title: PB_7d_3


title: 3ABDKO infected with DNMT3B3 control Day 5 post 24 treatment with 5-Aza-CdR

status: Public on Apr 08 2016

type: genomic

city: Los Angeles

first: Peter

middle: A

last: Jones

state: California

address: 1441 Eastlake Ave NOR7344

department: Urology

country: USA

institute: University of Southern California

description: 3ABDKO 3B3 DAY 5

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: MethylLumi Package

label: cy5 and cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: cell line

value: HCT derivative cell line 3ABDKO

tag: treatment


title: 3BKO infected with DNMT3L control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 3L DAY 42

data_processing:
MethylLumi Package
Unmethylated and methylated signal intensities in MethylationIntensities.txt file

label: Cy5 and Cy3


title: Ep.5wk.MEChi.Th#2

type: RNA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Affymetrix WT Sense Target Labeling Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Thymus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: tissue

value: Thymus

tag: age

value: 5 Weeks Old

tag: exclusion markers

value: PI- CD45-

tag: genetic background

tag: phenotype markers

value: EpCAM+ Ly51+ MHCII+ Sca1+

tag: separation method

value: FACSAria

tag: Sex

value: Male


title: 3BKO infected with EV control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 EV DAY 42


title: 3BKO infected with DNMT3B1M control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1M DAY 42


title: 3BKO infected with DNMT3B1 control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1 DAY 42


title: PB_7d_1

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: 10 µg of fragmented, biotinylated aRNA were hybridized for approximately 16 hrs at 45ºC to the GeneChip® Mouse430_2 arrays. The arrays were then washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were then scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix). The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

label: biotin

source_name: liver, Phenobarbital, 7 days, 0.05 % w/v

label_protocol: Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix, Santa Clara, CA). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3' IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented.

growth_protocol: 29- to 32-day-old male B6C3F1/Crl (C57BL/6 female × C3H/He male) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatize for 5 days prior to being randomly divided into treatment groups.

extract_protocol: Blood was withdrawn for PK analysis, and liver was removed, split into several sections, either frozen in liquid nitrogen and stored at −80°C for subsequent analyses or fixed in neutral phosphate-buffered formalin, and embedded in paraffin wax. To ensure sample homogeneity for different molecular profiling methods, frozen liver samples were reduced to powder with Covaris Cryoprep (Covaris Inc., Woburn, MA) system and aliquoted on dry ice. Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: PB (Sigma [St Louis, MO] #04710, 0.05% [wt/vol] in drinking water) was administered to one group through ad libitum access to drinking water. Mice were checked daily for activity and behavior and sacrificed on the indicated dates.

tag: strain

value: liver

value: PB

value: Phenobarbital

tag: group

tag: treatment_duration [days]

tag: treatment_dose [% w/v]


title: 3BKO infected with DNMT3L control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 3L DAY 10


title: Ep.5wk.MEC.Sca1+.Th#1


title: BA.Sp#4

source_name: Spleen

value: Spleen

value: 6 Weeks Old

value: FcER1a+ CD49b+


title: PB_3d_4

source_name: liver, Phenobarbital, 3 days, 0.05 % w/v


title: PB_3d_5


title: PB_7d_2


title: MC.PC#0

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: Mast+

value: Dissection / Trimming


title: Ep.8wk.CEC.Sca1+.Th#1

value: 8 Weeks Old


title: MC.Es#1

source_name: Whole Tissue

value: Whole Tissue

value: CD11b CD11c CD4 CD8 CD19

value: CD45+ CD117+ FcER1a+


title: 3BKO infected with DNMT3B3 control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B3 DAY 10


title: PB_3d_2


title: Ep.5wk.MEC.Sca1+.Th#2

value: Thymus

value: 5 Weeks Old

value: PI- CD45-


title: BA.Sp#3

source_name: Blood

value: Blood

value: CD3, CD19, CD11c

value: CD49b+ FcER1a+

value: FACSAria

value: Male


title: BA.Bl#2

value: 6 Weeks Old


title: BA.Bl#3

value: FcER1a+ CD49b+


title: BA.Sp#1

value: Spleen


title: BA.Bl#1

value: CD4 CD8 C19 NK1.1


title: 3BKO infected with DNMT3B4 control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B4 DAY 10


title: 3BKO infected with EV control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 EV DAY 10


title: 3BKO infected with DNMT3B1 control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1 DAY 10


title: PB_1d_3

source_name: liver, Phenobarbital, 1 days, 0.05 % w/v

value: liver

value: PB

value: Phenobarbital


title: PB_3d_1


title: 3BKO infected with DNMT3B1M control Day 10 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1M DAY 10


title: PB_1d_5


title: PY_24

city: Singapore

first: Regina

last: Hoo

address: 60, Nanyang Drive

department: School of Biological Science

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 2 fold median background intensity for either channel passed quality control and were accepted. Local  background correction using substraction, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium yoelii

source_name: Ex vivo, Blood stage, 24hr

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol:
Mice were infected by intraperitoneal injections of P. berghei ANKA, P. chabaudi AS or P. yoelii parasitized erythrocytes and parasitaemia and parasite stages were monitored by thin blood smears stained with Giemsa.
Mice infected with P. chabaudi were terminal bled every 2 hrs time-point under anesthesia over the course of 24 hr. Mice infected with P. berghei and P. yoelii were terminal bleed and the stage-specific parasitized erythrocytes were separated via Nycodenz density gradient. The ring stage interface was isolated, washed and subjected to ex vivo culture. The ex vivo parasite culture was then collected every 2 hr over the course of 24 hr over a complete IDC life-cycle.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: Ex vivo, Blood stage

