title: Ecoli_wild-type_rep3_Anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: Wild-type

value: normal


title: ArcA - Anaerobic - Affinity Purified -biological rep B

status: Public on Oct 17 2013

type: genomic

city: Madison

first: Dan

last: Park

state: WI

address: 440 Henry Mall

country: USA

institute: UW Madison

description: IP and INPUT (reference) for WT ArcA from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

hyb_protocol: Hybridized according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: ArcA IP from WT Escherichia coli MG1655 K-12

label_protocol: Labeled with Cy5 (ChIP) and Cy3 (INPUT) according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: strain

tag: antibody

value: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP

source_name: ArcA INPUT from WT Escherichia coli MG1655 K-12

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and no antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.


title: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.13 p21

type: RNA

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description:
Individual sample. Reanalysis of GSM1085049
VP-sp-CB_iPSC-6.13-7FE p21

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

molecule: total RNA

organism: Homo sapiens

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.13 passage 21

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: cell type

value: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.13, passage 21, generated in the Zambidis laboratory

tag: sample type

value: FACS-purified CD31+/CD146+ vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013).


title: Ecoli_wild-type_rep1_Anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridzation was performed following Roche NimbleGen standard opperator protocol.  See www.nimblegen.com.

scan_protocol: Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT of 480.

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

source_name: Escherichia coli MG1655 K-12 WT

label_protocol: Labeling was performed following Roche NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Escherichia coli MG1655 K-12 WT and ∆arcA were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).

extract_protocol: Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by gel electrophoresis and quantity was determined using a NanoDrop.

treatment_protocol: Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (Khodursky et al, 2003).

tag: genotype

tag: phenotype

tag: accession


title: -Fe 1d Replicate 3 (line 2i-3)

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

country: Japan

institute: Ishikawa Prefectural University

description: Biological/line replicate 3 of 3.

hyb_protocol: Performed according to the Agilent instruction.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US90500268. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

label_protocol: 400 ng of total RNA were primed withT7 Promoter Primer, then reverse transcribed with MMLV-RT, Cy-5 or Cy-3 labeled with T7 RNA polymerase, and purified by RNeasy mini kit (QIAGEN).

growth_protocol: NT and HRZ2i lines were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture.

extract_protocol: Total RNA extracted using using NucleoSpin RNA Plant Mini Kit (Macherey-Nagel).

tag: cultivar

value: Tsukinohikari

tag: line and replicate

value: HRZ2i line 3

tag: treatment

value: Iron deficiency for 1 day

tag: tissue

value: Root

source_name: NT -Fe 1d

value: Non-transformant replicate 2


title: -Fe 7d Replicate 3 (line 2i-3)

description: Biological/line replicate 3 of 3.

value: Iron deficiency for 7 days

source_name: NT -Fe 7d

value: Non-transformant replicate 3


title: FACS-purified CD31+/CD146+ vascular progenitors derived from hESC (H9) p52

description:
Individual sample. Reanalysis of GSM1085044
VP-hESC (H9) p52

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 52 (NIH Code WA09)


title: -Fe 7d Replicate 1 (line 2i-1)

description: Biological/line replicate 1 of 3.

value: Non-transformant replicate 1

value: HRZ2i line 1


title: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 4F stromal primed cord blood iPSC clone E17C6 p17

description:
Individual sample
VP-sp-CB_iPSC-E17C6-4FE p17

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 4F stromal primed cord blood iPSC clone E17C6 passage 17

value: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E17C6 passage 17,  generated in the Zambidis laboratory


title: Ecoli_wild-type_rep2_Anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: FACS-purified CD31+/CD146+ vascular progenitors derived from hESC (ES03) p80

description:
Individual sample. Reanalysis of GSM1085045
VP-hESC (ES03) p80

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from ES03 human Embryonic Stem Cells, Passage 80 (ES Cell International)


title: FACS-purified CD31+/CD146+ vascular progenitors derived from hESC (H9) p56

description:
Individual sample. Reanalysis of GSM1085043
VP-hESC (H9) p56

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 56 (NIH Code WA09)


title: -Fe 1d Replicate 2 (line 2i-2)

description: Biological/line replicate 2 of 3.

value: HRZ2i line 2


title: -Fe 7d Replicate 2 (line 2i-2)

description: Biological/line replicate 2 of 3.


title: FACS-purified CD31+/CD146+ vascular progenitors derived from hESC (H9) p51

description:
Individual sample. Reanalysis of GSM1085046
VP-hESC (H9) p51

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 51 (NIH Code WA09)


title: +Fe 7d Replicate 3 (line 2i-3)

description: Biological/line replicate 3 of 3.

value: Iron sufficiency for 7 days

source_name: NT +Fe 7d


title: Human dermal microvascular endothelial cells, sample 1

description:
Individual sample
HMVEC_Sample_1

value: Human dermal microvascular endothelial cells (neonatal), pooled (Lonza Cat # CC-2516), passage 2 after thawing

value: Human dermal microvascular endothelial cells, passage 2


title: -Fe 1d Replicate 1 (line 2i-1)

description: Biological/line replicate 1 of 3.


title: Sox2KO TSC Day4 biological rep2

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

description: On MEF feeders, with FGF4/heparin/Activin A

hyb_protocol: Samples were hybridized, stained, and washed according to the Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
The expression values were summarized and normalized by the robust multiarray analysis and quantile normalization method using by Expression Console(tm) software (Affymetrix).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mod.mm9.mps

label: biotin

organism: Mus musculus

source_name: 22CEROH2-TSC1 TS cells, +Tet, Day 4

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on gelatin-coated dishes. TS cells were maintained in GMEM/10% FBS supplemented with 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on the mitomycin C treated mouse embryonic fibroblasts (MEFs).

extract_protocol: Total RNA was isolated using QuickGene RNA cultured cell HC kit S (Fuji Film).

treatment_protocol: Tet-inducible Sox2 knockout ES and TS cells were cultured in ES and TS cell media, respectively, supplemented with 1 ug/ml Tet for 4 days on MEF feeders.

tag: cell line

value: Tet

tag: time

value: 4 days


title: Human dermal microvascular endothelial cells, sample 2

description:
Individual sample
HMVEC_Sample_2

value: Human dermal microvascular endothelial cells (neonatal), pooled (Invitrogen Cat # C-010-5C), passage 2 after thawing


title: Sox2KO TSC Day4 biological rep1


title: Sox2KO TSC Day4 biological rep3


title: +Fe 7d Replicate 1 (line 2i-1)

description: Biological/line replicate 1 of 3.

value: Tsukinohikari


title: Human dermal microvascular endothelial cells, sample 3

description:
Individual sample
HMVEC_Sample_3

value: Human dermal microvascular endothelial cells (neonatal), pooled (ATCC Cat # PCS-110-010), passage 2 after thawing


title: Sox2KO TSC Control biological rep3

source_name: 22CEROH2-TSC1 TS cells, untreated

value: control


title: Sox2KO ESC Day4 biological rep3

description: On MEF feeders

source_name: 2TS22C ES cells, +Tet, Day 4


title: Sox2KO TSC Control biological rep2


title: Sox2KO ESC Day4 biological rep2

description: On MEF feeders


title: +Fe 7d Replicate 2 (line 2i-2)

description: Biological/line replicate 2 of 3.

value: Root


title: Sox2KO TSC Control biological rep1


title: Human umbilical vein endothelial cells, sample 1

description:
Individual sample
HUVEC_Sample_1

source_name: Human umbilical vein endothelial cells

value: Human umbilical vein endothelial cells, pooled (Lonza, Cat # CC-2519), passage 2 after thawing

value: Human umbilical vein endothelial cells, passage 2


title: ESv6.5

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

institute: Kyoto University

description: Gene expression data from ESv6.5.

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Gene 1.0 ST arrays were normalised using GCRMA implemented in GeneSpring 12.0. The data were median transformed.

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM, 10% FBS, 50 units/ml penicillin and 50 mg/ml streptomycin. Pluripotent stem cells were grown in ES cell medium (DMEM containing 15% FBS, 1X non-essential amino acids (NEAA), 5.5 mM 2-mercaptoethanol (2-ME), 50 units/ml penicillin and 50 mg/ml streptomycin) on feeder layers of mitomycin-C-treated SNL cells stably expressing the puromycin-resistance gene.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

value: embryonic stem (ES) cells

tag: strain/background


title: Human umbilical vein endothelial cells, sample 2

description:
Individual sample
HUVEC_Sample_2


title: Sox2KO ESC Control biological rep2

description: On MEF feeders

source_name: 2TS22C ES cells, untreated


title: Human umbilical vein endothelial cells, sample 3

description:
Individual sample
HUVEC_Sample_3

value: Human umbilical vein endothelial cells, pooled (Invitrogen, Cat # C-015-5C), passage 2 after thawing


title: Sox2KO ESC Day4 biological rep1

description: On MEF feeders


title: Sox2KO ESC Control biological rep1

description: On MEF feeders


title: iPS492B4

description: Gene expression data from iPS492B4.

value: induced pluripotent stem cells

value: mixed genetic background (DBA/2, C57BL/6, 129S4)


title: iPS178B5

description: Gene expression data from iPS178B5.


title: Sox2KO ESC Control biological rep3

description: On MEF feeders


title: Mouse embryonic fibroblast

description: Gene expression data from mouse embryonic fibroblasts.

