city: Toronto

hyb_protocol: For array hybridization, 2ug of the labeled DNA material was hybridized per chip for 18 h at 45C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100?g/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Scanned at 0.7 microns/pixel.

data_processing: Data_Normalization_for_Expression_Arrays protocol. Three biological replicates were hybridized for this experiment. The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity given (e.g. 361).  Processed data are obtained using following parameters: median value is 361   Signal Graph generation protocol. The sliding window approach (bandwidth 50) has been used to estimate RNA abundance (signal which is listed in column #2). It was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch.  Processed data are obtained using following parameters: bandwidth is 50

molecule: polyA RNA

source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array5 channel_1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
This protocol was used for staging and collection of Drosophila melanogaster embryos by Dave Miller(Kaufman Lab, IU Bloomington) for transcriptome analysis by the Celniker group.

extract_protocol:
Protocol for extraction of polyA+ RNA starting from staged whole insects.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: Y cn bw sp

tag: developmental stage

value: Embryo 4-6h

tag: genotype


title: 5 STAT6KO control macrophage

status: Public on Nov 18 2010

type: RNA

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

description:
Gene expression data of bone marrow-derived macrophages derived from STAT6KO mouse
17_(Mouse430_2).CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Mouse Genome 430 2.0  Affymetrix microarrays according to Affymetric standardized protocol.

scan_protocol: Microarrays were scanned canned according to Affymetric standardized protocol.

data_processing: The data were generated with GCOS, and cel files were analyzed in GeneSpring 7.3 using GC-RMA.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: STAT6 KO bone marrow-derived macrophage

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

growth_protocol: Bone marrow cells were isolated from the femur, washed twice with PBS and cultured in RPMI+10% FCS supplemented with glutamine, penicillin and streptomycin and 20 ng/ml M-CSF. Fresh media and cytokines were added every other day for 10 days.

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

treatment_protocol: Cell were treated after plating into 6-well cell culture plates with the indicated cytokines (20 ng/ml M-CSF. 20 ng/ml IL-4 and vehicle (DMSO:ethanol) or 1 uM Rosiglitazone.

tag: mouse

tag: strain

tag: genotype/variation

value: STAT6 KO

tag: cell type

value: bone marrow-derived macrophage

tag: activation

value: Control

tag: treatment

tag: time

value: 10 days


first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

label: Biotin

organism: Drosophila melanogaster

source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array5 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array5 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array1 channel_1

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction2_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array2 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array2 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction1_array1 channel_1


title: Mouse pancreatic islets, biological replicate 1

city: Leuven

first: Katleen

last: Lemaire

address: Herestraat 49, bus 901

country: Belgium

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16h at 45C.

scan_protocol: The arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All images were analyzed using GCOS version 1.4 with the MAS5 algorithm

source_name: Mouse pancreatic isltes

label_protocol: Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). Two ug of total RNA was used to prepare biotinylated cRNA with IVT labeling kit (Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.5. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.

extract_protocol: Total RNA from mouse tussues was extracted using Trizol reagent according to the manufacturer's protocol (Invitrogen), followed by a cleanup procedure with Rneasy colmuns (Qiagen). RNA from mouse islets as well as mouse pituitary and adrenal gland was extracted using the absolutely RNA microprep (Stratagene). For MIN6 cells we used the PureLink micro-to-midi RNA kit (INvitrogen)

tag: tissue

value: pancreatic islets

tag: Sex

value: male

tag: age

value: 10-12 weeks old


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array2 channel_1


title: Mouse pancreatic islets, biological replicate 3


title: Mouse pancreatic acini, biological replicate 3

source_name: Mouse pancreatic acini

value: pancreatic acini


title: Mouse placenta, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252127

source_name: Mouse placenta

value: placenta


title: Mouse ovary, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252130

source_name: Mouse ovary

value: ovary


title: Mouse placenta, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252125


title: Mouse ovary, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252128


title: Mouse pancreatic acini, biological replicate 1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction2_array3 channel_1


title: Mouse pancreatic acini, biological replicate 2


title: Mouse pancreatic islets, biological replicate 2


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction1_array3 channel_1


title: Mouse eye, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252120

source_name: Mouse eye

value: eye


title: Mouse eye, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252119


title: Mouse small intestine, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252116

source_name: Mouse small intestine

value: small intestine


title: Mouse placenta, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252126


title: Mouse small intestine, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252118


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array3 channel_1


title: Mouse heart, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252113

source_name: Mouse heart

value: heart


title: Mouse eye, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252121


title: Mouse heart, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252115


title: Mouse small intestine, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252117


title: Mouse ovary, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252129


title: Mouse testis, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252112

source_name: Mouse testis

value: testis


title: Mouse heart, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252114


title: Mouse thymus, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252108

source_name: Mouse thymus

value: thymus


title: Mouse salivary gland, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252103

source_name: Mouse salivary gland

value: salivary gland


title: Mouse salivary gland, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252102


title: Mouse thymus, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252109


title: Mouse seminal vesicle, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252106

source_name: Mouse seminal vesicle

value: seminal vesicle


title: Mouse seminal vesicle, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252105


title: Mouse testis, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252110


title: Mouse pituitary gland, biological replicate 4

description:
CEL file uploaded in GSE9954
GSM252099

source_name: Mouse pituitary gland

value: pituitary gland


title: Mouse seminal vesicle, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252104


title: Mouse pituitary gland, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252096


title: Mouse pituitary gland, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252097


title: Mouse adipose tissue, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252094

source_name: Mouse adipose tissue

value: adipose tissue


title: Mouse pituitary gland, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252098


title: Mouse testis, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252111


title: Mouse adipose tissue, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252095


title: GPR54-suppressed Ishikawa, biological rep2

city: Kyoto

first: Tsukasa

last: Baba

address: 54 Shogoin Kawahara-cho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from Ishikawa cells that were introduced with GPR54 siRNA.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data were RMA normalized.

organism: Homo sapiens

source_name: Ishikawa cells introduced with GPR54 siRNA

label_protocol: Affymetrix one cycle IVT.

growth_protocol: Cells were grown in RPMI 1640 media with 10% FBS in a humidifed incubator maintained at 37 degrees Celsius with 5% CO2 until ~70% confluency.

extract_protocol: Qiagen Rneasy.

treatment_protocol: At ~70% confluence, cells were transfected with negative control siRNA or GPR54-specific siRNA for 48 hrs, and then treated with either 10 µM metastin-10 or control peptide for the following 24 hrs.

tag: cell line

value: Ishikawa

value: endometrial cancer cells

tag: sirna transfection

value: GPR54-specific siRNA

tag: peptide treatment

value: control peptide


title: GPR54-suppressed Ishikawa treated with metastin-10, biological rep2

description: Gene expression data from Ishikawa cells that were introduced with GPR54 siRNA and treated with metastin-10.

source_name: Ishikawa cells introduced with GPR54 siRNA and treated with metastin-10


title: Ishikawa non-treated, biological rep2

description: Gene expression data from Ishikawa cells that were not treated with metastin-10 and not introduced with GPR54 siRNA.

source_name: Ishikawa cells not introduced with GPR54 siRNA and not treated with metastin-10

value: negative control siRNA


title: GPR54-suppressed Ishikawa, biological rep1


title: Mouse bone marrow, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252090

source_name: Mouse bone marrow

value: bone marrow

value: male

value: 10-12 weeks old


title: Ishikawa non-treated, biological rep1


title: GPR54-suppressed Ishikawa treated with metastin-10, biological rep1


title: Mouse adipose tissue, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252093


title: Mouse adrenal gland, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252088

source_name: Mouse adrenal gland

value: adrenal gland


title: GPR54-suppressed Ishikawa, biological rep3


title: Mouse bone marrow, biological replicate 4

description:
CEL file uploaded in GSE9954
GSM252092


title: Ishikawa treated with metastin-10, biological rep1

description: Gene expression data from Ishikawa cells treated with metastin-10.