tag: time

source_name: Ex vitro culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle

tag: reference

value: P. yoelii 17X RNA reference pool

tag: train


title: PB_1d_4


title: PB_1d_2


title: PB_1d_1


title: PY_22

source_name: Ex vivo, Blood stage, 22hr


title: 3BKO infected with DNMT3L control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 3L DAY 5

tag: cell line


title: PB_3d_3


title: 3BKO infected with DNMT3B1M control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1M DAY 5

tag: treatment


title: PY_16

source_name: Ex vivo, Blood stage, 16hr


title: PY_18

source_name: Ex vivo, Blood stage, 18hr


title: PY_20

source_name: Ex vivo, Blood stage, 20hr


title: 3BKO infected with DNMT3B1 control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B1 DAY 5


title: H2O_91d_4

source_name: liver, Drinking water, 91 days, 0 % w/v

tag: tissue

value: Drinking water


title: PY_12

source_name: Ex vivo, Blood stage, 12hr


title: H2O_57d_5

source_name: liver, Drinking water, 57 days, 0 % w/v


title: H2O_91d_3


title: H2O_91d_1


title: H2O_91d_5


title: 3BKO infected with DNMT3B3 control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B3 DAY 5


title: 3BKO infected with DNMT3B4 control Day 0 PBS control

description: 3BK0 3B4 CTRL


title: PY_14

source_name: Ex vivo, Blood stage, 14hr


title: 3BKO infected with EV control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 EV DAY 5


title: H2O_91d_2


title: H2O_57d_3


title: PY_08

source_name: Ex vivo, Blood stage, 8hr


title: 3BKO infected with DNMT3B1M control Day 0 PBS control

description: 3BK0 3B1M CTRL


title: H2O_57d_2


title: H2O_57d_4


title: 3BKO infected with DNMT3L control Day 0 PBS control

description: 3BK0 3L CTRL


title: 3BKO infected with DNMT3B3 control Day 0 PBS control

description: 3BK0 3B3 CTRL


title: PY_04

source_name: Ex vivo, Blood stage, 4hr


title: H2O_28d_4

source_name: liver, Drinking water, 28 days, 0 % w/v


title: DKO8 infected with DNMT Delta 3B4

source_name: DKO8 infected with DNMT Delta 3B4

value: infected with DNMT Delta 3B4


title: 3BKO infected with EV control Day 0 PBS control

description: 3BK0 EV CTRL


title: PY_02

source_name: Ex vivo, Blood stage, 2hr


title: H2O_57d_1


title: 3BKO infected with DNMT3B1 control Day 0 PBS control

description: 3BK0 3B1 CTRL


title: DKO8 infected with DNMT3L

source_name: DKO8 infected with DNMT3L

value: infected with DNMT3L


title: H2O_28d_2


title: H2O_28d_3


title: PC_18

organism: Plasmodium chabaudi

source_name: In vivo, Blood stage, 18hr

value: AS

value: In vivo, Blood stage

source_name: In vivo culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle

value: P. chabaudi AS RNA reference pool


title: PC_20

source_name: In vivo, Blood stage, 20hr


title: PY_10

source_name: Ex vivo, Blood stage, 10hr

source_name: Ex vitro culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle


title: PY_06

source_name: Ex vivo, Blood stage, 6hr


title: H2O_28d_5


title: PC_24

source_name: In vivo, Blood stage, 24hr


title: PC_16

source_name: In vivo, Blood stage, 16hr


title: PC_22

source_name: In vivo, Blood stage, 22hr


title: H2O_14d_4

source_name: liver, Drinking water, 14 days, 0 % w/v


title: H2O_28d_1


title: DKO8 infected with DNMT Delta 3B2

source_name: DKO8 infected with DNMT Delta 3B2

value: infected with DNMT Delta 3B2


title: 3BKO infected with DNMT3B4 control Day 5 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B4 DAY 5