source_name: Mouse embryonic fibroblasts

value: mouse embryonic fibroblasts (MEFs)


title: SCI + delayed VHC graft 2dpi, biological rep1

status: Public on Oct 16 2013

city: Bellaterra

first: Xavier

last: Navarro

address: Edif. M, Campus UAB

country: Spain

institute: Univarsitat Autònoma de Barcelona

hyb_protocol: samples were hyb in Rat Gene Array 1.1 ST from Affymetrix, for 16 hours at 45 ºC and 60 rpm. Samples were washed and stained in the GeneTitan platform following manufacturer specifications.

scan_protocol: Arrays were scanned  in the GeneTitan platform following manufacturer specifications

data_processing: CEL files obtained from scanner were normalized with RMA algorithm using R software and bioconductor associated packages.

organism: Rattus norvegicus

source_name: 5mm segment of Spinal cord

label_protocol: samples were labeled with GeneChip Terminal Labeling kit following protocol specifications

extract_protocol: Spinal cord segment (5mm long) centered in the contusion epicenter was harvested and maintained in RNA-latter solution (Qiagen, Barcelona, Spain). The samples were processed for mRNA analysis following the manufacturer instructions. The total RNA of each sample was extracted with RNeasy mini kit (Qiagen), including a DNase step (RNase free DNase set, Qiagen, Barcelona, Spain).

treatment_protocol: vehicle (VHC), mesenchymal stromal cells (MSC) or olfactory ensheathing cells (OEC) transplantation after spinal cord injury

value: VHC graft

tag: time graft

value: delayed

tag: time extraction

value: 2 days post graft


title: SCI + acute VHC graft 7dpi, biological rep3

value: acute

value: 7 days post graft


title: SCI + acute VHC graft 7dpi, biological rep2


title: SCI + delayed VHC graft 2dpi, biological rep4


title: SCI + delayed VHC graft 2dpi, biological rep3


title: SCI + delayed VHC graft 7dpi, biological rep4


title: SCI + acute VHC graft 7dpi, biological rep1


title: SCI + delayed VHC graft 7dpi, biological rep3


title: SCI + delayed VHC graft 2dpi, biological rep2


title: SCI + acute VHC graft 7dpi, biological rep4


title: SCI + delayed OEC graft 7dpi, biological rep4

value: OEC graft


title: SCI + acute VHC graft 2dpi, biological rep4


title: SCI + delayed VHC graft 7dpi, biological rep2


title: SCI + acute VHC graft 2dpi, biological rep1


title: SCI + delayed VHC graft 7dpi, biological rep1


title: SCI + delayed OEC graft 7dpi, biological rep3


title: SCI + acute VHC graft 2dpi, biological rep3


title: SCI + delayed OEC graft 7dpi, biological rep2


title: SCI + acute OEC graft 7dpi, biological rep2


title: SCI + delayed OEC graft 2dpi, biological rep3


title: SCI + delayed OEC graft 2dpi, biological rep2


title: SCI + delayed OEC graft 2dpi, biological rep1


title: SCI + acute OEC graft 7dpi, biological rep3


title: SCI + delayed OEC graft 2dpi, biological rep4


title: SCI + acute OEC graft 7dpi, biological rep1


title: SCI + acute OEC graft 7dpi, biological rep4


title: SCI + acute VHC graft 2dpi, biological rep2


title: SCI + delayed OEC graft 7dpi, biological rep1


title: vegetative buds_893-12_0days_rep1

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution. Microarray scanner and image analysis software used are described in the Samples section

data_processing: Data processing was performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach. Further data analysis was performed using FlexArray v1.5  A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem juvenile). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

organism: Picea glauca

source_name: vegetative buds, genotype:893-12 ,0 days

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Buds were collected from branches of several clonal replicates of 9-year-old trees of P. glauca regenerated from two genetically distinct somatic embryogenesis lines as described (Klimaszewska et al. 2011) during the mid-Spring when the buds were just beginning to grow.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the tissue culture vessels, and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008).

treatment_protocol: For somatic embryogenesis induction, buds were disinfected, primordial shoots were excised and cut longitudinally into two or four equal parts, and the explants were placed onto semi-solid MLV-S medium containing 9.5 μM 2,4-dichlorophenoxyacetic acid and 4.5 μM benzyl adenine. Replicate explant samples were collected after 0 and 7 days of culture.  For each genotype, five biological samples each consisting of 6 buds (approximately 80 mg fresh weight) were collected.

value: vegetative buds

tag: age of trees

tag: days after induction

tag: replicate

tag: slide batch

tag: microarray scanner

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)

tag: image analysis program

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: SCI + acute OEC graft 2dpi, biological rep4


title: SCI + delayed MSC graft 7dpi, biological rep4

value: MSC graft


title: SCI + delayed MSC graft 7dpi, biological rep3


title: SCI + acute OEC graft 2dpi, biological rep2


title: M2nsf1∆ mutant at 85% total glucose fermented, biological rep3

city: Guelph

first: Kyrylo

last: Bessonov

state: ON

address: 50 Stone Rd East

department: Molecular Biology

institute: University of Guelph

description: Gene expression data from the mutant industrial M2 nsf1∆ strain grown in Riesling grape must. 85% of the total glucose fermented time point.

hyb_protocol: Total RNA samples were hybridized to the microarrays. The microarrays were washed several times to eliminate non-specific hybridization.

scan_protocol: The microarrays were subsequently scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were normalized with Robust Multi-array Analysis(RMA) algorithm using Affymetrix default analysis settings

organism: Saccharomyces cerevisiae

source_name: Mutant  M2nsf1∆ strain cells at 85% glucose fermented

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

growth_protocol: M2 and M2 nsf1∆ strains were cultured over-night in YPD broth to obtain a sufficient number of cells. 4 L of Riesling grape must purchased from Kamil Juices (http://www.kamiljuices.com/) in 2010 was sterile filtered into 1L bottles and left over-night at 18 °C in incubator. The following day, the M2 and M2 nsf1∆ cultures were briefly washed in sterile dH2O and the cell number calculated using a hemocytometer. Each 1L of Riesling grape must was inoculated to a final 2.6x10^6cells/mL that corresponded to OD600 of 0.1.  After inoculation, the 1L flasks were incubated at 18°C without shaking. 100 mL samples were taken at 3 time points: 24h after inoculation, 20% and 85% glucose fermentented. The isolated cells were used for total RNA extraction for microarray analysis. The overall experimental setup consisted of 2 stains and 3 sample time points.

extract_protocol: Phenol:Chloroform:Isoamyl Alcohol (25:24:1) pH 6.8 standard RNA extraction with NaCl precipitation protocol followed by the Qiagen™ RNeasy silica based column RNA cleanup

treatment_protocol: No additional treatments were applied to the M2 and M2 and M2 nsf1∆ strains

tag: strain

value: M2 nsf1∆ (mutant)

value: grown in Riesling grape must, 85% of the total glucose fermented time point


title: SCI + delayed MSC graft 2dpi, biological rep3


title: SCI + acute MSC graft 7dpi, biological rep3


title: SCI + acute OEC graft 2dpi, biological rep1


title: M2nsf1∆ mutant at 85% total glucose fermented, biological rep1


title: SCI + delayed MSC graft 2dpi, biological rep2


title: SCI + delayed MSC graft 7dpi, biological rep2


title: SCI + delayed MSC graft 2dpi, biological rep1


title: SCI + acute OEC graft 2dpi, biological rep3


title: SCI + acute MSC graft 7dpi, biological rep2


title: SCI + delayed MSC graft 2dpi, biological rep4


title: SCI + delayed MSC graft 7dpi, biological rep1


title: SCI + acute MSC graft 2dpi, biological rep4


title: M2nsf1∆ mutant at 85% total glucose fermented, biological rep2


title: SCI + acute MSC graft 7dpi, biological rep1


title: M2nsf1∆ mutant at 24hr, biological rep2

description: Gene expression data from the mutant industrial M2 nsf1∆ strain at 24hrs post Riesling grape must innoculation

source_name: Mutant  M2nsf1∆ strain cells at 24hrs


title: M2nsf1∆ mutant at 24hr, biological rep1

value: 24hrs post Riesling grape must innoculation


title: SCI + acute MSC graft 2dpi, biological rep2


title: M2nsf1∆ mutant at 20% total glucose fermented, biological rep2

description: Gene expression data from the mutant industrial M2 nsf1∆ strain grown in Riesling grape must. 20% of the total glucose fermented time point.

source_name: Mutant  M2nsf1∆ strain cells at 20% glucose fermented

value: grown in Riesling grape must, 20% of the total glucose fermented time point


title: M2 at 85% total glucose fermented, biological rep2

description: Gene expression data from the wild type industrial M2 strain grown in Riesling grape must. 85% of the total glucose fermented time point.

source_name: Wild type M2 strain cells at 85% glucose fermented

value: M2  (wild type)


title: SCI + acute MSC graft 2dpi, biological rep3


title: SCI + acute MSC graft 7dpi, biological rep4


title: M2nsf1∆ mutant at 20% total glucose fermented, biological rep1


title: M2 at 85% total glucose fermented, biological rep3


title: SCI + acute MSC graft 2dpi, biological rep1


title: MH63-ROOT, biological replicate 3

city: Beijing

first: Jie

last: Zhao

address: No. 2 Yuan Ming Yuan West Street

country: China

institute: Institute of Plant Protection, Chinese Academe of Agricultural Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C using an Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained at Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip® Scanner 3000 7G.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MH63 seedlings_roots

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

growth_protocol: Rice seeds were surface-disinfected and then soaked in distilled sterile water for germination at 28°C for 2 days. rice seedlings with similar size were selected and transplanted into 8 L plastic containers containing nutrient solution(Yoshida et al., 1976) in a controlled climate chamber at 16-h-light (30°C)/8-h-dark (26°C) cycle.