source_name: Ishikawa cells treated with metastin-10


title: GPR54-suppressed Ishikawa treated with metastin-10, biological rep3


title: Ishikawa treated with metastin-10, biological rep3


title: Mouse bone marrow, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252089


title: Ishikawa non-treated, biological rep3


title: Mouse salivary gland, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252101


title: Mouse adrenal gland, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252087


title: Ishikawa treated with metastin-10, biological rep2


title: Mouse adrenal gland, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252086


title: Mouse kidney, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252084

source_name: Mouse kidney

value: kidney


title: Mouse kidney, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252085


title: Mouse kidney, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252083


title: Mouse bone marrow, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252091


title: Mouse lung, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252080

source_name: Mouse lung

value: lung


title: Mouse lung, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252082


title: Mouse lung, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252081


title: Mouse brain, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252078

source_name: Mouse brain

value: brain


title: Mouse liver, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252076

source_name: Mouse liver

value: liver


title: 7 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 25.txt

hyb_protocol: Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

data_processing: The data were generated with ABI1700 and txt files were further analyzed in GeneSpring 7.3.

label: DIG

source_name: PPARg fl/-LysCre bone marrow-derived macrophage treated with IL-4

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

growth_protocol: Bone marrow cells were isolated from the femur, washed twice with PBS and cultured in RPMI+10% FCS supplemented with glutamine, penicillin and streptomycin and 20 ng/ml M-CSF+20 ng/ml IL-4 for macrophage or 20 ng/ml GM-CSF+20 ng/ml IL-4 for iDC differentiation. Fresh media and cytokines were added every other day for 9 days.

treatment_protocol: Cell were treated after plating into 6-well cell culture plates with the indicated cytokines and vehicle (DMSO:ethanol) or 1 uM Rosiglitazone.

value: PPARg fl/-LysCre

value: bone marrow-derived alternatively activated macrophage

value: Control

value: 9 days


title: Mouse liver, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252075


title: Mouse brain, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252077


title: 8 PPARg fl/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg fl/-LysCre mouse
Data Sample 31.txt

source_name: PPARg fl/-LysCre bone marrow-derived iDC

value: bone marrow-derived immature dendritic cell


title: 8 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 30.txt

source_name: PPARg fl/-LysCre bone marrow-derived macrophage treated with IL-4+RSG

value: Rosiglitazone


title: Mouse muscle, biological replicate 4

description:
CEL file uploaded in GSE9954
GSM252073

source_name: Mouse muscle

value: muscle


title: Mouse brain, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252079


title: Mouse liver, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252074


title: 7 PPARg fl/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg fl/-LysCre mouse
Data Sample 27.txt


title: 7 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 26.txt


title: Mouse muscle, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252070


title: Mouse muscle, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252071


title: 8 PPARg fl/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg fl/-LysCre mouse
Data Sample 32.txt

source_name: PPARg fl/-LysCre bone marrow-derived iDC treated with RSG


title: Mouse muscle, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252072


title: Mouse spleen, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252069

source_name: Mouse spleen

value: spleen


title: 8 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 29.txt


title: 6 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 21.txt


title: 6 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 22.txt


title: 6 PPARg fl/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg fl/-LysCre mouse
Data Sample 24.txt


title: 5 PPARg fl/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg fl/-LysCre mouse
Data Sample 20.txt


title: 7 PPARg fl/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg fl/-LysCre mouse
Data Sample 28.txt


title: Mouse spleen, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252068


title: 6 PPARg fl/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg fl/-LysCre mouse
Data Sample 23.txt


title: 5 PPARg fl/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg fl/-LysCre mouse
Data Sample 19.txt


title: 5 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 18.txt


title: 5 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
Data Sample 17.txt


title: 4 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 13.txt

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with IL-4

value: PPARg +/-LysCre


title: Mouse spleen, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252067


title: 3 PPARg +/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg +/-LysCre mouse
Data Sample 12.txt

source_name: PPARg +/-LysCre bone marrow-derived iDC treated with RSG


title: 3 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 9.txt


title: Mouse diaphragm, biological replicate 2

description:
CEL file uploaded in GSE9954
GSM252065

source_name: Mouse diaphragm

value: diaphragm


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array4 channel_1

value: Y cn bw sp

value: Embryo 4-6h


title: 4 PPARg +/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg +/-LysCre mouse
Data Sample 16.txt


title: 3 PPARg +/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg +/-LysCre mouse
Data Sample 11.txt

source_name: PPARg +/-LysCre bone marrow-derived iDC


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array4 channel_1


title: 4 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 14.txt

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with IL-4+RSG


title: Mouse diaphragm, biological replicate 3

description:
CEL file uploaded in GSE9954
GSM252066

value: male

value: 10-12 weeks old


title: Mouse diaphragm, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252064


title: 2 PPARg +/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg +/-LysCre mouse
Data Sample 8.txt


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array4 channel_1


title: 2 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 6.txt


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array4 channel_1


title: 1 PPARg +/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg +/-LysCre mouse
Data Sample 3.txt


title: 2 PPARg +/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg +/-LysCre mouse
Data Sample 7.txt


title: 1 PPARg +/-LysCre iDC+RSG

description:
Gene expression data of bone marrow-derived RSG-treated iDC derived from PPARg +/-LysCre mouse
Data Sample 4.txt


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction2_array4 channel_1


title: MCF10A Scramble

city: Turku

first: Karoliina

last: Vuoriluoto

address: Itäinen pitkäkatu 4C

country: Finland

institute: VTT Medical Biotechnology

description: siScr replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: MCF10A breast cancer cells

label_protocol: For the Illumina gene expression analysis, 300 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: MCF10A cells were grown in 1:1 DMEM:Ham's F-12 supplemented with 5 % horse serum, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, and 100 ng/ml choleratoxin.

extract_protocol: Three days after vimentin siRNA transfection, RNA was extracted with Trizol reagent. To ensure sufficient purity of the cellular RNA, the samples were further processed with RNeasy Mini kit (QIAGEN). The purity of the cellular RNA was controlled and the material was considered to be sufficiently pure when A260/A280 > 1.8.

treatment_protocol: An siRNA targeting vimentin (siGENOME SMARTpoolTM M-003551-01-005: Dharmacon, Inc.) or a scrambled control siRNA (AllStars Negative Control siRNA; Qiagen) was transfected to cells using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions.


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction1_array4 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array1 channel_1


title: 1 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 2.txt


title: 4 PPARg +/-LysCre iDC

description:
Gene expression data of bone marrow-derived iDC derived from PPARg +/-LysCre mouse
Data Sample 15.txt


title: 3 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 10.txt


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction2_array5 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array5 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction1_array5 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array3 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array3 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array3 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction2_array2 channel_1


title: MCF10A Scramble2

description: siScr replicate 2


title: 1 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 1.txt

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with IL-4


title: Mouse thymus, biological replicate 1

description:
CEL file uploaded in GSE9954
GSM252107

source_name: Mouse thymus

value: thymus


title: Mouse pituitary gland, biological replicate 5

description:
CEL file uploaded in GSE9954
GSM252100

source_name: Mouse pituitary gland

value: pituitary gland


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array2 channel_1


title: 2 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
Data Sample 5.txt


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction1_array2 channel_1


title: MCF10A KD2

description: siVim replicate 2

source_name: MCF10A breast cancer cells


title: MCF10A KD

description: siVim replicate 1


title: GDF15 treatment 2

city: Beijing

first: Wei

last: Yang

address: 6 Rong Jing Dong Jie

country: China

institute: Chinese Academy of Medical Sciences

hyb_protocol: standard Capitalbio Methods, http://www.capitalbio.com/marticle/Manual400010-Human_22k_oligo_array-070620.pdf

scan_protocol: CapitalBio manual. Using LuxScan 10KA two-channel scanner.