title: H2O_14d_5


title: DKO8 infected with DNMT3B3

source_name: DKO8 infected with DNMT3B3

value: infected with DNMT3B3


title: DKO8 infected with DNMT3B1

source_name: DKO8 infected with DNMT3B1

value: infected with DNMT3B1


title: H2O_14d_3


title: DKO8 infected with DNMT Delta 3B2-M

source_name: DKO8 infected with DNMT Delta 3B2-M

value: infected with DNMT Delta 3B2-M


title: H2O_14d_2


title: H2O_7d_5

source_name: liver, Drinking water, 7 days, 0 % w/v


title: PB_20

organism: Plasmodium berghei

source_name: Ex vivo, Blood stage, 20hr

value: ANKA

value: P. berghei ANKA RNA reference pool


title: PB_22

source_name: Ex vivo, Blood stage, 22hr


title: H2O_7d_3

value: liver


title: H2O_7d_2


title: PC_14

source_name: In vivo, Blood stage, 14hr


title: PC_10

source_name: In vivo, Blood stage, 10hr

source_name: In vivo culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle


title: PC_08

source_name: In vivo, Blood stage, 8hr


title: H2O_14d_1


title: DKO8 infected with EV control

source_name: DKO8 infected with EV control

value: infected with EV control


title: PB_12

source_name: Ex vivo, Blood stage, 12hr

source_name: Ex vitro culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle


title: PC_02

source_name: In vivo, Blood stage, 2hr


title: PB_18

source_name: Ex vivo, Blood stage, 18hr


title: H2O_3d_1

source_name: liver, Drinking water, 3 days, 0 % w/v


title: H2O_7d_4


title: H2O_3d_5


title: PB_10

source_name: Ex vivo, Blood stage, 10hr


title: PB_14

source_name: Ex vivo, Blood stage, 14hr


title: H2O_3d_2


title: H2O_3d_4


title: H2O_3d_3


title: PC_12

source_name: In vivo, Blood stage, 12hr


title: PB_16

source_name: Ex vivo, Blood stage, 16hr


title: PB_08

source_name: Ex vivo, Blood stage, 8hr


title: H2O_1d_4

source_name: liver, Drinking water, 1 days, 0 % w/v


title: PB_06

source_name: Ex vivo, Blood stage, 6hr


title: H2O_1d_3


title: PB_02

source_name: Ex vivo, Blood stage, 2hr


title: PB_04

source_name: Ex vivo, Blood stage, 4hr


title: H2O_1d_2


title: mouse melanoma 1011

status: Public on Apr 07 2016

city: Houston

first: Lawrence

middle: N

last: Kwong

state: TX

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description: cDNA from total mRNA isolated by Trizol from macrodissected frozen tumor

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw image files were converted to probe set data (.cel files) in Microarray Suite (MAS 5.0). The 18 probe set data files were normalized together, and expression values were determined, using the Robust Multi-chip Average (RMA) method as implemented in RMAExpress (Bolstad/Berkeley).

source_name: mouse melanoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: iBIP mice developed melanomas and dox was withdrawan from the water for the specified number of days.

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

treatment_protocol: Tumors were harvested from iBIP mice. Skin was trimmed off of the tumors and a small piece (10-50mg) of tumor parenchyma was placed into RNA Later preservation reagent, refrigerated overnight at 4oC, then stored at -80oC. Samples were later placed into Trizol after minimal thawing and homogenized using a hand-held electric tissue homogenizer.

value: iBIP

value: macrodissected frozen tumor

tag: days off dox


title: mouse melanoma 222


title: DKO8 infected with DNMT3B1-M

source_name: DKO8 infected with DNMT3B1-M

value: infected with DNMT3B1-M


title: mouse melanoma 143


title: H2O_1d_1

value: Drinking water


title: PC_06

source_name: In vivo, Blood stage, 6hr

source_name: In vivo culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle


title: mouse melanoma 216


title: mouse melanoma 3650


title: mouse melanoma 3630


title: mouse melanoma 3626


title: mouse melanoma 111


title: mouse melanoma 120


title: mouse melanoma 139


title: mouse melanoma 3651


title: mouse melanoma 160


title: mouse melanoma 1019


title: mouse melanoma 3625


title: H2O_7d_1

source_name: liver, Drinking water, 7 days, 0 % w/v


title: mouse melanoma 3481


title: mouse melanoma 3652


title: mouse melanoma 3653


title: mouse melanoma 1018


title: mouse melanoma 1098


title: mouse melanoma 1035


title: mouse melanoma 1094


title: mouse melanoma 1004


title: mouse melanoma 1089


title: mouse melanoma 3353


title: mouse melanoma 1058


title: mouse melanoma 1062


title: mouse melanoma 1072


title: mouse melanoma 3329


title: mouse melanoma 1027


title: mouse melanoma 1008


title: mouse melanoma 1007


title: PB_24

source_name: Ex vivo, Blood stage, 24hr

value: Ex vivo, Blood stage

source_name: Ex vitro culture, asexual blood stage, mixture of equal amounts of RNA harvested every 2 hours over the 24-hour parasite's intraerythrocytic life cycle


title: mouse melanoma 1036


title: mouse melanoma 1009


title: mouse melanoma 1037


title: mouse melanoma 1015


title: mouse melanoma 1016


title: mouse melanoma 1069


title: cell_M5A

city: Yokohama, Kanagawa

first: Takeya

last: Kasukawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Gene expression data of single apical progenitor (AP) cell overexpressed NICD+p18 derived from dorso-lateral portion of cerebral wall of E14 CD1 mouse

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Single apical progenitor (AP) cell overexpressed NICD+p18, derived from dorso-lateral portion of cerebral wall of E14 CD1 mouse

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

growth_protocol: For cell_W2G,W2O and W6D, cells from dorso-lateral portion of cerebral wall of E11 CD1 mice were cultured for 3 days in DMEM/F12 with N2, B27, 1mM N-acetylcysteine, 20ng/ml FGF2 and 20ng/ml EGF in suspension culture dish.

extract_protocol: Single cell was lysed in a PCR tube containing 4.5ul of cell lysis buffer containing spike RNA: poly(A)-tailed Bacillus subtilis lys, dap, phe, and thr RNAs at 1000,100, 20, and 5 copies per cell, respectively, and the clude lysate was used for cDNA synthesis and amplification as descibed (Kurimoto et al.Nucreic Acid Res.34:e42, 2006).

treatment_protocol: For cell_M5A, M5K, M6C, M6H, pCAG-NICD and pEF-p18 was co-electroporated into dorso-lateral part of cerebral wall at E11 by in vivo electroporation. Dorso-lateral portion of cerebral wall of CD1 mice at E11,E12, small VZ/SVZ fragments of the same portion at E14 (3 days after electroporation), E16, or 3 days-in-vitro neurospheres were digested in 100ul of 0.25%Trypsin/0.5% Glucose /PBS for 5min at 37°C and triturated. After adding Hanks solution (Nakarai, Japan) with trypsin inhibitor (Ovomucoid, Sigma), singly-isolated cells were randomly picked up manually by glass-capillary under inverted microscope and transferred into PCR tubes containing 4.5ul of cell lysis buffer.