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

tag: cultivar (background)

value: Minghui 63

tag: genotype/variation

value: non-transgenic control

value: roots

tag: age

value: 30 days


title: M2 at 20% total glucose fermented, biological rep2

description: Gene expression data from the wild type industrial M2 strain grown in Riesling grape must. 20% of the total glucose fermented time point.

source_name: Wild type M2 strain cells at 20% glucose fermented


title: MH63-ROOT, biological replicate 1


title: M2 at 85% total glucose fermented, biological rep1


title: M2 at 24hr, biological rep1

description: Gene expression data from the wild type industrial M2 strain at 24hrs post Riesling grape must innoculation

source_name: Wild type M2 strain cells at 24hr


title: intact animal, biological rep2

tag: treatment


title: HH1-ROOT, biological  replicate 2

source_name: HH1 seedlings_roots

value: transgenic Huahui 1 (HH1)

tag: tissue


title: M2 at 20% total glucose fermented, biological rep1


title: intact animal, biological rep4


title: intact animal, biological rep1


title: intact animal, biological rep3


title: MH63-ROOT, biological replicate 2


title: HH1-ROOT, biological  replicate 1


title: HH1-ROOT, biological  replicate 3


title: M2 at 24hr, biological rep2


title: Gata1 0h rep3

status: Public on Oct 15 2013

city: Lund

first: Shamit

last: Soneji

address: Sölvegatan 19

country: Sweden

institute: BMC

hyb_protocol: Each Cy3-labeled cRNA sample (1.6ug as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.

scan_protocol: Scanning and feature extraction was performed as per Agilent protocols

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent v10.1.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: FDCPmix_Gata1 0h

label_protocol: Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.

growth_protocol: FDCPmix were grown in 20% Fischer's medium.

extract_protocol: Total RNA was isolate using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).

treatment_protocol: GATA1ERT and Pu.1ERT were subcloned into the pHR-SIN-CSGWEmGFP lentiviral expression construct under control of the SFFV promoter. Gata2 and Pu.1 shRNAs were subcloned into Lentilox 3.7. Recombinant plasmids were packaged into lentiviral particles esssentially by published procedures. FDCPmix cells were transduced at an MOI of between 50 and 200. For gene expression analysis,  samples of FDCPmix cells in self-renewal conditions were transduced with lentiviral particles encoding GATA1ERT or PU.1ERT fusion proteins linked to ires-GFP, with empty virus used as a control. GFP+ cells were sorted after 3 days and expanded for a further 7 days under standard conditions, before re-sorting on GFP and addition of 2M 4OH-tamoxifen. Cells were harvested after 0h and 24h of induction and total RNA analyzed by microarray.

tag: cell line

value: FDCPmix

tag: infected with


title: Gata1 24h rep2

source_name: FDCPmix_Gata1 24h


title: Gata1 0h rep1


title: Pu1 24h rep1

source_name: FDCPmix_Pu1 24h


title: Gata1 24h rep1


title: Pu1 0h rep2

source_name: FDCPmix_Pu1 0h


title: Cont 0h rep1

source_name: FDCPmix_Cont 0h

value: Empty vector


title: Cont 24h rep2

source_name: FDCPmix_Cont 24h


title: Cont 24h rep3


title: Pu1 shRNA rep3

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent 10.1.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

extract_protocol: Total RNA was isolated using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).

treatment_protocol: Triplicate samples of FDCPmix cells in self-renewal conditions were transduced with lentiviral particles encoding shRNA directed against Gata2 or Pu.1; empty virus was used as a control. Five days after transduction, cells were washed and viable GFP+ cells isolated by flow sorting. Sorted cells were lysed in TRIzol and total RNA analyzed by microarray.

value: shPu1 LLX


title: Gata1 0h rep2


title: EV rep2


title: Pu1 shRNA rep2


title: Cont 24h rep1


title: Pu1 24h rep2


title: Gata1 24h rep3


title: Gata2 shRNA rep3

value: shGata2 LLX


title: Pu1 0h rep1


title: Cont 0h rep3


title: EV rep3


title: Pu1 shRNA rep1


title: Mac1Gr1 rep3

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent v10.7.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Bone Marrow

extract_protocol: Total RNA was isolated from samples using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).

treatment_protocol: Cells were extracted from mouse bone marrow and sorted according to the markers stated in the sample descriptions.

value: bone Marrow

tag: cell type

value: primary hematopoietic cells

tag: fraction

value: Mac1Gr1 (Mac1+ Gr1+)


title: Mac1Gr1 rep1


title: Mac1Gr1 rep2


title: Gata2 shRNA rep2


title: EV rep1


title: GMP rep3

value: GMP (lin- ckit+ sca1+ CD150- FCGrI/II+)


title: GMP rep2


title: Gata2 shRNA rep1


title: Ter119 rep3


title: GMP rep1


title: PreGM rep2

value: PreGM (lin- ckit+ sca1+ CD150- CD105- FGCrI/II-)


title: CFUe rep2

value: CFUe (lin- ckit+ sca1+ CD150- CD105- FCGrI/II-)


title: Ter119 rep1


title: Ter119 rep2


title: CFUe rep1


title: PreGM rep3


title: CFUe rep3


title: PreGM rep1


title: KLS rep2

value: KLS (lin- ckit+ sca1+)


title: PreMegE rep2

value: PreMegE (lin- ckit+ sca1+ CD150+ CD105-  FGCrI/II-)


title: PreMegE rep3


title: Ndiff 120h rep1

source_name: FDCPmix_Ndiff 120h

growth_protocol: FDCPmix were routinely maintained in Fischer's medium.

extract_protocol: Total RNA was isolated from triplicates using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).

treatment_protocol: For differentiation, cells were washed and then triplicate samples were cultured in IMDM plus 10% FCS and low IL-3 supplemented with either Epo and hemin (erythroid output) or G-CSF and SCF (neutrophil output).

tag: cytokine condition

value: GCSF+SCF

tag: differentiation stage

value: Myeloid


title: KLS rep3


title: Ndiff 72h rep2

source_name: FDCPmix_Ndiff 72h


title: Ndiff 168h rep2

source_name: FDCPmix_Ndiff 168h


title: Ndiff 120h rep3


title: Ndiff 96h rep3

source_name: FDCPmix_Ndiff 96h


title: Ndiff 120h rep2


title: PreMegE rep1


title: Ndiff 168h rep3


title: Ndiff 168h rep1


title: Ndiff 96h rep1


title: KLS rep1


title: Ndiff 96h rep2


title: Ndiff 72h rep1


title: Ndiff 72h rep3


title: Ndiff 68h rep3

source_name: FDCPmix_Ndiff 68h


title: Ndiff 68h rep2


title: Cont 0h rep2


title: Ndiff 64h rep1

source_name: FDCPmix_Ndiff 64h


title: Ndiff 64h rep2


title: Ndiff 64h rep3


title: Ndiff 68h rep1


title: Ndiff 60h rep2

source_name: FDCPmix_Ndiff 60h


title: Ndiff 60h rep1


title: Ndiff 60h rep3


title: Ndiff 56h rep1

source_name: FDCPmix_Ndiff 56h


title: Ndiff 56h rep3


title: Ndiff 52h rep2

source_name: FDCPmix_Ndiff 52h


title: Ndiff 52h rep1


title: Ndiff 45h rep3

source_name: FDCPmix_Ndiff 45h


title: DCIS_sample50

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: 50 DCIS

hyb_protocol: Labeled test DNA was combined with labeled reference DNA, diluted to 150 µl with nuclease free water, and combined with 50 µl Cot-1 DNA (Invitrogen), 50 µl 10X Blocking Agent (Agilent, Santa Clara, CA), and 250 µl 2X Hybridization Buffer (Agilent).  Labeled DNAs were heat-denatured and pre-blocked at 37°C for 30 min.  The microarray was hybridized in a rotisserie at 65°C for 40 hrs.  Washing was according to the manufacturers instructions.

scan_protocol: Arrays were scanned in an Agilent DNA Microarray Scanner.

data_processing: Arrays were processed with Feature Extraction Software (Agilent, CGH-v4_95_Feb07) using build HG18.

source_name: Amplified DNA from laser capture microdissected DCIS

label_protocol: DNA was labelled using the Bioprime Array CGH Labeling Module (Invitrogen) with modifications. Specifically, 20 µl 2.5X Random Primer Mix was combined with 10 µg DNA in 21 µl nuclease free water and heat-denatured.  To the cooled DNA was added: 5 µl of nucleotide mix (1.2 mM each of dATP, dGTP, dCTP, and 0.6 mM dTTP), 3 nmol of appropriate labelled nucleotide (test DNA and reference DNA labeled with Cy5-dUTP and Cy3-dUTP respectively), and 1 µl Exo- Klenow.  Reaction was incubated at 37°C for 2 hrs, acidified with 10 µl 3 M Sodium Acetate (pH 5.2), and purified using QIAquick PCR Purification Kit (Qiagen, Germantown, MD, USA).