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy.

source_name: Huh7.5.1 cells/PBS

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Huh7.5.1 cells were grown in Dulbecco's Modified Eagle Medium (Invitrogen, Carlsbad, CA) supplemented with 1% penicillin and streptomycin (Gibco), 1% NEAA (Gibco), and 10% fetal bovine serum (Gibco) in a 37°C 5% CO2 atmosphere.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Recombinant human GDF15 was obtained from R&D Systems (Minneapolis, MN).For the GDF15 treatment, the recombinant protein was added to Huh7.5.1 cells 24 hours prior to microarray analysis.

value: PBS

source_name: Huh7.5.1 cells/GDF


title: GDF15 treatment 1


title: Sample T61

status: Public on Nov 17 2010

city: Barcelona

first: Sophie

last: Domingues

address: Pg Vall d’Hebron 119-129

department: Department of Neurology

country: Spain

institute: Institut de Recerca Hospital Vall d’Hebron

description: Gene expression data from human blood samples

hyb_protocol: cRNA was hybridizated in Human Genome U133 Plus 2.0 Affymetrix microarrays.

scan_protocol: Microarrays were scanned in Affymetrix Genechip Scanner 3000 7G.

data_processing: Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized. Log2 RMA signal estimates were obtained using R-2.8 and Bioconductor 2.3 Packages

source_name: Human blood sample

label_protocol:
Samples were amplified using Two Cycle cDNA Synthesis Affymetrix kit.
Samples were chemically fragmented and biotinylated using the IVT Labelling Kit (Affymetrix)

growth_protocol: Blood samples from 12 sujects were obtained.

extract_protocol: Total RNA was extracted from fresh peripheral blood mononuclear cells using a RiboPureTM -Blood kit from Ambion (Ambion, Woodward st. Austin, USA).

treatment_protocol: EDTA tubes were centrifuged at 3500rpm for 15 min to obtain the white blood cell fraction and the samples were stored at -80ºC until RNA isolation.

tag: sample id

value: blood

tag: gender

value: Male

tag: rs7956957 genotype

value: GG


title: Hec50_mock_rep_3

city: Aurora

first: Erin

middle: N.

last: Howe

state: CO

address: UCD AMC, Mail Stop 8104 PO Box 6511

department: Pathology

institute: University of Colorado at Denver, Anschutz Medical Campus

description: Endometrial cancer cell line (Hec50) mock transfected, or transfected with scrambled negative control or miR-200c

hyb_protocol: 20 ug biotin-labeled cDNA was fragmented and hybridized.

scan_protocol: Microarray analysis was performed using Affymetrix gene chips (HuFL-U133 plus2) and scanned using Affymetrix Genechip Scanner 3000

data_processing: All entities: Data normalized to chip. 1_5 fold 200c vs mock and neg: Data was analyzed using Genespring GX 9.0 (Agilent). Data was filtered using a 1.5 fold change cutoff and a p value of 0.05 (ANOVA, with Benjamini Hochberg FDR multiple testing correction).

source_name: mock

label_protocol: Labeled complementary RNA was made using the GeneChip_IVT labeling kit (Affymetrix, Inc., Santa Clara, CA)

growth_protocol: Cells were grown in DMEM supplemented with L-glutamine and 10% FBS in an incubator at 37 degrees and 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's directions. RNA integrity was confirmed using an Agilent Bioanalyzer (Agilent, Palo Alto, CA)

treatment_protocol: Cells were treated with 60 nM miR-200c mimic or scrambled negative control (Applied Biosystems) for 48 hrs prior to extraction

value: endometrial cancer


title: Hec50_neg_rep_3

source_name: scrambled negative control


title: breast tumor, stage I, explant, Patient 8, rep 3

city: Pittsburgh

first: Jean

middle: Johanna

last: Latimer

state: Pennsylvania

address: 5150 Centre Avenue

department: Obstetrics and Gynecology

institute: University of Pittsburgh

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome HGU133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were analyzed with GeneSpring GX 10.0.1 using the PLIER algorithm and default analysis settings.

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents assay (Affymetrix Corp, Santa Clara, CA) starting with 1 ug of purified total RNA.

growth_protocol: Samples were cultured in MWRI medium and expanded until 10-20 ug of total RNA were obtainable.

extract_protocol: Total RNA was extracted using the RNAEasy kit from Qiagen according to manufacturer's instructions.

tag: patient

tag: replicate

value: breast tumor explant

tag: breast tumor stage

value: stage I


title: Sample T46

value: Female


title: Sample T35

value: CG


title: breast tumor, stage I, explant, Patient 8, rep 1


title: breast tumor, stage I, explant, Patient 4, rep 1


title: breast reduction mammoplasty tissue explant, Patient 5, rep 1


title: Hec50_200c_rep_1

source_name: miR-200c mimic


title: Sample T41

value: CC


title: Sample T17


title: Hec50_200c_rep_2


title: Sample T48


title: breast reduction mammoplasty tissue explant, Patient 1, rep 1


title: breast reduction mammoplasty tissue explant, Patient 6, rep 2


title: Sample R179


title: Sample R199


title: breast tumor, stage I, explant, Patient 33, rep 1


title: Hec50_mock_rep_2


title: breast reduction mammoplasty tissue explant, Patient 6, rep 3


title: Hec50_200c_rep_3


title: Sample T12


title: Sample T29


title: Hec50_neg_rep_1


title: Sample 14054


title: breast reduction mammoplasty tissue explant, Patient 6, rep 1


title: Sample 14140


title: Hec50_neg_rep_2


title: breast tumor, stage I, explant, Patient 8, rep 2


title: L428_2

city: Berlin

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

country: Germany

institute: Max-Delbrueck-Centre for Molecular Medicine

hyb_protocol: Hybridization was done according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning was done according to the manufacturer's recommendations (Affymetrix). Scanner Model was GeneChip® Scanner 3000 7G, GeneChip® Command Console® 2.0.1 was used as software.

data_processing: Raw data were background corrected with RMA and normalized using quantile normalization. All processeing was done in R/Bioconductor.

source_name: lymphoid cell line

label_protocol: Labeling was done according to the manufacturer's recommendations (Affymetrix).

extract_protocol: Total RNA was extracted using RNeasy Mini-Kit from QIAGEN according to the manufacturer's recommendations.

tag: malignancy (disease state)

value: classical Hodgkin Lymphoma


title: Namalwa_2

value: Burkitt lymphoma


title: SU-DHL-4

value: B non Hodgkin lymphoma


title: HDLM2_2


title: UNI-2

city: Granada

first: Angel

last: Concha

address: 2 Fuerzas Armadas

institute: Servicio Andaluz de Salud

hyb_protocol: Amersham Biosciences CodeLink protocol (Ramakrishnan et al, 2002)

scan_protocol: Axon GenePix 4000B scanner (Axon Instruments, Foster City, CA) with 10 uM resolution. CodeLink™ Expression Analysis software v 5.0

data_processing: Normalization: 1) Background correction: saddle-point approximation (offset = 50); 2) quantile normalization method

source_name: adult tissue cells

label_protocol: linear amplification method using Ambion’s MessageAmp™ II‐Biotin Enhanced Single Round aRNA Amplification Kit

growth_protocol: MES3 mESC line was derived by whole blastocyst culture from the inner cell mass of a C57BLxCBA mouse embryo. Culture cells were maintained on Mitomicin C inactivated mouse embryonic fibroblasts (MEF) in knock-out DMEM (Gibco, Invitrogen) supplemented with 10% FBS (Gibco, Invitrogen), 2mM non-essential amino acids, 2 mM L-glutamine, 50 mg/mL Penn-Strep, 10 nM b-mercaptoethanol and 1000 units/mL LIF (ESGRO, Chemicon). EBs were obtained by excising clusters of undifferentiated stem cells from growing colonies and transferring them to low-adhesion culture plates, where they were maintained in the same medium as the mESCs but without b-mercaptoethanol and LIF.