value: dorso-lateral portion of cerebral wall

tag: developmental stage


title: cell_M6C


title: mouse melanoma 172


title: cell_M5K


title: cell_M6H


title: mouse melanoma 1005


title: PC_04

source_name: In vivo, Blood stage, 4hr

value: AS


title: cell_109B

description: Gene expression data of single apical progenitor (AP) cell derived from dorso-lateral portion of cerebral wall of E12 CD1 mouse

source_name: Single apical progenitor (AP) cell derived from dorso-lateral portion of cerebral wall of E12 CD1 mouse


title: cell_W2O

description: Gene expression data of single apical progenitor (AP) cell  in 3-day-cultured neurosphere derived from dorso-lateral portion of cerebral wall of E11 CD1 mouse

source_name: Single apical progenitor (AP) cell from 3 days-in-vitro neurosphere derived from dorso-lateral portion of cerebral wall of E11 CD1 mouse


title: cell_E16-82H

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E16 CD1 mouse

source_name: Single cell from VZ/SVZ of cerebral wall, E16, CD1 mouse

treatment_protocol: Dorso-lateral portion of cerebral wall of a CD1 mouse at E11 or small VZ/SVZ fragments of the same portion at E16 were digested in 100ul of 0.25%Trypsin/0.5% Glucose /PBS for 5min at 37°C and triturated. After adding Hanks solution (Nakarai, Japan) with trypsin inhibitor (Ovomucoid, Sigma), singly-isolated cells were randomly picked up manually by glass-capillary under inverted microscope and transferred into PCR tubes containing 4.5ul of cell lysis buffer.

value: VZ/SVZ of cerebral wall


title: cell_W2G


title: cell_W6D


title: cell_E16-81i


title: cell_E16-81O


title: cell_E16-82P


title: cell_E16-81A


title: cell_E16-81J


title: mouse melanoma 209


title: cell_E16-82O


title: cell_103L


title: cell_E16-81C


title: cell_E16-76F


title: cell_E16-78O


title: cell_E16-81P


title: cell_E16-81L


title: cell_E16-81E


title: cell_E16-80K


title: cell_E16-76J


title: cell_E16-81G


title: cell_E16-75O


title: cell_E16-77M


title: cell_E16-78C


title: cell_105M


title: cell_E16-76C


title: cell_E16-81M


title: cell_E16-78G


title: cell_E16-81H


title: cell_E16-72J


title: cell_E16-75A


title: cell_E11-45E

description: Gene expression data of single cell derived from dorso-lateral portion of cerebral wall of E11 CD1 mouse

source_name: Single cell derived from dorso-lateral portion of cerebral wall of E11 CD1 mouse


title: cell_E11-45D


title: cell_E11-45G


title: cell_E11-45B


title: cell_E11-45F


title: cell_E11-45K


title: cell_E16-73A


title: cell_E11-42O


title: cell_E11-42P


title: cell_E11-42J


title: mouse melanoma 1002


title: cell_E11-42C


title: cell_E16-71E


title: cell_E11-37N


title: cell_E11-41G


title: cell_E11-44D


title: cell_E11-43D


title: cell_E11-38O


title: cell_E11-42D


title: cell_E11-42B


title: cell_E11-40F


title: cell_E11-38B


title: cell_E11-37M


title: cell_E11-42N


title: cell_E16-75H


title: cell_E11-41B


title: cell_E11-42M


title: ATII_control_LR138

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data from human adult alveolar type II cells day 3

hyb_protocol: The cDNA was hybridized to Human Gene 1.0 ST arrays

scan_protocol: Affymetrix Standard protocol

data_processing: Gene level analysis was performed using the Affymetrix® Expression Console™ software with the default settings of the RMA-sketch workflow.

source_name: Human adult alveolar type II cells, control

label_protocol: Fragmentation and labeling was performed using the Affymetrix GeneChip WT terminal Labeling Kit.

growth_protocol: Human adult alveolar type II cells were extracted from lung resection tissue specimens. 0.5 Million cells were seeded onto 24 well plates and grown in DCCM-1 (Biological Industries Ltd. Kibbutz Beit-Haemek, Israel) media supplemented with fetal calf serum (FCS).

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen)

value: control

tag: cell type

value: alveolar type II cells

tag: patient


title: cell_E11-37C


title: cell_E11-31i


title: ATII_vitaminD_LR132

description: Gene expression data from vitamin D-treated human adult alveolar type II cells day 3

source_name: Human adult alveolar type II cells, treated with 100nM vitamin D

value: 100nM vitamin D


title: cell_E11-32J


title: ATII_vitaminD_LR133


title: ATII_vitaminD_LR138


title: ATII_control_LR133


title: ATII_control_LR134


title: cell_E11-30F


title: cell_E11-37D


title: ATII_vitaminD_LR134


title: day 8 Gr1+/Cx3cr1low biological replicate 1

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data of muscle-derived macrophages

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: muscle-derived tissue macrophage

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Muscle injury was caused by cardiotoxin ijection in the Tibialis anterior muscle. Macrophages were separated after 1, 2 , 4 and 8 days post-injury from the regenerating muscle.

treatment_protocol: CD45+ hematopoietic cells from regenerating muscles were isolated with a magnetic bead selection (Miltenyi). Cells were labeled with PE-conjugated Gr1+ and APC-conjugated Cx3cr1 antibodies and then sorted into Ly6C+ F4/80low and Ly6C- F4/80high subsets.