extract_protocol: DNA was extracted using the QIAamp DNA Micro Kit (Qiagen) according to manufacturer's instructions. DNA amplification was performed using the GenomiPhi DNA amplification kit (Amersham-Biosciences).

value: ductal carcinoma in situ (DCIS) of the breast

source_name: Amplified normal male DNA (Promega)

tag: sample type

value: Reference DNA


title: Ndiff 48h rep3

source_name: FDCPmix_Ndiff 48h


title: Ndiff 48h rep1


title: Ndiff 45h rep2


title: DCIS_sample39

description: 39 DCIS


title: LCIS_sample46

description: 46 LCIS

source_name: Amplified DNA from laser capture microdissected LCIS

value: lobular carcinoma in situ (LCIS) of the breast


title: DCIS_sample48

description: 48 DCIS


title: Ndiff 45h rep1

value: FDCPmix


title: DCIS_sample29

description: 29 DCIS


title: DCIS_sample21

description: 21 DCIS


title: Ndiff 48h rep2


title: DCIS_sample26

description: 26 DCIS


title: DCIS_sample24

description: 24 DCIS


title: Ndiff 52h rep3


title: Ndiff 42h rep1

source_name: FDCPmix_Ndiff 42h


title: DCIS_sample19

description: 19 DCIS


title: DCIS_sample11

description: 11 DCIS


title: Ndiff 42h rep2


title: Ndiff 39h rep3

source_name: FDCPmix_Ndiff 39h


title: Ndiff 56h rep2


title: DCIS_sample17

description: 17 DCIS


title: DCIS_sample9

description: 9 DCIS


title: Ndiff 39h rep1


title: DCIS_sample7

description: 7 DCIS


title: Ndiff 39h rep2


title: Ndiff 42h rep3


title: DCIS_sample1

description: 1 HG DCIS


title: Ndiff 36h rep3

source_name: FDCPmix_Ndiff 36h


title: Ndiff 36h rep2


title: Ndiff 33h rep2

source_name: FDCPmix_Ndiff 33h


title: Ndiff 22h rep2

source_name: FDCPmix_Ndiff 22h


title: Ndiff 22h rep3


title: DCIS_sample1.1

description: 1.1 IG DCIS


title: Ndiff 30h rep1

source_name: FDCPmix_Ndiff 30h


title: Ndiff 27h rep1

source_name: FDCPmix_Ndiff 27h


title: Ndiff 24h rep1

source_name: FDCPmix_Ndiff 24h


title: Ndiff 27h rep2


title: Ndiff 36h rep1


title: Ndiff 20h rep3

source_name: FDCPmix_Ndiff 20h


title: Ndiff 20h rep2


title: Ndiff 24h rep3


title: Ndiff 30h rep3


title: Ndiff 18h rep3

source_name: FDCPmix_Ndiff 18h


title: Ndiff 20h rep1


title: Ndiff 22h rep1


title: Ndiff 33h rep1


title: Ndiff 30h rep2


title: Ndiff 33h rep3


title: Ndiff 24h rep2


title: Ndiff 18h rep1


title: Ndiff 27h rep3


title: Ndiff 14h rep3

source_name: FDCPmix_Ndiff 14h


title: Ndiff 18h rep2


title: Ndiff 16h rep1

source_name: FDCPmix_Ndiff 16h


title: Ndiff 8h rep3

source_name: FDCPmix_Ndiff 8h


title: Ndiff 10h rep1

source_name: FDCPmix_Ndiff 10h


title: Ndiff 14h rep2


title: Ndiff 12h rep2

source_name: FDCPmix_Ndiff 12h


title: Ndiff 12h rep1


title: Ndiff 16h rep3


title: Ndiff 12h rep3


title: Ndiff 16h rep2


title: Ndiff 6h rep3

source_name: FDCPmix_Ndiff 6h


title: Ndiff 4h rep3

source_name: FDCPmix_Ndiff 4h


title: Ndiff 6h rep2


title: Ndiff 4h rep2


title: Ndiff 4h rep1


title: Ndiff 6h rep1


title: Ndiff 8h rep2


title: Ndiff 14h rep1


title: Ndiff 10h rep3


title: Ndiff 8h rep1


title: Ndiff 10h rep2


title: Ediff 168h rep1

source_name: FDCPmix_Ediff 168h

value: Epo+hemin

value: Erythroid


title: Ediff 168h rep3


title: Ndiff 2h rep2

source_name: FDCPmix_Ndiff 2h


title: Ediff 120h rep2

source_name: FDCPmix_Ediff 120h


title: Ediff 120h rep1


title: pUCA1501_3, biological rep3

city: Bei Jing

first: Liang

last: Li

state: Bei Jing

address: Zhongguan Cun Nanda Jie No.12

department: Biotechnology Research Institute

institute: Chinese Academy of Agricultural Sciences

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli 2.0 array at 45ºC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4  Details: Intra-chip normalizations were performed using Affymetrix Gene Chip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2.

organism: Escherichia coli

source_name: E. coli K12 strain JM109 harboring pUCA1501

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

growth_protocol: E.coli cells with pUC18/pUCA1501 grown with aeration in LB media at 37º C until early log phase (0.4), after that the cells were harvested to M9 media.

extract_protocol: Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.

treatment_protocol: Treatment protocol- E.coli cells with pUC18/pUCA1501 grown in M9 media with  at 37ºC for 1 h,after that the cells were harvested to extract RNA.

tag: plasmid vector


title: pUCA1501_2, biological rep2


title: Ediff 168h rep2


title: Ndiff 2h rep3


title: Ediff 96h rep2

source_name: FDCPmix_Ediff 96h


title: Ediff 120h rep3


title: Ediff 96h rep1


title: Ndiff 2h rep1


title: pUCA1501_1, biological rep1


title: Ediff 96h rep3


title: pUC18_1, biological rep1

source_name: E. coli K12 strain JM109 harboring pUC18


title: pUC18_3, biological rep3


title: Ediff 72h rep3

source_name: FDCPmix_Ediff 72h


title: pUC18_2, biological rep2


title: Ediff 72h rep2


title: Wildtype triclosan treated biological rep 3

city: Dublin

first: Julieanne

last: Molloy

address: Ashtown

department: Food Safety

country: Ireland

institute: Teagasc Food Research Centre

hyb_protocol: Performed by Source BioScience imaGenes, Berlin, Germany - imaGenes Affymetrix expression profiling full service on GeneChip E. coli Genome 2.0 Array

data_processing: Microarray analysis including pre-processing, normalisation anmd statistical analysis were performed using R (R, 2007) version 2.6 and Bioconductor (Gentleman et al. 2004, Genome Biol. 5:R80) version 2.1 as previously described by Morris et al.(2009, Physiol. Genomics 39:28-37). Propagating uncertainty in microarray analysis (puma) method was used to estimate fold changes and P-like values of differential gene expression analysis (Pearson et al. 2009, BMC Bioinformatics 10:211).

organism: Escherichia coli O157

source_name: Wildtype E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 3

growth_protocol: The wildtype and mutant E. coli O157:H19 strains were grown on LB agar incubated at 37c x 24h. A single isolated colony for each strain was selected and inoculated into 20 ml LB broth and incubated at 37c until growth reached an optical density of 0.6 at 600nm.

extract_protocol: Total RNA was stabilised and subsequently purified from a 500 ul portion of each bacterial culture using a RNAprotect Bacterial Reagent Mini Kit (Qiagen, Crawley, UK)

treatment_protocol: The subculture was split into two 10 ml portions, one of which was treated with 6ug/ml triclosan and the other retained as an untreated control. Treated and untreated samples were incubated at 37c for 30 min.

tag: genotype

value: wild type

tag: genetic background

value: triclosan


title: Wildtype untreated biological rep 2

scan_protocol: Performed by Source BioScience imaGenes, Berlin, Germany - imaGenes Affymetrix expression profiling full service on GeneChip E. coli Genome 2.0 Array

source_name: Wildtype E. coli O157 untreated, biological rep 2

value: untreated


title: Wildtype untreated biological rep 1

source_name: Wildtype E. coli O157 untreated, biological rep 1

label_protocol: Performed by Source BioScience imaGenes, Berlin, Germany - imaGenes Affymetrix expression profiling full service on GeneChip E. coli Genome 2.0 Array


title: Wildtype triclosan treated biological rep 2

source_name: Wildtype E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 2


title: Wildtype untreated biological rep 3

source_name: Wildtype E. coli O157 untreated, biological rep 3


title: Ediff 68h rep3

source_name: FDCPmix_Ediff 68h


title: Ediff 72h rep1


title: Ediff 64h rep3

source_name: FDCPmix_Ediff 64h


title: Triclosan tolerant mutant untreated biological rep 2

source_name: Mutant E. coli O157 untreated, biological rep 2

value: T3 5H5 M

value: triclosan tolerant mutant


title: Ediff 68h rep2


title: Ediff 68h rep1


title: Wildtype triclosan treated biological rep 1

source_name: Wildtype E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 1


title: Triclosan tolerant mutant untreated biological rep 1

source_name: Mutant E. coli O157 untreated, biological rep 1


title: Ediff 64h rep2


title: Triclosan tolerant mutant untreated biological rep 3

source_name: Mutant E. coli O157 untreated, biological rep 3


title: Triclosan tolerant mutant triclosan treated biological rep 3

source_name: Mutant E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 3


title: Triclosan tolerant mutant triclosan treated biological rep 1

source_name: Mutant E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 1


title: Triclosan tolerant mutant triclosan treated biological rep 2

source_name: Mutant E. coli O157 treated with 6 ug/ml triclosan for 30 min, biological rep 2


title: Ediff 64h rep1


title: Ediff 60h rep1

source_name: FDCPmix_Ediff 60h


title: Ediff 60h rep2


title: Ediff 60h rep3


title: Ediff 56h rep1

source_name: FDCPmix_Ediff 56h


title: Ediff 56h rep3


title: Ediff 52h rep2

source_name: FDCPmix_Ediff 52h


title: Ediff 48h rep3

source_name: FDCPmix_Ediff 48h


title: Ediff 52h rep1


title: Ediff 52h rep3


title: Ediff 56h rep2


title: Ediff 48h rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge mRNA rep3