extract_protocol: Total RNA was extracted from ESC cultures by the Trizol® method (Invitrogen). All samples were treated with an RNase-free DNase set (Qiagen, Valencia, CA)

treatment_protocol: Mouse stem cells were differentiated spontaneously in cell culture to form Ebs

tag: developmental stage

value: adult

tag: cell type

value: adult tissue cells


title: L540Cy


title: 7 Days-1-1

source_name: embryoid bodies

value: 7 days

value: embryoid bodies


title: Hec50_mock_rep_1


title: KM-H2_2


title: 7 Days-2-2


title: UNI-1


title: 3 Days-1-1

value: 3 days


title: L1236_2


title: L428_1


title: 7 Days-2-1


title: Stem Cell-1-2

source_name: stem cells

value: embryo

value: stem cells


title: L540


title: Reh_2

value: B acute lymphoblastic leukemia


title: L1236_1


title: 7 Days-1-2


title: KM-H2_1


title: Reh_1


title: Namalwa_1


title: 3 Days-1-2


title: HDLM2_1


title: 3 Days-2-1


title: Stem Cell-1-1


title: 3 Days-2-2


title: constitutively active Stat3, replicate 2

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: For the hybridization step, the samples are applied to the arrays and assembled into the BeadChip Hyb Chamber. The BeadChip is hybridized at 58°C overnight, and then washed the following day.

scan_protocol: Scanning was performed using the Illumina Beadarray scanner.

data_processing: Raw expression data were obtained with BeadStudio, version 3.1.7. Normalization was performed with the lumi package of Bioconductor 2.2 and default parameters.

source_name: Mouse embryonic fibroblasts, Stat3

label_protocol: RNA amplification and labelling were performed using the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were cultured in DMEM supplemented with FCS 10%, 2 mM Glutamax, 100 U/ml Pennicillin, 100 ug/ml Streptomycin and maintained at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) followed by purification on a Qiagen RNAeasy midi column.

treatment_protocol: None.

tag: strain

value: BALB/c

value: mouse embryonic fibroblasts (MEFs)

value: constitutively active


title: constitutively active Stat3, replicate 3


title: constitutively active Stat3, replicate 1


title: MIAML167T_primary human: blood or bone marrow, FACS sort-purified AML blasts

type: genomic

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturers’ recommendations.

scan_protocol: According to Affymetrix protocol

data_processing:
Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in text format. Call rates for the entire group of samples included in this report were between 93.57% and 99.45% with mean and median call rates of 98.35% and 98.58%, respectively; none of the DNA samples gave out-of-bounds results. Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.
primary data description: dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.

molecule: genomic DNA

label_protocol: According to Affymetrix protocol

extract_protocol:
Liquid nitrogen-cryopreserved (liquid phase) peripheral blood or bone marrow mononuclear cells derived from AML patients were washed and recovered by centrifugation and then treated with anti-human CD3 (Miltenyi Biotec #130-050-101), anti-human CD14 microbeads (if blasts were negative for CD14 expression; Miltenyi Biotec #130-050-201), anti-human CD19 (if blasts were negative for CD19 expression; Miltenyi Biotec #130-050-301) and anti-human CD235a (Miltenyi Biotec #130-050-501) per manufacturer’s recommendations.  Cell suspensions were run through Miltenyi MACS LS separation columns (#130-042-401) in order to negatively enrich for AML blasts.  All blast preps were analyzed by cytospins for purity. This schema always resulted in greater than 90% blast purity.  AML blast DNA used for SNP 6.0 profiling and RNA used for expression analysis (Q-PCR) was extracted from samples that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter(20).  CD33 and CD13 were then used in order to further discriminate blasts versus erythroid lineage and mature myeloid lineage cells.
Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

tag: disease state

value: tumor


title: wild-type, replicate 3

source_name: Mouse embryonic fibroblasts, wild-type

value: wild-type


title: MIAML159N_primary human: buccal

source_name: buccal swabs

value: normal


title: MIAML160N_primary human: buccal


title: MIAML167N_BU_primary human: buccal


title: MIAML164N_primary human: buccal


title: MIAML163T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML149T_021709_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML145T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML153T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML160T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML150N_primary human: buccal


title: MIAML153N_primary human: buccal


title: MIAML157T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: wild-type, replicate 2


title: MIAML157N_primary human: buccal


title: MIAML159T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML149N_primary human: buccal


title: MIAML150T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML147N_primary human: buccal


title: MIAML145N_primary human: buccal


title: MIAML151T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: 7 Days-3-1

scan_protocol: Axon GenePix 4000B scanner (Axon Instruments, Foster City, CA) with 10 M resolution. CodeLink™ Expression Analysis software v 5.0


title: 7 Days-3-2


title: MIAML143T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML147T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML158N_primary human: buccal


title: 3 Days-3-2


title: MIAML151N_primary human: buccal


title: 3 Days-3-1


title: Stem Cell-2-1


title: wild-type, replicate 1


title: MIAML164T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML140T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML143N_primary human: buccal


title: MIAML140N_primary human: buccal


title: Radiation with FTY, rep2

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from lung tissue of animal with FTY under radiation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Probeset present calls were determined by Affymetrix GCOS software; the chip data were normalized by rank invariant set method (Li and Wong, 2001) using dChip software.

source_name: Lung, radiation and FTY

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: Standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity).

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

treatment_protocol: Single thoracic radiation (25Gy) with intraperitoneal injection, 2X/wk, 0.1mg/kg FTY.

tag: genotype

value: wildtype

value: female

tag: weight

value: 14-17 weeks

tag: tissue

value: lung

tag: treatment

value: radiation and FTY720


title: Radiation with FTY, rep3

tag: age


title: MIAML136T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML130T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML131T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML132N_primary human: buccal


title: MIAML132T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML138N_primary human: buccal


title: MIAML130N_primary human: buccal


title: MIAML127T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML131N_primary human: buccal


title: MIAML124T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML129N_primary human: buccal


title: Radiation with SEW, rep3

description: Gene expression data from lung tissue of animal with SEW under radiation

source_name: Lung, radiation and SEW

treatment_protocol: Single thoracic radiation (25Gy) with intraperitoneal injection, 2X/wk, 0.1mg/kg SEW.

value: radiation and SEW-2871


title: Radiation with FTY, rep1


title: MIAML128N_primary human: buccal


title: Radiation with SEW, rep2


title: MIAML128T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML129T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML137N_primary human: buccal


title: Stem Cell-2-2


title: MIAML158T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML126N_primary human: buccal


title: Radiation with SEW, rep1


title: MIAML127N_primary human: buccal


title: Radiation with fTyS, rep3

description: Gene expression data from lung tissue of animal with fTyS under radiation

source_name: Lung, radiation and fTyS

treatment_protocol: Single thoracic radiation (25Gy) with intraperitoneal injection, 2X/wk, 0.1mg/kg fTyS.

value: radiation and (S)-FTY-phosphonate


title: MIAML124N_primary human: buccal


title: Radiation with fTyS, rep1


title: Radiation with fTyS, rep2


title: Radiation alone, rep1

description: Gene expression data from lung tissue of animal under radiation

source_name: Lung, radiation

treatment_protocol: Single thoracic radiation (25Gy).

value: radiation


title: Radiation alone, rep3


title: Radiation alone, rep2


title: MIAML121N_primary human: buccal


title: MIAML122T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Drug control FTY, rep2

description: Gene expression data from lung tissue of drug control animal with FTY

source_name: Lung, FTY

treatment_protocol: Intraperitoneal injection, 2X/wk, 0.1mg/kg FTY.


title: Drug control FTY, rep3


title: MIAML120T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Drug control FTY, rep1


title: MIAML126T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML138T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Drug control SEW, rep3

description: Gene expression data from lung tissue of drug control animal with SEW.

source_name: Lung, SEW

treatment_protocol: Intraperitoneal injection, 2X/wk, 0.1mg/kg SEW.


title: MIAML121T_021709_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML123T_021709_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML117T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML110N_primary human: buccal


title: Drug control SEW, rep2


title: MIAML109N_032009_primary human: buccal


title: MIAML113N_primary human: buccal


title: MIAML110T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML115N_primary human: buccal


title: MIAML163N_primary human: buccal


title: MIAML137T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML123N_031910_primary human: buccal


title: MIAML120N_060908_primary human: buccal


title: MIAML107T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML115T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML109T_072208_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML122N_primary human: buccal


title: Drug control fTyS, rep3

description: Gene expression data from lung tissue of drug control animal with fTyS.