tag: cell surface marker

value: day 8


title: day 4 Gr1+/Cx3cr1low biological replicate 3

value: day 4


title: day 8 Gr1-/Cx3cr1high biological replicate 2


title: cell_E11-30L


title: day 4 Gr1-/Cx3cr1high biological replicate 3


title: ATII_control_LR132


title: day 4 Gr1-/Cx3cr1high biological replicate 2


title: day 8 Gr1-/Cx3cr1high biological replicate 3


title: day 2 Gr1-/Cx3cr1high biological replicate 3

value: day 2


title: day 4 Gr1-/Cx3cr1high biological replicate 1


title: day 8 Gr1-/Cx3cr1high biological replicate 1


title: day 2 Gr1+/Cx3cr1low biological replicate 3


title: day 2 Gr1-/Cx3cr1high biological replicate 2


title: day 4 Gr1+/Cx3cr1low biological replicate 2


title: day 2 Gr1-/Cx3cr1high biological replicate 1


title: day 2 Gr1+/Cx3cr1low biological replicate 1


title: day 1 Gr1-/Cx3cr1high biological replicate 3

value: day 1


title: day 1 Gr1+/Cx3cr1low biological replicate 2


title: day 1 Gr1+/Cx3cr1low biological replicate 3


title: day 1 Gr1-/Cx3cr1high biological replicate 2


title: day 1 Gr1-/Cx3cr1high biological replicate 1


title: day 2 Gr1+/Cx3cr1low biological replicate 2


title: day 1 Gr1+/Cx3cr1low biological replicate 1


title: Mouse-Naïve-replicate-6

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Mouse-Naïve-replicate-6

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip mouse gene 1.0 ST arrays according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with EC 1.1 using Affymetrix default analysis with an RMA-sketech normalization method.

source_name: Mouse-Naïve

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: Female mice 6-8 weeks’ old were bred and kept in the specific pathogen–free facility at the National Institute for Medical Research, or National Institutes of Health.

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: Percutaneous infections were carried out with S. mansoni cercariae or mice were infected in the ear dermis with L. major metacyclic promastigotes using a 27.5 G needle in a volume of 10μl

tag: background strain

tag: treg cell type


title: HOS miR23a overexpression 2

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: Human HOS cell line

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

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

treatment_protocol: HOS cells were transfected with human hsa-miR-23a, or negative control mimic for 72h. 150ng of each RNA was amplified and labeled. 750ng biotin-labeled cRNA was hybridized to Illumina HumanHT-12- V4 Expression BeadChip microarrays. BeadChips were scanned in an Illumina Scanner.

value: HOS

value: osteosarcoma

tag: mir23a status

value: Overexpression


title: HOS miR23a overexpression 3


title: HOS miR23a overexpression 1


description: Gene expression data from_Mouse-infected with-Leishmania major-replicate-1

source_name: Mouse-infected with-Leishmania major


title: Mouse-Naïve-replicate-1

description: Gene expression data from_Mouse-Naïve-replicate-1


description: Gene expression data from_Mouse-infected with-Schistosoma mansoni-replicate-4

source_name: Mouse-infected with-Schistosoma mansoni


description: Gene expression data from_Mouse-infected with-Schistosoma mansoni-replicate-1


description: Gene expression data from_Mouse-infected with-Leishmania major-replicate-3


title: Mouse-Naïve-replicate-3

description: Gene expression data from_Mouse-Naïve-replicate-3


title: Mouse-Naïve-replicate-7

description: Gene expression data from_Mouse-Naïve-replicate-7


description: Gene expression data from_Mouse-infected with-Schistosoma mansoni-replicate-3


title: Mouse-Naïve-replicate-5

description: Gene expression data from_Mouse-Naïve-replicate-5


title: Mouse-Naïve-replicate-2

description: Gene expression data from_Mouse-Naïve-replicate-2


title: HOS negative control mimic 1

value: Negative


title: HOS negative control mimic 2


title: Mouse-Naïve-replicate-4

description: Gene expression data from_Mouse-Naïve-replicate-4


title: HOS negative control mimic 3


description: Gene expression data from_Mouse-infected with-Leishmania major-replicate-2


description: Gene expression data from_Mouse-infected with-Schistosoma mansoni-replicate-2


title: HOS BGP treatment 1

treatment_protocol: HOS cells were grown to got 100% confluence, followed by differentiation induced by bone inducing agents, that include L-ascorbic acid 50ug/ml and beta-glycerophosphate 5mM. Cells were harvested at indicated times for mRNA extraction.

value: BGP


title: HOS BGP treatment 3


title: cell_E11-45O

description: Gene expression data of single cell derived from dorso-lateral portion of cerebral wall of E11 CD1 mouse

tag: strain


title: HOS negative control 1


title: HOS negative control 3


title: K562 NTC 3

city: Ghent

first: Hetty

middle: Hilde

last: Helsmoortel

address: De Pintelaan 185

department: Department of Pediatric Hematology-Oncology and Stem Cell Transplantation

country: Belgium

institute: Ghent University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization after background correction was performed with the normalizeBetweenArrays function (Limma).

source_name: K562 NTC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were selected with puromycin after transduction and allowed to grow for several days until enough cells could be harvested.

extract_protocol: RNA was extracted from stored, frozen cells using Trizol and the miRNeasy mini kit (Qiagen)

treatment_protocol: Retroviral transduction with shRNA GN36578 and non-targeting TRH1103

tag: transduced with

value: shRNA-miR non-targeting control TRH1103


title: Oci-AML3 empty 3

source_name: Oci-AML3 empty

treatment_protocol: Retroviral transduction with MSCV-PIG-LIN28B or MSCV-PIG-empty

value: MSCV-PIG-empty vector


title: HOS negative control 2


title: HOS BGP treatment 2


title: K562 LIN28B-KD 2

source_name: K562 LIN28B-KD

value: shRNA GN36578 against LIN28B


title: gastric mucosa_normal_patient_9

city: Hangzhou

first: Qinshu

last: Shao

state: ZheJiang

address: 158 Shangtang Road

country: China

institute: Zhejiang Provincial People’s Hospital

description: Gene expression data of gastric mucosa from patient 9

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) was used to control the scanner  with default settings.

