: Brain_PostNatalDay2_rep1

description: replicate 1


title: Brain_PostNatalDay3_rep2

description: replicate 2


title: Brain_PostNatalDay2_rep4

description: replicate 4


title: Brain_PostNatalDay1_rep6

description: replicate 6

source_name: brain, right hemisphere, day 1

value: postnatal day 1


title: Healthy control 8

description: healthy control 8


title: Brain_PostNatalDay1_rep4

description: replicate 4

value: Sprague Dawley


title: Brain_PostNatalDay1_rep3

description: replicate 3


title: Brain_PostNatalDay1_rep5

description: replicate 5


title: Brain_Embryo_Day21_rep5

description: replicate 5

source_name: embryo, day 21, brain, right hemisphere

value: embryo, day 21


title: Brain_Embryo_Day21_rep3

description: replicate 3

value: brain, right hemisphere


title: Brain_PostNatalDay1_rep1

description: replicate 1


title: Brain_Embryo_Day21_rep4

description: replicate 4


title: Colon_PostNatalDay22_rep1

description: replicate 1

source_name: colon, day 22

value: postnatal day 22

value: colon


title: Brain_PostNatalDay1_rep2

description: replicate 2


title: Brain_Embryo_Day21_rep1

description: replicate 1


title: Brain_Embryo_Day21_rep6

description: replicate 6


title: Healthy control 7

description: healthy control 7


title: Colon_PostNatalDay22_rep4

description: replicate 4


title: Colon_PostNatalDay22_rep6

description: replicate 6


title: Colon_PostNatalDay22_rep3

description: replicate 3


title: Colon_PostNatalDay22_rep5

description: replicate 5


title: Colon_PostNatalDay15_rep6

description: replicate 6

source_name: colon, day 15

value: postnatal day 15


title: Colon_PostNatalDay15_rep2

description: replicate 2


title: Colon_PostNatalDay15_rep4

description: replicate 4


title: Colon_PostNatalDay22_rep2

description: replicate 2


title: Colon_PostNatalDay10_rep6

description: replicate 6

source_name: colon, day 10

value: postnatal day 10


title: Brain_Embryo_Day21_rep2

description: replicate 2


title: Colon_PostNatalDay10_rep5

description: replicate 5


title: Colon_PostNatalDay15_rep3

description: replicate 3


title: Colon_PostNatalDay15_rep1

description: replicate 1


title: Brain_PostNatalDay15_rep4

description: replicate 4


title: Colon_PostNatalDay10_rep4

description: replicate 4


title: Colon_PostNatalDay15_rep5

description: replicate 5


title: Colon_PostNatalDay10_rep2

description: replicate 2


title: Colon_PostNatalDay7_rep2

description: replicate 2

source_name: colon, day 7

value: postnatal day 7


title: Colon_PostNatalDay10_rep3

description: replicate 3


title: Colon_PostNatalDay7_rep5

description: replicate 5


title: Colon_PostNatalDay7_rep3

description: replicate 3


title: Colon_PostNatalDay7_rep1

description: replicate 1


title: Colon_PostNatalDay5_rep6

description: replicate 6

source_name: colon, day 5

value: postnatal day 5


title: Colon_PostNatalDay5_rep5

description: replicate 5


title: Colon_PostNatalDay7_rep4

description: replicate 4


title: Colon_PostNatalDay5_rep2

description: replicate 2


title: Colon_PostNatalDay7_rep6

description: replicate 6


title: Colon_PostNatalDay3_rep5

description: replicate 5

source_name: colon, day 3


title: Colon_PostNatalDay3_rep3

description: replicate 3


title: Colon_PostNatalDay3_rep4

description: replicate 4


title: Colon_PostNatalDay10_rep1

description: replicate 1


title: Colon_PostNatalDay5_rep1

description: replicate 1


title: Colon_PostNatalDay5_rep3

description: replicate 3


title: Colon_PostNatalDay2_rep6

description: replicate 6

source_name: colon, day 2


title: Colon_PostNatalDay3_rep6

description: replicate 6