source_name: Lung, fTyS

treatment_protocol: Intraperitoneal injection, 2X/wk, 0.1mg/kg (S)-FTY-phosphonate.

value: (S)-FTY-phosphonate


title: MIAML106T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML103T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML107N_primary human: buccal


title: Drug control fTyS, rep2


title: Drug control fTyS, rep1


title: MIAML101T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML113T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML105T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Control, rep2

description: Gene expression data from lung tissue of control animal.

source_name: Lung, control

treatment_protocol: PBS.

value: PBS


title: Control, rep4


title: Drug control SEW, rep1


title: MIAML103N_primary human: buccal


title: Control, rep3


title: MIAML105N_primary human: buccal


title: MIAML117N_primary human: buccal


title: MIAML106N_primary human: buccal


title: MIAML101N_primary human: buccal


title: MIAML099T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: D2_P90_liver_rep2

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues and each time points separately.

label_protocol: The synthesis of cRNA was performed using the GeneChip® One-Cycle cDNA Synthesis according to the manufacturer' protocol (Affymetrix, Santa Clara, CA, USA). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: Inbred mice of the strains C57BL/6J and DBA/2J were obtained directly from The Jackson Laboratory, whereas strain 129S2 animals were purchased from Charles River, France. Tissue samples used for the experiments described in this report are from purchased animals (P90 stage) or from the F1 generation (E14.5, P1 and P7 stages). E14.5 and P1 individuals were sexed molecularly.

extract_protocol: Whole brain and liver from E14.5, P1, P7 and P90 males were dissected and immediately frozen on dry ice. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, NM, USA), cleaned on RNeasy columns (Qiagen) according to the manufacturers' protocols.

value: male

value: 11-14 weeks of age

value: liver


title: B6_P90_liver_rep3


title: MIAML099N_primary human: buccal


title: D2_P90_liver_rep3


title: Control, rep1


title: MIAML098N_primary human: buccal


title: MIAML097T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML096T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML092N_primary human: buccal


title: MIAML095N_primary human: buccal


title: B6_P90_liver_rep1


title: D2_P90_liver_rep1


title: MIAML097N_primary human: buccal


title: MIAML093T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML095T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML092T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: 129_P90_liver_rep3


title: 129_P90_liver_rep2


title: MIAML091N_primary human: buccal


title: 129_P90_liver_rep1


title: B6_P90_liver_rep2


title: MIAML091T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML090N_primary human: buccal


title: MIAML088T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML090T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML085T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML088N_primary human: buccal


title: MIAML086T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML086N_primary human: buccal


title: MIAML085N_primary human: buccal


title: MIAML098T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML087T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: D2_P90_brain_rep1

value: brain


title: B6_P90_brain_rep3


title: MIAML080T_primary human: blood or bone marrow, FACS sort-purified AML blasts

value: tumor


title: D2_P90_brain_rep3


title: 5ug/ml IL-1F9, 24h, replicate 2

first: Andrew

last: Johnston

state: Michigan

address: 1301 East Catherine Street

department: Dermatology

description: 5ug/ml rhIL-1F9, 24h

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Normal human keratinocytes

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN exon module, encore end-labeling module).

growth_protocol: Reconstituted human epidermal cultures were obtained from MatTek (EPI-200, MatTek Inc,  Ashland, MA). After overnight equilibration in 5ml normal maintenance medium (MatTek), medium was refreshed and supplemented with recombinant human cytokines as indicated.

extract_protocol: Cultures were removed from their support filters and dissolved in RLT buffer (Qiagen), homogenized using glass beads (Biospec) and total RNA was isolated (RNeasy Mini kit, Qiagen).

treatment_protocol: 24hr with human recombinant cytokine as indicated

value: Reconstituted human epidermis

tag: treatment group

value: 5ug/ml IL-1F9, 24h


title: B6_P90_brain_rep2


title: B6_P90_brain_rep1


title: D2_P90_brain_rep2


title: 5ug/ml IL-1F9, 24h, replicate 1

description: 5ug/ml rhIL-1F9, 24h


title: MIAML079N_primary human: buccal

value: normal


title: 129_P90_brain_rep3


title: MIAML077T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML081T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML078N_primary human: buccal


title: MIAML079T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: 5ug/ml IL-1F8, 24h, replicate 1

description: 5ug/ml IL-1F8, 24h

value: 5ug/ml IL-1F8, 24h


title: MIAML076N_primary human: buccal


title: 129_P90_brain_rep2


title: MIAML078T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML074N_primary human: buccal


title: 5ug/ml IL-1F8, 24h, replicate 3

description: 5ug/ml IL-1F8, 24h


title: MIAML071T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: D2_P7_liver_rep3

value: 7 days post-natal


title: 5ug/ml IL-1F6, 24h, replicate 2

description: 5ug/ml rhIL-1F6, 24h

value: 5ug/ml IL-1F6, 24h


title: 5ug/ml IL-1F6, 24h, replicate 3

description: 5ug/ml rhIL-1F6, 24h


title: MIAML074T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: D2_P7_liver_rep2


title: 5ug/ml IL-1F6, 24h, replicate 1

description: 5ug/ml rhIL-1F6, 24h


title: D2_P7_liver_rep1


title: MIAML093N_primary human: buccal


title: 5ug/ml IL-1F5, 24h, replicate 3

description: 5ug/ml rhIL-1F5, 24h

value: 5ug/ml IL-1F5, 24h


title: B6_P7_liver_rep3


title: MIAML068N_primary human: buccal


title: B6_P7_liver_rep2


title: 5ug/ml IL-1F5, 24h, replicate 2

description: 5ug/ml rhIL-1F5, 24h


title: 129_P90_brain_rep1


title: MIAML067T_031910_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML071N_BU_031910_primary human: buccal


title: B6_P7_liver_rep1


title: MIAML068T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML064T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML087N_primary human: buccal


title: MIAML081N_primary human: buccal


title: MIAML067N_primary human: buccal


title: MIAML062T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML063T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: 5ug/ml IL-1F8, 24h, replicate 2

description: 5ug/ml IL-1F8, 24h


title: MIAML063N_primary human: buccal


title: 129_P7_liver_rep2


title: MIAML077N_primary human: buccal


title: MIAML062N_primary human: buccal


title: 5ug/ml IL-1F5, 24h, replicate 1

description: 5ug/ml rhIL-1F5, 24h


title: MIAML080N_primary human: buccal


title: 129_P7_liver_rep3


title: MIAML064N_primary human: buccal


title: 10ng/ml IL-1a treated 24h replicate 3

description: 10ng/ml rhIL-1a 24h

value: 10ng/ml IL-1a treated 24h


title: MIAML076T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML060N_primary human: buccal


title: D2_P7_brain_rep2


title: 10ng/ml IL-1a treated 24h replicate 1

description: 10ng/ml rhIL-1a 24h


title: D2_P7_brain_rep1


title: 10ng/ml IL-1a treated 24h replicate 2

description: 10ng/ml rhIL-1a 24h


title: 129_P7_liver_rep1


title: thymus rep1

first: Lieven

last: Thorrez

address: Kasteelpark Arenberg 10

institute: Katholieke Universiteit Leuven

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data were analyzed with RMA sketch using the standard settings for Gene 1.0 ST arrays of Expression Console in the AGCC software (affymetrix).

source_name: thymus

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol Reagent according to the manufacturer's protocol (Gibco BRL, Carlsbad, CA), followed by a cleanup procedure with RNeasy columns (Qiagen, Cologne, Germany).The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

value: thymus


title: B6_P7_brain_rep2


title: D2_P7_brain_rep3


title: B6_P7_brain_rep3


title: Untreated, 24h replicate 1

description: Untreated culture

value: Untreated, 24h


title: thymus rep2


title: thymus rep3


title: Untreated, 24h replicate 2

description: Untreated culture


title: testis rep3

source_name: testis

value: testis


title: B6_P7_brain_rep1


title: 129_P7_brain_rep3


title: 129_P7_brain_rep2


title: MIAML060T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: testis rep2


title: 129_P7_brain_rep1


title: small intestine rep1

source_name: small intestine

value: small intestine


title: small intestine rep3


title: D2_P1_liver_rep2

value: male

value: 1 day post-natal


title: small intestine rep2


title: D2_P1_liver_rep3

value: liver


title: B6_P1_liver_rep3


title: placenta rep2

source_name: placenta

value: placenta


title: tamoxifen replicate 4

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: replicate 4

data_processing:
The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.
Detection p-value not provided

source_name: MCF-7 cell line treated with  tamoxifen

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

growth_protocol: MCF-7 human cell lines were grown as described previously (Neve et al. 2006, Cancer Cell 10:515–527).