source_name: gastric mucosa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions.

treatment_protocol: This study was approved by the ethics committee of Zhejiang Provincial People's Hospital and all patients signed an informed consent. Paired fresh specimens were collected from 10 patients who underwent radical gastrectomy for GC at Zhejiang Provincial People’s Hospital. Both the tumor lesions and adjacent non-tumor mucosa were rapidly frozen in liquid nitrogen after resection and stored at −80°C.

value: gastric mucosa


title: gastric mucosa_normal_patient_10

description: Gene expression data of gastric mucosa from patient 10


title: gastric adenocarcinoma_tumor_patient_9

description: Gene expression data of gastric adenocarcinoma from patient 9

source_name: gastric adenocarcinoma

value: gastric adenocarcinoma


title: K562 NTC 1


title: Oci-AML3 empty 2


title: gastric adenocarcinoma_tumor_patient_10

description: Gene expression data of gastric adenocarcinoma from patient 10


title: gastric adenocarcinoma_tumor_patient_7

description: Gene expression data of gastric adenocarcinoma from patient 7


title: gastric adenocarcinoma_tumor_patient_8

description: Gene expression data of gastric adenocarcinoma from patient 8


title: Oci-AML3 LIN28B 1

source_name: Oci-AML3 LIN28B


title: K562 LIN28B-KD 1


title: Oci-AML3 LIN28B 3


title: Oci-AML3 LIN28B 2


title: gastric mucosa_normal_patient_6

description: Gene expression data of gastric mucosa from patient 6


title: gastric mucosa_normal_patient_7

description: Gene expression data of gastric mucosa from patient 7


title: K562 NTC 2


title: Oci-AML3 empty 1


title: K562 LIN28B-KD 3


title: gastric adenocarcinoma_tumor_patient_6

description: Gene expression data of gastric adenocarcinoma from patient 6


title: gastric mucosa_normal_patient_8

description: Gene expression data of gastric mucosa from patient 8


title: gastric mucosa_normal_patient_4

description: Gene expression data of gastric mucosa from patient 4


title: gastric adenocarcinoma_tumor_patient_4

description: Gene expression data of gastric adenocarcinoma from patient 4


title: gastric mucosa_normal_patient_5

description: Gene expression data of gastric mucosa from patient 5


title: gastric mucosa_normal_patient_3

description: Gene expression data of gastric mucosa from patient 3


title: gastric mucosa_normal_patient_2

description: Gene expression data of gastric mucosa from patient 2


title: gastric adenocarcinoma_tumor_patient_2

description: Gene expression data of gastric adenocarcinoma from patient 2


title: gastric adenocarcinoma_tumor_patient_3

description: Gene expression data of gastric adenocarcinoma from patient 3


title: gastric mucosa_normal_patient_1

description: Gene expression data of gastric mucosa from patient 1


title: gastric adenocarcinoma_tumor_patient_1

description: Gene expression data of gastric adenocarcinoma from patient 1


title: gastric adenocarcinoma_tumor_patient_5

description: Gene expression data of gastric adenocarcinoma from patient 5


title: C2-C1

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

institute: KU Leuven

description: Control locust midgut/caeca sample replicate 2 vs Control locust midgut/caeca sample replicate 1

hyb_protocol: The labeled samples were hybridized onto the microarrays according to the design described under 'Overall design', and by using the Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions. Hybridization was performed during 17 hr at 65°C. Next, the microarrays were washed twice in GE Wash Buffer 1 (Agilent) for 1 minute each, in GE Wash Buffer 2 (Agilent) at 37°C for 1 minute and in acetonitrile for 1 minute. Finally, the slides were immersed in Stabilization & Drying Solution (Agilent).

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments) at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm. The PMT voltages for each wavelength were adjusted to obtain an overall green/red ratio as close as possible to 1. Spot identification and quantification of the fluorescent signal was carried out using GenePix Pro 6.0 software (Axon Instruments).

data_processing: The data obtained from all eight hybridizations were used for statistical analysis by means of the R package limma. Spots where the median foreground intensity was less than the average local background intensity (calculated over the complete microarray) plus twice its standard deviation on all arrays were deleted before analysis. Median intensities were background corrected using a normal-exponential convolution model (offset +50) and normalized by a Locally Weighed Scatterplot Smoothing (Lowess) function.

organism: Locusta migratoria

label_protocol: Labeling of the samples was performed by using the Quick Amp Labeling Kit (Two Color, Agilent Technologies), according to the manufacturer’s instructions. For each sample, 1µg total RNA was used for labeling. The fluorescently labeled samples were purified by means of the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

growth_protocol: Gregarious locusts were reared under crowded conditions with controlled temperature (32 ± 1°C), light (14h photoperiod) and relative humidity (40-60%). Locusts were fed daily with grass.

extract_protocol: Total RNA was extracted by using RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. In addition, a DNase treatment (RNase-free DNase set, Qiagen) was performed to eliminate potential genomic DNA contamination.

treatment_protocol: After two days of normal feeding, individual 5th instar locusts received a single meal of 1.5% agar based artificial diet containing 2.4% Wesson salt mixture, 0.5% linoleïc acid, 0.6% cholesterol, 18.8% Vanderzant vitamin mixture, 50% cellulose, 14% dextrin, 8.1% caseïne, 2.8% peptone and 2.8% albumin. One group received a meal containing plant derived PI (SBTI, SBBI: 1% of total protein content), while another group received a control diet, where BSA was added to achieve equal total protein contents in the diets. 4 hours after ingestion of the meal, midgut and caeca samples were dissected for RNA extraction.