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45 ˚C on the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX 11.5 using RMA normalization, then normalized to the median of all samples

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).

growth_protocol: Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA).

extract_protocol:
Extrahepatic bile ducts and gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injection and stabilized with RNAlater (QIAGEN, CA).
3 sets of samples were generated for each time point (experimental and control groups), with each set containing 2-6 extrahepatic bile ducts.
Total RNA was isolated from extrahepatic bileducts of RRV- or saline-injected mice using miRNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

treatment_protocol: Newborn mice were injected with 20 μL of a solution containing 1.5x10^6 fluorescent-forming units of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth.

value: Extrahepatic Bileduct and gallbladder

value: Balb/c

tag: time

value: 14 days

value: Rhesus rotavirus injection


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge mRNA rep1

tag: strain


title: Ediff 48h rep1


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection mRNA rep1

value: Normal saline injection


title: Ediff 45h rep2

source_name: FDCPmix_Ediff 45h


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge mRNA rep3

value: 7 days


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection mRNA rep3


title: Ediff 45h rep3


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection mRNA rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge mRNA rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection mRNA rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge mRNA rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection mRNA rep3


title: Ediff 42h rep2

source_name: FDCPmix_Ediff 42h


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge mRNA rep1


title: Ediff 42h rep3


title: Ediff 45h rep1


title: Ediff 39h rep3

source_name: FDCPmix_Ediff 39h


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection mRNA rep1


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge mRNA rep3

value: 3 days


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge mRNA rep1


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection mRNA rep1


title: Ediff 36h rep3

source_name: FDCPmix_Ediff 36h


title: Ediff 42h rep1


title: Ediff 36h rep1


title: Ediff 39h rep2


title: Ediff 39h rep1


title: Ediff 33h rep2

source_name: FDCPmix_Ediff 33h


title: Ediff 36h rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection mRNA rep2


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection mRNA rep3


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge mRNA rep2


title: Ediff 33h rep1


title: Expt2_kd_R3

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

source_name: Adult mouse round spermatids

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

tag: genotype (brdt)

value: Th2b kd

value: Round spermatids (post-meiotic)

tag: replicate

value: Replicate 3


title: Expt2_kd_R5

value: Replicate 5


title: Ediff 30h rep2

source_name: FDCPmix_Ediff 30h

value: FDCPmix

value: Epo+hemin

value: Erythroid


title: Expt2_kd_R2

value: Replicate 2


title: Ediff 30h rep1


title: Ediff 33h rep3


title: Ediff 30h rep3


title: Expt2_kd_R1

value: Replicate 1


title: Expt2_wt_R5

value: wild type


title: Ediff 27h rep1

source_name: FDCPmix_Ediff 27h


title: Expt2_wt_R4

value: Replicate 4


title: Expt2_wt_R2


title: Ediff 22h rep3

source_name: FDCPmix_Ediff 22h


title: Expt2_kd_P4

source_name: Adult mouse spermatocytes

value: Spermatocytes (meiotic)


title: Expt2_kd_P2


title: Ediff 27h rep3


title: Ediff 27h rep2


title: Expt2_kd_P3


title: Expt2_wt_R3


title: Expt2_kd_P5


title: Expt2_wt_R1


title: Ediff 22h rep2


title: Expt2_wt_P5


title: Expt2_kd_P1


title: Ediff 24h rep3

source_name: FDCPmix_Ediff 24h


title: Ediff 24h rep1


title: Ediff 20h rep3

source_name: FDCPmix_Ediff 20h


title: Ediff 22h rep1


title: Ediff 24h rep2


title: Expt2_wt_P4


title: Expt2_wt_P3


title: Ediff 20h rep1


title: Ediff 20h rep2


title: Expt2_kd_R4


title: Ediff 18h rep1

source_name: FDCPmix_Ediff 18h


title: Expt2_wt_P2


title: Expt1_tag_R5


title: Expt1_tag_R4


title: Ediff 18h rep2


title: Ediff 18h rep3


title: Expt2_wt_P1


title: Ediff 16h rep2

source_name: FDCPmix_Ediff 16h


title: Ediff 12h rep3

source_name: FDCPmix_Ediff 12h


title: Ediff 14h rep2

source_name: FDCPmix_Ediff 14h


title: Ediff 14h rep1


title: Ediff 12h rep2


title: Expt1_wt_R6

value: Replicate 6


title: Expt1_tag_R2


title: Expt1_tag_R3


title: Expt1_wt_R5


title: Ediff 16h rep3


title: Ediff 16h rep1


title: Ediff 14h rep3


title: Expt1_tag_R1


title: Expt1_wt_R3


title: Ediff 10h rep3

source_name: FDCPmix_Ediff 10h


title: Ediff 12h rep1


title: Expt1_wt_R2


title: Expt1_wt_R1


title: Ediff 10h rep2


title: Ediff 8h rep3

source_name: FDCPmix_Ediff 8h


title: Ediff 10h rep1


title: Expt1_tag_P3


title: Ediff 6h rep3

source_name: FDCPmix_Ediff 6h


title: Expt1_tag_P5


title: Expt1_tag_P6


title: Ediff 8h rep2


title: Expt1_tag_P4


title: Ediff 4h rep3

source_name: FDCPmix_Ediff 4h


title: Ediff 6h rep1


title: Expt1_wt_P6


title: Expt1_tag_P1


title: Expt1_tag_P2


title: Ediff 8h rep1


title: Expt1_wt_P4


title: Ediff 2h rep3

source_name: FDCPmix_Ediff 2h


title: Expt1_wt_P2


title: Ediff 4h rep2


title: Expt1_wt_P5


title: Ediff 2h rep2


title: FDCP T0 rep3

source_name: FDCPmix_FDCP T0

value: Multipotential


title: Ediff 2h rep1


title: Ediff 4h rep1


title: Expt1_wt_P1


title: Expt1_wt_P3


title: FDCP T0 rep1


title: FDCP T0 rep2


title: Ediff 6h rep2


title: TSA_rep3

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression arrays were normalized in Bioconductor, using RMA and median polish settings in the expresso package.

source_name: Spleen Sorted Cells

label_protocol: Affymetrix protocol

growth_protocol: Cells were harvested from 6-8wk old mice that had been administered Flt3L expressing B.16 tumors.  DC were purified by MACS Miltenyi CD11c beads.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructions.

value: Flt3L-elicited DC

value: TSA treated


title: Butyrate_rep3

value: Butyrate treated


title: Butyrate_rep1


title: Control_rep1

value: untreated


title: Control_rep2


title: Butyrate_rep2


title: TSA_rep2


title: TSA_rep1


title: Expt1_tag_R6

source_name: Adult mouse round spermatids

value: Round spermatids (post-meiotic)


title: Bmel Infected vs Control 120 min PI, Calf 3

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

description: 10484 Inf Data 2hrs S3::10482 Co Data 2hrs S3::t=120

hyb_protocol: Prior to hybridization, the microarrays were denatured by exposing to steam from boiling water for three seconds, UV cross-linked and then immersed in pre-hybridization buffer [5X sodium chloride, sodium citrate buffer (SSC), 0.1% sodium dodecyl sulfate (SDS) (Ambion, Austin, TX), 1% bovine serum albumin (BSA)] at 42ºC for a minimum of 45 min.  The arrays were then washed four times in RNase-, DNase-free, distilled water, immersed in 100% isopropanol for 10 seconds, and dried by centrifugation. Slides were hybridized at 42ºC for approximately 40 hours in a dark, humid chamber (Corning, Corning, NY), washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] and then washed twice for 5-min each wash in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature with agitation.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). Scans were performed using the autoscan feature with the percent saturated pixels set at 0.03%.

data_processing: Global scaling to 200 across all arrays, LOWESS normalized, background subtracted data. Channel 2 (Cy5) was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with experiment condition (Bmel Infected) versus Uninfected as the control.

label: Cy3: Infected Array; Cy5: Uref

organism: Bos taurus

source_name: Distal ileum, inoculated with Bmel 16M collected at 2 h, calf 3 (vs Uref_Cy5)

label_protocol: Briefly, cDNA from bovine experimental samples (i.e. from infected and control loops)  and cDNA generated from the bovine reference RNA sample were co-hybridized to the previously described custom 13K bovine 70-mer oligoarray. The cDNA was reverse-transcribed using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) and labeled with amino-allyl-UTP (Ambion, Austin, TX).  Cy3 and Cy5 dye esters were covalently linked to the amino-allyl group by incubating the samples with the dye esters in 0.1M sodium carbonate buffer.