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. A DNase I digestion was included. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Estrogen was added at a final concentration of 100 nM and tamoxifen at 1 microM

value: tamoxifen

tag: cell line


title: placenta rep3


title: MIAML057N_primary human: buccal


title: pituitary rep3

source_name: pituitary

value: pituitary


title: placenta rep1


title: estrogen and tamoxifen replicate 4

description: replicate 4

source_name: MCF-7 cell line treated with estrogen and tamoxifen

value: estrogen and tamoxifen


title: MIAML056N_primary human: buccal

source_name: buccal swabs

value: normal


title: B6_P1_liver_rep2

tag: gender


title: testis rep1


title: estrogen replicate 4

description: replicate 4

source_name: MCF-7 cell line treated with  estrogen

value: estrogen


title: D2_P1_liver_rep1


title: MIAML053T_primary human: blood or bone marrow, FACS sort-purified AML blasts

value: tumor


title: MIAML059T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: pituitary rep2


title: MIAML056T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: B6_P1_liver_rep1


title: vehicle replicate 4

description: replicate 4

source_name: MCF-7 cell line treated with vehicle (control)

value: vehicle (control)


title: pituitary rep1


title: tamoxifen replicate 3

description: replicate 3


title: MIAML053N_primary human: buccal


title: lung rep3

source_name: lung

value: lung


title: MIAML054N_primary human: buccal


title: MIAML054T_010908_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML059N_primary human: buccal


title: MIAML050T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: 129_P1_liver_rep1


title: lung rep2


title: MIAML057T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML049T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML050N_primary human: buccal


title: estrogen and tamoxifen replicate 3

description: replicate 3


title: 129_P1_liver_rep3


title: liver rep3

source_name: liver


title: lung rep1


title: 129_P1_liver_rep2


title: D2_P1_brain_rep2

value: brain


title: MIAML047T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: tamoxifen replicate 2

description: replicate 2


title: D2_P1_brain_rep3


title: vehicle replicate 3

description: replicate 3


title: MIAML048N_primary human: buccal


title: MIAML047N_010908_primary human: buccal


title: MIAML048T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: liver rep2


title: estrogen and tamoxifen replicate 2

description: replicate 2


title: B6_P1_brain_rep3


title: estrogen replicate 2

description: replicate 2


title: D2_P1_brain_rep1


title: liver rep1


title: kidney rep3

source_name: kidney

value: kidney


title: B6_P1_brain_rep2


title: MIAML049N_primary human: buccal


title: vehicle replicate 2

description: replicate 2


title: 129_P1_brain_rep3


title: MIAML045N_primary human: buccal


title: kidney rep1


title: kidney rep2


title: estrogen replicate 3

description: replicate 3


title: estrogen replicate 1

description: replicate 1


title: heart rep3

source_name: heart

value: heart


title: MIAML045T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: heart rep2


title: estrogen and tamoxifen replicate 1

description: replicate 1


title: 129_P1_brain_rep2


title: 129_P1_brain_rep1


title: tamoxifen replicate 1

description: replicate 1


title: MIAML044T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: vehicle replicate 1

description: replicate 1


title: heart rep1


title: MIAML043N_primary human: buccal


title: MIAML043T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: B6_P1_brain_rep1


title: muscle rep3

source_name: muscle

value: muscle


title: muscle rep2


title: D2_E14.5_liver_rep3

value: embryonic stage E14.5


title: Sample13661-EAC-early stage-good prognosis

city: Buffalo

first: song

last: liu

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

description: good prognosis

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v3 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: Fresh frozen tissue

label_protocol: Initially, 250ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy midi kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

tag: type

value: EAC

tag: stage

value: early stage


title: Sample12878-EAC-early stage-good prognosis

description: good prognosis


title: muscle rep1


title: MIAML044N_primary human: buccal


title: D2_E14.5_liver_rep2

value: male

value: liver


title: Sample16613-EAC-early stage-bad prognosis

description: bad prognosis


title: Sample14124-EAC-early stage-good prognosis

description: good prognosis


title: B6_E14.5_liver_rep2


title: brain rep3

source_name: brain


title: B6_E14.5_liver_rep3


title: Sample10623-EAC-early stage-bad prognosis

description: bad prognosis


title: MIAML041T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: B6_E14.5_liver_rep1


title: 129_E14.5_liver_rep3


title: MIAML036N_primary human: buccal


title: MIAML041N_primary human: buccal


title: MIAML036T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: brain rep1


title: islets rep4

source_name: islets

value: islets


title: Sample13700-USC-late stage-good prognosis

description: good prognosis

value: USC

value: late stage


title: 129_E14.5_liver_rep2


title: 129_E14.5_liver_rep1


title: MIAML040N_primary human: buccal

value: normal


title: Sample11339-USC-late stage-bad prognosis

description: bad prognosis


title: islets rep3


title: D2_E14.5_brain_rep3


title: Sample16682-USC-late stage-good prognosis

description: good prognosis


title: MIAML040T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML035T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: D2_E14.5_liver_rep1


title: MIAML035N_primary human: buccal


title: islets rep2


title: Sample17050-EAC-late stage-good prognosis

description: good prognosis


title: Sample15579-USC-late stage-good prognosis

description: good prognosis


title: islets rep1


title: adipose tissue rep3

source_name: adipose tissue

value: adipose tissue


title: MIAML032T_primary human: blood or bone marrow, FACS sort-purified AML blasts

value: tumor


title: Sample11801-EAC-late stage-good prognosis

description: good prognosis


title: B6_E14.5_brain_rep3


title: D2_E14.5_brain_rep2


title: D2_E14.5_brain_rep1


title: MIAML031T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Sample16398-EAC-late stage-bad prognosis

description: bad prognosis


title: MIAML030T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: adipose tissue rep2


title: si FoxA1 and estrogen replicate 3

description: replicate 3

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package. Detection p-val not provided.

source_name: MCF-7 cell line treated with FoxA1 siRNA and estrogen

treatment_protocol: Estrogen was added at a final concentration of 100 nM.

tag: cell

value: FoxA1 siRNA and estrogen


title: si Control and estrogen replicate 3

description: replicate 3

source_name: MCF-7 cell line treated with control siRNA and estrogen

value: control siRNA and estrogen


title: adipose tissue rep1


title: B6_E14.5_brain_rep1

value: brain


title: Sample15901-EAC-late stage-good prognosis

description: good prognosis


title: 129_E14.5_brain_rep3


title: MIAML031N_primary human: buccal


title: MIAML032N_primary human: buccal


title: MIAML028N_primary human: buccal


title: MIAML024T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: B6_E14.5_brain_rep2


title: MIAML030N_primary human: buccal


title: Sample11205-EAC-late stage-bad prognosis

description: bad prognosis


title: 129_E14.5_brain_rep2


title: Sample13773-USC-late stage-bad prognosis

description: bad prognosis


title: si Control and vehicle replicate 3

description: replicate 3

source_name: MCF-7 cell line treated with control siRNA and vehicle (control)

value: control siRNA and vehicle (control)


title: 129_E14.5_brain_rep1


title: Sample13377-USC-early stage-bad prognosis

description: bad prognosis


title: si FoxA1 and vehicle replicate 3

description: replicate 3

source_name: MCF-7 cell line treated with FoxA1 siRNA and vehicle (control)

value: FoxA1 siRNA and vehicle (control)


title: si Control and estrogen replicate 2

description: replicate 2


title: si FoxA1 and estrogen replicate 2

description: replicate 2


title: brain rep2


title: Sample10963-USC-early stage-good prognosis

description: good prognosis


title: si FoxA1 and estrogen replicate 1

description: replicate 1


title: si Control and vehicle replicate 2

description: replicate 2


title: Sample16302-USC-early stage-bad prognosis

description: bad prognosis


title: MIAML028T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: si FoxA1 and vehicle replicate 2

description: replicate 2


title: si Control and estrogen replicate 1

description: replicate 1


title: Sample16936-USC-early stage-good prognosis

description: good prognosis


title: MIAML012T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Experimental Sample (WT vs BPS treated) replicate 3; Dye Swap