value: midgut and caeca

tag: diet

value: Control diet


title: day 4 Gr1+/Cx3cr1low biological replicate 1

description: Gene expression data of muscle-derived macrophages

tag: time


title: C3-C2

description: Control locust midgut/caeca sample replicate 3 vs Control locust midgut/caeca sample replicate 2


title: Normal_Fibroblasts_Vehicle_Patient_45

city: Madrid

first: Maria Jesus

last: Larriba

state: Madrid

address: Arturo Duperier 4

department: Cancer Biology

country: Spain

institute: Instituto de Investigaciones Biomedicas "Alberto Sols"

description: Gene expression profile of colon normal fibroblast primary culture established from patient 45 and treated with vehicle for 48 h

hyb_protocol: Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µl. Temperature (ºC): 65. Duration: 17 h.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. Normexp background subtraction was performed.

data_processing: Quantile normalization was performed using limma package available at Bioconductor

source_name: Colon normal fibroblasts, vehicle-treated, patient 45

label_protocol: Amount of nucleic acid labeled: 100 ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit following manufacturer's instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.

growth_protocol: Primary cultures of colon normal and tumor fibroblasts were established following the explant outgrowth technique from fresh surgical specimens of normal colon mucosa and colon primary tumor resected from colorectal cancer patients.

extract_protocol: Total RNA was extracted using the NucleoSpin miRNA extraction kit (Macherey-Nagel, Düren, Germany) following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary human colon normal and tumor fibroblasts cultured in Fibroblast Growth Medium 2 (Lonza, Basel, Switzerland) were treated with 1,25(OH)2D3 (Sigma-Aldrich, San Louis, MO) or vehicle (ethanol) and incubated for 48 h at 37 ºC in a humidified incubator with 5% CO2.

value: Vehicle

value: Colon normal fibroblasts

value: Patient 45


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_38

description: Gene expression profile of colon normal fibroblast primary culture established from patient 38 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 38

value: Patient 38


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_44

description: Gene expression profile of colon normal fibroblast primary culture established from patient 44 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 44

value: Patient 44


title: PI1-C3

description: Protease inhibitor-fed locust midgut/caeca sample replicate 1 vs Control locust midgut/caeca sample replicate 3

value: Protease inhibitor supplied diet


title: PI2-C3

description: Protease inhibitor-fed locust midgut/caeca sample replicate 2 vs Control locust midgut/caeca sample replicate 3


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_45

description: Gene expression profile of colon normal fibroblast primary culture established from patient 45 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 45


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_43

description: Gene expression profile of colon normal fibroblast primary culture established from patient 43 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 43

value: Patient 43


title: Normal_Fibroblasts_Vehicle_Patient_44

description: Gene expression profile of colon normal fibroblast primary culture established from patient 44 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 44


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_16

description: Gene expression profile of colon normal fibroblast primary culture established from patient 16 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 16

value: Patient 16


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_11

description: Gene expression profile of colon normal fibroblast primary culture established from patient 11 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 11

value: Patient 11


title: Normal_Fibroblasts_Vehicle_Patient_43

description: Gene expression profile of colon normal fibroblast primary culture established from patient 43 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 43


title: C3-PI3

description: Control locust midgut/caeca sample replicate 3 vs protease inhibitor-fed locust midgut/caeca sample replicate 3

source_name: Protease inhibitor-fed locust midgut/caeca sample replicate 3


title: C1-PI1

description: Control locust midgut/caeca sample replicate 1 vs protease inhibitor-fed locust midgut/caeca sample replicate 1

source_name: Protease inhibitor-fed locust midgut/caeca sample replicate 1


title: PI3-C1

description: Protease inhibitor-fed locust midgut/caeca sample replicate 3 vs Control locust midgut/caeca sample replicate 1


title: Normal_Fibroblasts_Vehicle_Patient_27

description: Gene expression profile of colon normal fibroblast primary culture established from patient 27 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 27

value: Patient 27


title: Normal_Fibroblasts_1,25(OH)2D3_Patient_27

description: Gene expression profile of colon normal fibroblast primary culture established from patient 27 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon normal fibroblasts, 1,25(OH)2D3-treated, patient 27


title: Normal_Fibroblasts_Vehicle_Patient_38

description: Gene expression profile of colon normal fibroblast primary culture established from patient 38 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 38


title: Ppr1 gain of function (GOF) mutant vs. wild type Replicate 2

status: Public on Apr 06 2016

city: Montreal

first: Walters

middle: Aji

last: Tebung

state: Quebec

address: 7141 Rue Sherbrooke Ouest

department: Chemistry and Biochemistry

country: Canada

institute: Concordia University

hyb_protocol: Microarray slides were hybridized with labeled cDNAs overnight at 42°C DIG easy Hyb solution (Roche) containing 0.5 ug/ul of Bakers tRNA and 0.5 ug/ul of salmon sperm DNA. The slides were washed twice with 1X SSC/0.1% SDS and 3 times with 0.1X SSC and spin dry.

scan_protocol: The scanning was done using GenePix4000B microarray scanner Images were quantified using GenePix Pro 7

data_processing: Normalized Red signal/normalized Green signal. GenePix Pro 7 software was used for image normalization and final normalization and inspection of the data was done using MultiExperiment Viewer.