extract_protocol: Total RNA was extracted after dissection of the ileal loops obtained at 15 min, 30 min and at 1, 2 and 4 hours post-infection. A 6 mm biopsy punch was used to collect 8 tissue pieces of Peyer’s patch from the excised loop. The mucosa of the samples were immediately dissected, the tissue pieces finely minced with a scalpel blade, and two biopsy punches (0.1 mg of tissue) transferred to 1 ml of Trizol reagent (Molecular Research Center, Cincinnati, OH).  Tissues were further disrupted with an RNase, DNase free plastic disposable pestle.  The RNA extraction was performed using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion, Austin, TX).  Genomic DNA was removed by RNase-free DNase I treatment (DNA-free, Ambion) according to the manufacture’s instructions, and samples were stored at −80ºC until used. The quality of the RNA was initially assessed by measurement of the lambda 260/280 ratio and agarose gel electrophoresis. RNA concentration was quantified by measuring absorbance at lambda 260nm using a NanoDrop® ND-1000 (NanoDrop, Wilmington, DW), and the RNA quality was determined using a Nano-Chip® on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).  The RNA analyzed in all samples was of good to excellent quality (results not shown).  Samples were characterized by distinct 18S and 28S rRNA peaks and RNA size distribution.  Ten micrograms of RNA was used as starting material for each array.To generate the reference RNA (which was labeled with Cy3), total RNA was isolated from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines (American Type Culture Collection, Manassas, VA) and fresh bovine brain cortex and cerebellum collected from surgery calves following euthanasia at the conclusion of each experiment.  Cell lines were grown in 150 cm2 cell culture flasks with Eagle’s minimum essential medium (E-MEM) (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS). Tissues were homogenized in ice-cold Tri-reagent® (Ambion, Austin, TX). RNA concentration and quality from each sample was determined before and after pooling the samples. Total RNA isolated from three samples was pooled together in equal amounts, aliquoted and stored at −80ºC until needed.

tag: animal

value: Outbred male calf, 3 to 6 month old

value: Distal ileum, inoculated with Bmel

value: bovine reference RNA

label: Cy3: Control Array; Cy5: Uref

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 2 h, calf 3 (vs Uref_Cy5)

value: intestinal loops inoculated with cell culture medium


title: Bmel Infected vs Control 120 min PI, Calf 4

description: 10509 Inf Data 2hrs S4::10507 Co Data 2hrs S4::t=120

source_name: Distal ileum, inoculated with Bmel 16M collected at 2 h, calf 4 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 2 h, calf 4 (vs Uref_Cy5)


title: Bmel Infected vs Control 120 min PI, Calf 1

description: 10438 Inf Data 2hr S1::10436 Co Data 2hr S1::t=120

source_name: Distal ileum, inoculated with Bmel 16M collected at 2 h, calf 1 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 2 h, calf 1 (vs Uref_Cy5)


title: Bmel Infected vs Control 240 min PI, Calf 2

description: 10463 Inf Data 4hrs S2::10461 Co Data 4hrs S2::t=240

source_name: Distal ileum, inoculated with Bmel 16M collected at 4 h, calf 2 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 4 h, calf 2 (vs Uref_Cy5)


title: Control_rep3

tag: treatment


title: Bmel Infected vs Control 240 min PI, Calf 1

description: 10441 Inf Data 4hr S1::10439 Co Data 4hr S1::t=240

source_name: Distal ileum, inoculated with Bmel 16M collected at 4 h, calf 1 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 4 h, calf 1 (vs Uref_Cy5)


title: Bmel Infected vs Control 120 min PI, Calf 2

description: 10460 Inf Data 2hrs S2::10458 Co Data 2hrs S2::t=120

source_name: Distal ileum, inoculated with Bmel 16M collected at 2 h, calf 2 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 2 h, calf 2 (vs Uref_Cy5)


title: Bmel Infected vs Control 60 min PI, Calf 2

description: 10457 Inf Data 1hrs S2::10455 Co Data 1hrs S2::t=60

source_name: Distal ileum, inoculated with Bmel 16M collected at 1 h, calf 2 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 1 h, calf 2 (vs Uref_Cy5)


title: Bmel Infected vs Control 30 min PI, Calf 4

description: 10502 Inf Data 30min S4::10500 Co Data 30min S4::t=30

source_name: Distal ileum, inoculated with Bmel 16M collected at 30 min, calf 4 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 30 min, calf 4 (vs Uref_Cy5)


title: Bmel Infected vs Control 60 min PI, Calf 1

description: 10435 Inf Data 1hr S1::10433 Co Data 1hr S1::t=60

source_name: Distal ileum, inoculated with Bmel 16M collected at 1 h, calf 1 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 1 h, calf 1 (vs Uref_Cy5)


title: HF-20341-(1) Xba

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the DNAcopy package for the R statistical environment.

label_protocol: Affymetrix 100K protocol

growth_protocol: Patient samples

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions

treatment_protocol: Untreated

tag: braf status

tag: sample id

tag: tissue

value: melanoma tumor


title: Bmel Infected vs Control 60 min PI, Calf 3

description: 10480 Inf Data 1hrs S3::10478 Co Data 1hrs S3::t=60

source_name: Distal ileum, inoculated with Bmel 16M collected at 1 h, calf 3 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 1 h, calf 3 (vs Uref_Cy5)


title: HF-20339-(1) Xba


title: Bmel Infected vs Control 60 min PI, Calf 4

description: 10505 Inf Data 1hrs S4::10503 Co Data 1hrs S4::t=60

source_name: Distal ileum, inoculated with Bmel 16M collected at 1 h, calf 4 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 1 h, calf 4 (vs Uref_Cy5)


title: Bmel Infected vs Control 30 min PI, Calf 3

description: 10477 Inf Data 30min S3::10475 Co Data 30 min S3::t=30

source_name: Distal ileum, inoculated with Bmel 16M collected at 30 min, calf 3 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 30 min, calf 3 (vs Uref_Cy5)


title: Bmel Infected vs Control 30 min PI, Calf 2

description: 10454 Inf Data 30min S2::10452 Co Data 30min S2::t=30

source_name: Distal ileum, inoculated with Bmel 16M collected at 30 min, calf 2 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 30 min, calf 2 (vs Uref_Cy5)


title: Bmel Infected vs Control 240 min PI, Calf 3

description: 10487 Inf Data 4hrs S3::10485 Co Data 4hrs S3::t=240

source_name: Distal ileum, inoculated with Bmel 16M collected at 4 h, calf 3 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 4 h, calf 3 (vs Uref_Cy5)


title: Bmel Infected vs Control 30 min PI, Calf 1

description: 10432 Inf Data 30min S1::10430 Co Data 30min S1::t=30

source_name: Distal ileum, inoculated with Bmel 16M collected at 30 min, calf 1 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 30 min, calf 1 (vs Uref_Cy5)


title: Bmel Infected vs Control 240 min PI, Calf 4

description: 10512 Inf Data 4hrs S4::10510 Co Data 4hrs S4::t=240

source_name: Distal ileum, inoculated with Bmel 16M collected at 4 h, calf 4 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 4 h, calf 4 (vs Uref_Cy5)


title: HF-20337-(1) Xba


title: Expt1_wt_R4

source_name: Adult mouse round spermatids

tag: cell type


title: PBMC expression profile of IPF patient_P107

city: New Haven

first: JOSE

middle: DAVID

last: HERAZO MAYA

state: CT

address: 300 Cedar Street

department: Medicine

institute: Yale University

description: PBMC expression profile of IPF patient

hyb_protocol: Five µg of biotin labeled sense target samples were hybridized to Affymetrix Human Exon 1.0 ST array using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute • Transfer 200μl of hyb solution to each array, then tape holes and parafilm • Hybridize in hybridization oven 640 for 16-18 hours at 45° at 60rpm • Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The cel files were processed using dCHip software: Model method =Average; Normalization =Quantile; Smoothing method = Running median
Data is processed by mapping HuExon 1.0 st exon probesets to HG-U133 2.0 probesets where the exon probesets are fully contained within the HG-U133 2.0 consensus/exemplar. The output file is the average of exon expression value for each U133 probe set/gene (not a log transformation value).
probe group file: HuEx-1_0-st-v2.r2.pgf from Affymetrix
meta-probeset file: U133_to_exon_mapping file, which is from Affymetrix and maps exon array probe sets to U133 consensus or exemplar sequences.

source_name: RNA isolated from PBMC of IPF patient

label_protocol: One hundred fifty ng of total RNA per samples was processed to amplified cRNA and reverse transcribed to single stranded DNA using Affymetrix GeneChip WT cDNA Synthesis Kit according to Genechip Expression analysis technical manual (Affymetrix, USA).  5.5 µg of the single stranded DNA was enzymatically fragmented and biotin labled with GeneChip WT terminal Labeling Kit (Affymetrix, cat#900671)

growth_protocol: not applicable

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were purified from 10 ml of blood using the Ficoll-Paque™ PLUS followed by protocols described by Todd M. Bull et al., Am J Respir Crit Care Med. 170:911–919, 2004. Total RNA was extracted using TriZol Reagent (Invitrogen, Carlsbad, CA) based on manufacturer’s recommendations followed by sodium acetate/ethanol precipitation.