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: Biological Replicate 3 of 3

hyb_protocol: Labeled cDNA was mixed with hybridization buffer and applied immediately on the microarray slide. It was covered with 24x60 mm coverslip, sealed in Corning hybridization chambers and allowed to incubate overnight at 42° C. Slides were washed and scanned.

scan_protocol: Scanned on Scan Array Express microarray scanner from Perkin Elmer.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal using ScanArray Express v2.

organism: Candida albicans

source_name: BPS treated Candida cells

label_protocol: 10 µg of total RNA were primed with 2 µg of oligo dT at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 800 U SuperScript II Gibco BRL.

growth_protocol: All Candida strains were grown at 30°C

treatment_protocol: Treated Candida cells were grown at 30°C till OD600 of 1.0 with 150uM BPS to induce iron deprivation .

value: BPS treated (iron deprived)

source_name: WT Candida cells

value: WT (control)


title: Sample17344-USC-early stage-good prognosis

description: good prognosis


title: Experimental Sample (WT vs BPS treated) replicate 2

description: Biological Replicate 2 of 3


title: Experimental Sample (WT vs BPS treated) replicate 1

description: Biological Replicate 1 of 3


title: MIAML024N_primary human: buccal

source_name: buccal swabs


title: E_coli_AL371_vivo_rep2

status: Public on Nov 16 2010

first: Harry

last: Mobley

address: 5641 Medical Sciences II  1150 W. Medical Center Dr.

description: Second of three technical replicates of  E. coli patient isolate 371 directly from human urine.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Chip 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 (Roche NimbleGen, Inc.).

organism: Escherichia coli

source_name: Escherichia coli, 371, vivo

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

extract_protocol: Total RNA was extracted using the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the RNeasy Mini kit (Qiagen) and DNA was removed by TURBO DNase digestion (Ambion Inc., Austin, TX, USA). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer at the University of Michigan Affymetrix and Microarray Core Facility (University of Michigan Medical School, Ann Arbor, MI USA) and RNA concentration determined with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Rockford, IL, USA).

tag: isolate

tag: condition

value: patient urine in vivo


title: si FoxA1 and vehicle replicate 1

description: replicate 1

scan_protocol: Standard Illumina scanning protocol


title: E_coli_AL371_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 371 directly from human urine.


title: E_coli_AL291_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 291 directly from human urine.

source_name: Escherichia coli, 291, vivo


title: E_coli_AL361_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 361 directly from human urine.

source_name: Escherichia coli, 361, vivo


title: si Control and vehicle replicate 1

description: replicate 1


title: E_coli_AL361_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 361 directly from human urine.


title: E_coli_AL241_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 241 directly from human urine.

source_name: Escherichia coli, 241, vivo


title: E_coli_AL291_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 291 directly from human urine.


title: E_coli_AL241_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 241 directly from human urine.


title: MIAML012N_primary human: buccal


title: E_coli_AL371_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 371 directly from human urine.


title: MIAML014T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: E_coli_AL231_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 231 directly from human urine.

source_name: Escherichia coli, 231, vivo


title: MIAML014N_primary human: buccal


title: E_coli_AL231_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 231 directly from human urine.


title: MIAML009T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MIAML009N_primary human: buccal


title: E_coli_AL151_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 151 directly from human urine.

source_name: Escherichia coli, 151, vivo


title: E_coli_AL291_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 291 directly from human urine.


title: EGD-e / ∆LiaRLM Replicate 4

city: Würzburg

first: Frederike

last: Fritsch

address: Am Hubland

institute: Uni Würzburg

description: Biological replicate 2 of 2

hyb_protocol: The slides were hybridized according to the manufacturers protocol (BF-BIOlabs)

scan_protocol: slides were scanned using Axon GenePix 4200 Microarray scanner and analyzed using the Genepix Pro 6.0 software

data_processing: normalized using vsn, limma in R

organism: Listeria monocytogenes EGD-e

source_name: EGD-e ∆LiaRLM

label_protocol: 30 µg of total RNA were primed with 9 µg Random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 20 mM each dATP, dTTP, dGTP, with 10 µM dCTP, 50 nmol Cy3/Cy5-labelled dCTP

growth_protocol: bacteria were grown until OD600nm of 1.0

extract_protocol: RNA from the L. monocytogenes strains grown to an OD600 of 1.0 was extracted using the RNA-Mini-Kit (Seqlab, Göttingen, Germany) according to the manufacturer’s protocol. Residual DNA was removed on a column with RNase-free DNase (QIAGEN, Hilden, Germany) and TurboDNase (Ambion)

treatment_protocol: L. monocytogenes strains were grown under aerobic conditions in brain heart infusion (BHI from BD Biosciences, contains 2 g dextrose/l) at 37°C.

value: wild type

source_name: EGD-e

value: ∆LiaRLM


title: EGD-e / ∆LiaSLM Replicate 1

description: Biological replicate 1 of 5.

source_name: EGD-e ∆LiaSLM

value: ∆LiaSLM


title: E_coli_AL231_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 231 directly from human urine.


title: MIAML006T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: EGD-e / ∆LiaRLM Replicate 2

description: Biological replicate 1 of 2


title: EGD-e / ∆LiaRLM Replicate 3

description: Biological replicate 2 of 2


title: MIAML008N_primary human: buccal


title: E_coli_AL241_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 241 directly from human urine.


title: EGD-e / ∆LiaSLM Replicate 2

description: Biological replicate 1 of 5.


title: EGD-e / ∆LiaRLM Replicate 1

description: Biological replicate 1 of 2


title: E_coli_AL121_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 121 directly from human urine.

source_name: Escherichia coli, 121, vivo


title: E_coli_AL051_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 051 directly from human urine.

source_name: Escherichia coli, 051, vivo


title: EGD-e / ∆LiaSLM Replicate 3

description: Biological replicate 2 of 5.


title: EGD-e / ∆LiaSLM Replicate 7

description: Biological replicate 5 of 5.


title: EGD-e / ∆LiaSLM Replicate 6

description: Biological replicate 4 of 5.


title: MIAML007N_primary human: buccal


title: MIAML007T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: E_coli_AL151_vivo_rep2

description: Second of three technical replicates of  E. coli patient isolate 151 directly from human urine.


title: E_coli_AL051_vivo_rep2

description: Second of three technical replicates of E. coli patient isolate 051 directly from human urine.


title: E_coli_AL051_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 051 directly from human urine.


title: E_coli_AL121_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 121 directly from human urine.


title: E_coli_AL121_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 121 directly from human urine.


title: E_coli_AL151_vivo_rep1

description: First of three technical replicates of E. coli patient isolate 151 directly from human urine.


title: MIAML005T_primary human: blood or bone marrow, FACS sort-purified AML blasts


title: E_coli_AL371_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 371 cultured in vitro.

source_name: Escherichia coli, 371, vitro

value: urine in vitro culture


title: 2,000 CFU, t=15h, replicate 2

city: Nijmegen

first: Peter

last: Burghout

address: Kapittelweg 29

department: Laboratory of Pediatric Infectious Diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: n.a.