treatment_protocol: not applicable

tag: race

value: Caucasian

tag: gender

value: Male

tag: age of blood draw

tag: outcome

tag: time to outcome

value: 1.586 years


title: PBMC expression profile of IPF patient_P102

description: PBMC expression profile of IPF patient

value: 1.663 years


title: PBMC expression profile of IPF patient_P104

description: PBMC expression profile of IPF patient

value: 1.624 years


title: PBMC expression profile of IPF patient_P105

description: PBMC expression profile of IPF patient


title: PBMC expression profile of IPF patient_P101

description: PBMC expression profile of IPF patient

value: non-Caucasian

value: 1.679 years


title: PBMC expression profile of IPF patient_P97

description: PBMC expression profile of IPF patient

value: 0.008 years


title: PBMC expression profile of IPF patient_P94

description: PBMC expression profile of IPF patient

value: 2.172 years


title: PBMC expression profile of IPF patient_P98

description: PBMC expression profile of IPF patient

value: Female

value: 1.778 years


title: PBMC expression profile of IPF patient_P95

description: PBMC expression profile of IPF patient

value: 2.021 years


title: Bmel Infected vs Control 15 min PI, Calf 3

description: 10473 Inf Data 15min S3::10471 Co Data 15min S3::t=15

source_name: Distal ileum, inoculated with Bmel 16M collected at 15 min, calf 3 (vs Uref_Cy5)

value: Outbred male calf, 3 to 6 month old

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 15 min, calf 3 (vs Uref_Cy5)


title: HF-20013-(1) Xba


title: HF-18692-(1) Xba


title: HF-19011-(1) Xba


title: HF-19008-(1) Xba


title: PBMC expression profile of IPF patient_P82

description: PBMC expression profile of IPF patient

value: 0.139 years


title: HF-20011-(1) Xba


title: Bmel Infected vs Control 15 min PI, Calf 1

description: 10429 Inf Data 15min S1::10427 Co Data 15min S1::t=15

source_name: Distal ileum, inoculated with Bmel 16M collected at 15 min, calf 1 (vs Uref_Cy5)

value: Distal ileum, inoculated with Bmel

value: bovine reference RNA

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 15 min, calf 1 (vs Uref_Cy5)


title: Bmel Infected vs Control 15 min PI, Calf 4

description: 10498 Inf Data 15min S4::10496 Co Data 15min S4::t=15

source_name: Distal ileum, inoculated with Bmel 16M collected at 15 min, calf 4 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 15 min, calf 4 (vs Uref_Cy5)

value: intestinal loops inoculated with cell culture medium


title: PBMC expression profile of IPF patient_P81

description: PBMC expression profile of IPF patient

value: Caucasian

value: 0.035 years


title: PBMC expression profile of IPF patient_P80

description: PBMC expression profile of IPF patient

value: Male

value: 1.424 years


title: HF-19099-(1) Xba

value: melanoma tumor


title: HF-20335-(1) Xba


title: PBMC expression profile of IPF patient_P100

description: PBMC expression profile of IPF patient

value: 1.695 years


title: HF-18884-(1) Xba


title: HF-18886-(1) Xba


title: HF-18789-(1) Xba


title: Bmel Infected vs Control 15 min PI, Calf 2

description: 10451 Inf Data 15min S2::10449 Co Data 15min S2::t=15

source_name: Distal ileum, inoculated with Bmel 16M collected at 15 min, calf 2 (vs Uref_Cy5)

source_name: Distal ileum, inoculated with Neg Ctrl (F12K medium), collected at 15 min, calf 2 (vs Uref_Cy5)


title: HF-18882-(1) Xba


title: HF-18787-(1) Xba


title: HF-18782-(1) Xba


title: HF-18788-(1) Xba


title: PBMC expression profile of IPF patient_P79

description: PBMC expression profile of IPF patient

value: 2.482 years


title: PBMC expression profile of IPF patient_P78

description: PBMC expression profile of IPF patient

value: 0.539 years


title: PBMC expression profile of IPF patient_P76

description: PBMC expression profile of IPF patient


title: PBMC expression profile of IPF patient_P73

description: PBMC expression profile of IPF patient

value: non-Caucasian

value: 2.6 years


title: HF-18790-(1) Xba


title: PBMC expression profile of IPF patient_P74

description: PBMC expression profile of IPF patient

value: 0.701 years


title: PBMC expression profile of IPF patient_P72

description: PBMC expression profile of IPF patient

value: 1.764 years


title: PBMC expression profile of IPF patient_P69

description: PBMC expression profile of IPF patient

value: 2.027 years


title: PBMC expression profile of IPF patient_P65

description: PBMC expression profile of IPF patient

value: 2.734 years


title: HF-18689-(1) Xba


title: HF-17690-(1) Xba


title: PBMC expression profile of IPF patient_P66

description: PBMC expression profile of IPF patient

value: Female

value: 2.728 years


title: HF-18719-(1) Xba


title: PBMC expression profile of IPF patient_P62

description: PBMC expression profile of IPF patient

value: 2.764 years


title: PBMC expression profile of IPF patient_P63

description: PBMC expression profile of IPF patient

value: Caucasian

value: 2.756 years


title: HF-18686-(1) Xba


title: PBMC expression profile of IPF patient_P64

description: PBMC expression profile of IPF patient

value: Male

value: 2.202 years


title: HF-17691-(1) Xba

value: melanoma tumor


title: PBMC expression profile of IPF patient_P58

description: PBMC expression profile of IPF patient

value: 1.169 years


title: HF-17688-(1) Xba


title: PBMC expression profile of IPF patient_P57

description: PBMC expression profile of IPF patient

value: 2.783 years


title: HF-17687-(1) Xba


title: HF-17588-(1) Xba


title: HF-17684-(1) Xba


title: PBMC expression profile of IPF patient_P54

description: PBMC expression profile of IPF patient

value: 2.794 years


title: HF-16922-(1) Xba


title: HF-18713-(1) Xba


title: PBMC expression profile of IPF patient_P51

description: PBMC expression profile of IPF patient

value: 1.561 years


title: PBMC expression profile of IPF patient_P49

description: PBMC expression profile of IPF patient

value: non-Caucasian

value: 2.75 years


title: HF-16894 Xba


title: HF-16873 Xba


title: PBMC expression profile of IPF patient_P46

description: PBMC expression profile of IPF patient

value: 2.846 years


title: PBMC expression profile of IPF patient_P47

description: PBMC expression profile of IPF patient


title: HF-16890 Xba


title: PBMC expression profile of IPF patient_P45

description: PBMC expression profile of IPF patient

value: 2.884 years


title: HF-16888 Xba


title: PBMC expression profile of IPF patient_P44

description: PBMC expression profile of IPF patient

value: 2.117 years


title: HF-16884 Xba


title: HF-17686-(1) Xba


title: Average 5 healthy controls

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

hyb_protocol: Radioactive cDNA probes were hybridized to the microarrays at 68°C overnight in ExpressHyb solution (BD Biosciences Clontech) and washed according to the manufacturer’s instructions.

scan_protocol: Arrays were exposed to a phosphoimager screen at room temperature for 3 days.

data_processing: Arrays were analyzed using Atlas Image 2.0 software (Clontech Laboratories, Inc., Palo Alto, CA), according to the manufacturer’s instructions. All astronaut arrays (L-10 and R+0) were normalized to an average of 5 control arrays from the whole blood of healthy non-astronaut control subjects. Arrays were normalized using the following housekeeping genes: ubiquitin C (UBC), liver glyceraldehyde 3-phosphate dehydrogenase (GAPDH), tubulin alpha 1 (TUBA1), and major histocompatability complex class I C (HLAC). After background subtraction for each array, the ratio of the post-flight adjusted intensity values (R+0) to the pre-flight adjusted intensity values (L-10) was calculated. Only genes for astronauts with at least four data points pre-flight and post-flight were taken into consideration for data analysis.

source_name: Five Healthy Non-Astronaut Controls

label_protocol: Total RNA was converted to 32P-labeled first-strand cDNA by reverse transcription.  Reaction volumes were optimized for increased detection on the arrays as follows: 4 μg of total RNA was combined with 2 μl gene-specific CDS primer mix (BD Biosciences Clontech). A master mix was prepared at room temperature including 4 μl 5X Reaction Buffer, 2 μl 10X dNTP Mix (for dATP label), 5 μl [α-32P]dATP (10uCi/ul), and 1 μl 100mM DTT. Two microliters of MMLV Reverse Transcriptase was added to the master mix, and was combined with the RNA, primer mix.  All incubations were performed according to the manufacturer’s instructions.  Labeled probes were purified using column chromatography (BD Biosciences Clontech).

extract_protocol: Whole blood was collected into a Vacutainer Blood collection tubes and then transferred into PAXgene tubes (PreAnalytiX, Hombrechtikon), according to the manufacturer’s instructions.  Two separate 2.5 ml samples were collected from crewmembers in order to obtain enough RNA for processing for microarrays. Total RNA was isolated from whole blood samples using the PAXgene Blood RNA Kit (PreAnalytiX, Hombrechtikon, CH), according to the manufacturer’s instructions.  Duplicate RNA samples were combined and DNase treated using a DNA-free kit (Ambion).  RNA was quantitated by ultraviolet absorbance, concentrated by ethanol precipitation and re-suspended in deionized water (BD Biosciences Clontech) to yield a 4 μg sample of RNA for each astronaut at L-10 and R+0.  RNA integrity was confirmed using denaturing Formaldehyde-Agarose gel electrophoresis.

treatment_protocol: Consenting astronauts from several shuttle missions provided whole blood samples 10 days prior to shuttle launch (L-10) and several hours after return to earth (R+0).

value: Whole Blood

tag: fold change in epstein barr virus reactivation (post-spaceflight, relative to pre-flight levels)


title: Astronaut E R+0

data_processing: Arrays were analyzed using Atlas Image 2.0 software (Clontech Laboratories, Inc., Palo Alto, CA), according to the manufacturer’s instructions. Arrays were normalized to the following housekeeping genes: ubiquitin C (UBC), liver glyceraldehyde 3-phosphate dehydrogenase (GAPDH), tubulin alpha 1 (TUBA1), and major histocompatability complex class I C (HLAC). After background subtraction for each array, the ratio of the post-flight adjusted intensity values (R+0) to the pre-flight adjusted intensity values (L-10) was calculated. Only genes with at least four data points pre-flight and post-flight were taken into consideration for data analysis.

source_name: Astronaut E 2-3 hours post-landing


title: Astronaut E L-10

source_name: Astronaut E 10 days prior to launch

value: N/A (pre-flight)


title: HF-20341-(1) Hind


title: HF-20337-(1) Hind


title: PBMC expression profile of IPF patient_P41

description: PBMC expression profile of IPF patient

value: 3.005 years


title: Astronaut D R+0

source_name: Astronaut D 2-3 hours post-landing


title: Astronaut F L-10

source_name: Astronaut F 10 days prior to launch


title: PBMC expression profile of IPF patient_P40

description: PBMC expression profile of IPF patient

value: Caucasian

tag: years to outcome

value: 3.057 years


title: Astronaut D L-10

source_name: Astronaut D 10 days prior to launch

value: Male


title: Astronaut F R+0

source_name: Astronaut F 2-3 hours post-landing


title: PBMC expression profile of IPF patient_P39

description: PBMC expression profile of IPF patient

value: 3.079 years


title: HF-20335-(1) Hind

value: melanoma tumor


title: HF-20011-(1) Hind


title: PBMC expression profile of IPF patient_P43

description: PBMC expression profile of IPF patient

value: Female

value: 2.958 years


title: PBMC expression profile of IPF patient_P38

description: PBMC expression profile of IPF patient


title: Astronaut C L-10

source_name: Astronaut C 10 days prior to launch


title: Astronaut B R+0

source_name: Astronaut B 2-3 hours post-landing


title: PBMC expression profile of IPF patient_P36

description: PBMC expression profile of IPF patient

source_name: RNA isolated from PBMC of IPF patient

value: 0.961 years


title: Astronaut B L-10

source_name: Astronaut B 10 days prior to launch


title: Astronaut C R+0

source_name: Astronaut C 2-3 hours post-landing


title: PBMC expression profile of IPF patient_P34

description: PBMC expression profile of IPF patient

value: 0.597 years


title: PBMC expression profile of IPF patient_P35

description: PBMC expression profile of IPF patient

value: non-Caucasian

value: 3.172 years


title: Astronaut A R+0

source_name: Astronaut A 2-3 hours post-landing


title: HF-20013-(1) Hind


title: Astronaut A L-10

source_name: Astronaut A 10 days prior to launch


title: HF-20339-(1) Hind


title: HF-19011-(1) Hind


title: HF-18692-(1) Hind


title: HF-19099-(1) Hind


title: HF-19008-(1) Hind


title: PBMC expression profile of IPF patient_P37

description: PBMC expression profile of IPF patient

value: 0.23 years


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge miRNA rep3

description: Experimental group  at day 14

data_processing:
Expression was calculated using the comparative Ct method (Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3: 1101-8)
Normalization was done using average of 4 MammU6 probes on each plate.
The deltaCt values (Ct_Target − Ct_MammU6) were imported to GeneSpring GX 11.5 platform (Agilent Technologies, CA), converted to log2-based values and used for statistical analyses.
Fold Change worksheet reports each sample/average of 9 normal controls (i.e., D3_NS_1~3, D7_NS_1~3, D14_NS_1~3) ratios.

label: FAM

label_protocol:
Reverse transcription into first strand cDNA was performed using reagents from TaqMan® MicroRNA RT Kit and Megaplex RT Primer Pools (Applied Biosystems, CA).
Quantitative real-time PCR was performed using the TaqMan® Array Rodent MicroRNA Card v2.0 (A and B) with the Universal PCR Master Mix, No AmpErase UNG using 7900 HT Fast Real-Time PCR System (Applied Biosystems).

extract_protocol:
Extrahepatic bile ducts and gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injection and stabilized with RNAlater (QIAGEN, CA).
3 sets of samples were generated for each time point (experimental and control groups), with each set containing 2-6 extrahepatic bileducts.
Total RNA was isolated from extrahepatic bileducts of RRV- or saline-injected mice using miRNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

value: Extrahepatic Bileduct and gallbladder

value: Balb/c

tag: time

value: 14 days

value: Rhesus rotavirus


title: HF-16892 Xba


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge miRNA rep1

description: Experimental group  at day 14

tag: strain


title: HF-18886-(1) Hind


title: Plastic_noFGF2_replicate2, S12_H036

city: Worcester

first: Tanja

last: Dominko

state: MA

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

hyb_protocol: aRNA was hybridized at 50C overnight using the HybBag mixing system with 1x OneArray Hybridization Buffer (Phalanx Biotech), 0.01mg/ml sheared salmon spearm DNA and 0.025mg/ml of labeled target. After hybridization, arrays were washed according to OneArray protocol.

scan_protocol: Raw intensity signals were captured using Molecular Dynamics Axon 4100A scanner, were measured using GenePixPro Software, and were stored in GPR format.

data_processing: R/Bioconductor was used to normalize and filter data. Background corrected data was normalized by adjusting columns to the same median value. Filtering was performed to leave probes with maximum intensity value across samples higher than 100. Intensity values lower than 5 were substituted with 5 to remove negative values. Data was log2 transformed and filtered to leave gene probes with standard deviation above median. Only gene probes belonging to groups 1 and 4 (group assignment by Phalanx Biotech) were selected for further analysis.

source_name: Adult human dermal fibroblasts, plastic, no FGF2

label_protocol: High-quality RNA (RIN>7.0) was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The product ws conjugated with Cy5 NHS ester.

growth_protocol: Adult human dermal fibroblasts (CRL-2352, ATCC) were expanded at ambient oxygen on tissue culture plastic in DMEM/F12 + 10%FBS. At passage 7, they were cultured for seven days at 5% oxygen in DMEM/F12+10%FCIII at four experimental conditions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).

treatment_protocol: The four experimental conditions included growing adult human dermal fibroblasts in indicated conditions on glass; on tissue culture plastic; on glass with addition of 4ng/ml FGF2 (PeproTech); and on tissue culture plastic with addition of 4ng/ml FGF2 (PeproTech). Media was changed every three days.

tag: cell line

value: ATCC CRL-2352

value: adult human dermal fibroblasts

tag: surface

value: plastic


title: PBMC expression profile of IPF patient_P108

description: PBMC expression profile of IPF patient

value: Caucasian

value: Male

value: 1.528 years


title: HF-18882-(1) Hind

value: melanoma tumor


title: NFX1-123 shRNA2 replicate 6

city: Seattle

first: Rachel

last: Katzenellenbogen

state: WA

address: 1900 Ninth Ave

department: Adolescent Medicine

institute: Seattle Children's Research Institute

description:
condition 4
NHK6 sh3NFX1-123

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control was initially analyzed using GenomeStudio.  Box-whisker plots of raw signal intensity values for each sample showed that the distribution of intensities in each sample was similar.  Data were all log2 transformed followed by quantile normalization. Data were filtered based on the detection p-value, and only those probes with a detection p-value less than 0.01 across all samples were carried forward for analysis. Comparative analysis was performed to determine fold-change values between the normalized probe intensities, using the isogenic scramble shRNA control as the baseline.  We required a fold change of greater than or equal to 2 and the gene had to be detected in at least two of the three conditions.  Subsequent analyses were performed using GeneSpring GX11.5.1, and Excel.

source_name: NFX1-123 shRNA2

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

growth_protocol: NHKs were derived from neonatal foreskins and grown in EpiLife medium supplemented with calcium chloride (60 μM), human keratinocyte growth supplement (Life Technologies, Carlsbad, CA), and penicillin-streptomycin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol

treatment_protocol: Cells were grown as above and harvested at 70-80% confluence.

value: neonatal foreskin

value: keratinocytes


title: Plastic_noFGF2_replicate1, S11_H033


title: Plastic_noFGF2_replicate2, S12_H034


title: Plastic_noFGF2_replicate2, S12_H035


title: PBMC expression profile of IPF patient_P99

description: PBMC expression profile of IPF patient

value: 1.775 years


title: NFX1-123 shRNA control replicate 6

description:
condition 2
NHK6 scramble

source_name: NFX1-123 shRNA control


title: HF-18788-(1) Hind


title: HF-18884-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection miRNA rep3

description: Control group at day 14

value: Normal saline


title: HF-18789-(1) Hind


title: NFX1-123 shRNA1 replicate 6

description:
condition 3
NHK6 sh1NFX1-123

source_name: NFX1-123 shRNA1


title: HF-18790-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection miRNA rep1

description: Control group at day 14


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after rhusus rotvirus challenge miRNA rep2

description: Experimental group  at day 14