hyb_protocol: Fluorescently labeled DNA probes were combined and hybridized in Slidehyb buffer 1 (Ambion) to pneumococcal microarrays, which are super-amine glass slides spotted with duplicates of amplicons representing 2,087 S. pneumoniae TIGR4 ORFs and 184 ORFs unique to R6 (PMID: 16787930 ).The microarrays were incubated for 16 hours at 45°C, and then washed with 2xSSC (Invitrogen) containing 0.25% SDS for 5 min, followed by 2 washes in 1xSSC and 0.5xSSC for 5 min each. Finally, slides were dipped into H2O and dried by centrifugation.

scan_protocol: Dual channel array images were acquired on a GenePix 4200AL microarray scanner and analyzed with GenePix Pro software (Axon Instruments, Union City, CA, USA). Spots were screened visually to identify those of low quality.

data_processing: Microarray scan files were analyzed with GenePix Pro software (Axon Instruments, Union City, CA). Spots were screened visually to identify those of low quality and removed from the data set prior to analysis. A net mean intensity filter based on hybridization signals obtained with oligomer-spots representing open reading frames unique for S. pneumoniae strain R6 that were present on the pneumococcal microarray as well, was applied in all experiments. Slide data were processed and normalized using MicroPreP Slide data were processed and normalized using MicroPreP as described (PMID: 15130795). Further analysis was performed using a Cyber-T implementation of the Student’s t test (cybert.microarray.ics.uci.edu). This web-based program lists the ratios of all intra-replicates (duplicate spots) and inter-replicates (different slides), the mean ratios per gene, and standard deviations and (Bayesian) p values assigned to the mean ratios. For identification of conditionally essential genes, only genes with a minimum of 6/8 reliable measurements and a Bayesian p-value < 0.001 were included.

organism: Streptococcus pneumoniae

source_name: GAF control 2,000 CFU mutant library

label_protocol: Chromosomal DNA extracts was digested with AluI (New England Biolabs). The resulting DNA fragments were used as a template for an in vitro T7 RNA polymerase reaction (T7 MegaScript, Ambion). After removal of template DNA by DNAseI treatment, fluorescent Cy3/Cy5-labeled dUTP nucleotides (GE Healthcare) were incorporated by reverse transcription using Superscript III (Invitrogen).

growth_protocol: Control and CSF samples obtained during the experimental rabbit meningitis experiments were defrosted, diluted in GM17 medium supplemented with spectinomycin, and grown to mid-log phase.

extract_protocol: Chromosomal DNA was isolated from pneumococcal cultures by cetyl-trimethylammonium bromide (CTAB) extraction as described previously (PMID: 8057895).

value: TIGR4 marinerT7 mutant library

tag: mutant library size

tag: sample type

value: control

source_name: GAF 2,000 CFU mutant library t=15h replicate 2

value: CSF


title: 2,000 CFU, t=9h, replicate 3

description: n.a.

source_name: GAF 2,000 CFU mutant library t=9h replicate 3

treatment_protocol: Chromosomal DNA extracts was digested with AluI (New England Biolabs). The resulting DNA fragments were used as a template for an in vitro T7 RNA polymerase reaction (T7 MegaScript, Ambion). After removal of template DNA by DNAseI treatment, fluorescent Cy3/Cy5-labeled dUTP nucleotides (GE Healthcare) were incorporated by reverse transcription using Superscript III (Invitrogen).

tag: strain


title: E_coli_AL371_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 371 cultured in vitro.


title: E_coli_AL371_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 371 cultured in vitro.


title: EGD-e / ∆LiaSLM Replicate 4

description: Biological replicate 3 of 5.


title: EGD-e / ∆LiaSLM Replicate 5

description: Biological replicate 3 of 5.


title: MIAML008T_primary human: blood or bone marrow, FACS sort-purified AML blasts

tag: disease state


title: 2,000 CFU, t=15h, replicate 3

description: n.a.

source_name: GAF 2,000 CFU mutant library t=15h replicate 3


title: 2,000 CFU, t=9h, replicate 2

description: n.a.

source_name: GAF 2,000 CFU mutant library t=9h replicate 2


title: MIAML005N_primary human: buccal

source_name: buccal swabs

value: normal


title: 2,000 CFU, t=9h, replicate 1

description: n.a.

source_name: GAF 2,000 CFU mutant library t=9h replicate 1


title: 2,000 CFU, t=3h, replicate 1

description: n.a.

source_name: GAF 2,000 CFU mutant library t=3h replicate 1


title: 2,000 CFU, t=15h, replicate 1

description: n.a.

source_name: GAF 2,000 CFU mutant library t=15h replicate 1


title: 1,500(2) CFU, t=15h, replicate 4

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=15h replicate 4

source_name: GAF control 1,500(2) CFU mutant library


title: 2,000 CFU, t=3h, replicate 2

description: n.a.

source_name: GAF 2,000 CFU mutant library t=3h replicate 2


title: 1,500(2) CFU, t=15h, replicate 3

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=15h replicate 3


title: 2,000 CFU, t=3h, replicate 3

description: n.a.

source_name: GAF 2,000 CFU mutant library t=3h replicate 3


title: 1,500(2) CFU, t=15h, replicate 2

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=15h replicate 2


title: 1,500(2) CFU, t=15h, replicate 1

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=15h replicate 1


title: E_coli_AL361_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 361 cultured in vitro.

source_name: Escherichia coli, 361, vitro


title: E_coli_AL361_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 361 cultured in vitro.


title: E_coli_AL361_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 361 cultured in vitro.


title: E_coli_AL291_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 291 cultured in vitro.

source_name: Escherichia coli, 291, vitro


title: E_coli_AL361_vivo_rep3

description: Third of three technical replicates of E. coli patient isolate 361 directly from human urine.

source_name: Escherichia coli, 361, vivo


title: 1,500(2) CFU, t=9h, replicate 1

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=9h replicate 1


title: 1,500(2) CFU, t=3h, replicate 4

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=3h replicate 4


title: E_coli_AL291_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 291 cultured in vitro.


title: 1,500(2) CFU, t=3h, replicate 2

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=3h replicate 2


title: E_coli_AL241_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 241 cultured in vitro.

source_name: Escherichia coli, 241, vitro


title: 1,500(2) CFU, t=9h, replicate 2

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=9h replicate 2


title: 1,500(2) CFU, t=9h, replicate 3

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=9h replicate 3


title: 1,500(2) CFU, t=3h, replicate 1

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=3h replicate 1


title: 1,500(1) CFU, t=15h, replicate 4

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=15h replicate 4

source_name: GAF control 1,500(1) CFU mutant library


title: E_coli_AL241_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 241 cultured in vitro.


title: 1,500(2) CFU, t=9h, replicate 4

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=9h replicate 4

source_name: GAF control 1,500(2) CFU mutant library


title: E_coli_AL241_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 241 cultured in vitro.


title: 1,500(2) CFU, t=3h, replicate 3

description: n.a.

source_name: GAF 1,500(2) CFU mutant library t=3h replicate 3


title: 1,500(1) CFU, t=15h, replicate 3

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=15h replicate 3


title: 1,500(1) CFU, t=15h, replicate 2

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=15h replicate 2


title: 1,500(1) CFU, t=15h, replicate 1

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=15h replicate 1


title: E_coli_AL231_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 231 cultured in vitro.

source_name: Escherichia coli, 231, vitro


title: 1,500(1) CFU, t=9h, replicate 2

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=9h replicate 2


title: 1,500(1) CFU, t=9h, replicate 1

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=9h replicate 1


title: 1,500(1) CFU, t=3h, replicate 4

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=3h replicate 4


title: E_coli_AL231_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 231 cultured in vitro.


title: 1,500(1) CFU, t=9h, replicate 3

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=9h replicate 3


title: 1,500(1) CFU, t=9h, replicate 4

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=9h replicate 4


title: E_coli_AL231_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 231 cultured in vitro.


title: E_coli_AL151_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 151 cultured in vitro.

source_name: Escherichia coli, 151, vitro