organism: Candida albicans

source_name: Total RNA extracted from wild type

label_protocol: Direct cDNA labelling with Cy3-5 dCTP

growth_protocol: YPD medium at 30°C

extract_protocol: Total RNA extracted using QIAGEN RNeasy minikit protocol

value: Yeast cells

tag: genotype/variation

value: wild type

source_name: Total RNA extracted from Ppr1 GOF

value: Ppr1 gain of function (GOF) mutant


title: Ppr1 gain of function (GOF) mutant vs. wild type Replicate 1


title: WT vs mga2D 1.5h -O2 replicate 1

city: Baltimore

first: Risa

last: Burr

address: 725 N Wolfe St, Physiology 107B

department: Cell Biology

institute: Johns Hopkins University School of Medicine

description: Biological replicate 1 of 2. Exponentially growing mga2 delete S. pombe harvested after 1.5 hours hypoxia

hyb_protocol: 825 ng labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Arrays were scanned by Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 Software

data_processing: Features were examined and saved as Feature Extraction files using Agilent Feature Extraction software.  These data were imported into Partek Genomics Suite as the median of the arrays' three replicate probes' g/rProcessed signals.   These log2 signal values were quantile normalized and the dye-swapped samples compared in a 1-way ANOVA.

organism: Schizosaccharomyces pombe

source_name: ESY173 S. pombe

label_protocol: 400 ng total RNA was amplified and labeled using RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: Yeast were grown at log phase in complete (YES) media for 1.5hours -O2 in an in vivo anaerobic chamber.

extract_protocol: Total RNA was isolated using RNA STAT-60 reagent and chloroform followed by ethanol precipitation according to manufacturer’s instructions. RNA was treated with DNaseI to eliminate genomic DNA contamination.

source_name: KGY425 S. pombe


title: WT vs mga2D 1.5h -O2 replicate 2

description: Biological replicate 2 of 2. Exponentially growing mga2 delete S. pombe harvested after 1.5 hours hypoxia


title: C1-PI2

description: Control locust midgut/caeca sample replicate 1 vs protease inhibitor-fed locust midgut/caeca sample replicate 2

source_name: Protease inhibitor-fed locust midgut/caeca sample replicate 2


title: Normal_Fibroblasts_Vehicle_Patient_11

description: Gene expression profile of colon normal fibroblast primary culture established from patient 11 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 11


title: Glycerol control

first: Robert

middle: C

last: Angerer

address: 30 Convent Drive

institute: NIDCR

hyb_protocol: Hybridization was performed by Nimblegen.

scan_protocol: Scanning was performed by Nimlbegen.

data_processing:
Data processing was performed by Nimblegen.
Expression value were subject to RMA and quantile normalization.
The final normalized values were derived from the *RMA_calls.txt files. Because there were two blocks on the slide, the expression number was the average of two blocks and rounded. In addition, for each Seq_ID, there were 5 probes and the values were also averaged.

molecule: polyA RNA

organism: Strongylocentrotus purpuratus

source_name: Embryos injected with glycerol as control

label_protocol: Labeling was performed by Nimblegen.

growth_protocol: Sea urchin embryos were grown in 15 degree artificail sea water.

extract_protocol: Total RNA was extracted with Machere-Nagel NucleoSpin RNA II kit.

treatment_protocol: Fertilized eggs were injected with either glycerol or FoxQ2 morpholino oligo.

value: control

value: embryo

value: RNA extracted 27 hours post fertilization


title: Patient 30, Replicate 3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description:
SAMPLE 92
Normal bone marrow

hyb_protocol: Hybridization using standard hybridization protocols from Illumina.

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader.

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm.

source_name: Bone marrow stem cells, normal

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924).

extract_protocol: RNA was extracted using RNeasy Mini kit (Qiagen) including the DNaseI treatment.

tag: disease state

value: healthy

tag: age

value: adult

tag: population

value: Colombian

value: bone marrow stem cells

tag: patient identifier


title: Normal_Fibroblasts_Vehicle_Patient_16

description: Gene expression profile of colon normal fibroblast primary culture established from patient 16 and treated with vehicle for 48 h

source_name: Colon normal fibroblasts, vehicle-treated, patient 16

tag: treatment

value: Vehicle

tag: tissue

value: Colon normal fibroblasts


title: Patient 29, Replicate 1

description:
SAMPLE 88
Normal bone marrow

tag: cell type


title: FoxQ2 morpholino

source_name: Embryos injected with FoxQ2 morpholino oligo

value: FoxQ2 knockdown


title: Patient 30, Replicate 2

description:
SAMPLE 91
Normal bone marrow


title: Patient 30, Replicate 1

description:
SAMPLE 90
Normal bone marrow


title: Patient 29, Replicate 2

description:
SAMPLE 89
Normal bone marrow


title: Patient 27, Replicate 3

description: SAMPLE 84

source_name: Bone marrow stem cells, complete remission after inductive therapy

value: B-acute lymphoblastic leukemia (B-ALL)

value: inductive therapy

tag: response to therapy

value: complete remission


title: Patient 28, Replicate 3

description:
SAMPLE 87
Normal bone marrow


title: Patient 25, Replicate 2

description: SAMPLE 77


title: Patient 26, Replicate 2

description: SAMPLE 80


title: Patient 27, Replicate 1

description: SAMPLE 82


title: Patient 26, Replicate 3

description: SAMPLE 81


title: Patient 24, Replicate 2

description: SAMPLE 74


title: Patient 28, Replicate 2

description:
SAMPLE 86
Normal bone marrow


title: Patient 28, Replicate 1

description:
SAMPLE 85
Normal bone marrow


title: Patient 23, Replicate 2

description: SAMPLE 71


title: Patient 26, Replicate 1

description: SAMPLE 79


title: Patient 24, Replicate 1

description: SAMPLE 73


title: Patient 24, Replicate 3

description: SAMPLE 75


title: Patient 27, Replicate 2

description: SAMPLE 83


title: Patient 25, Replicate 1

description: SAMPLE 76


title: Patient 23, Replicate 3

description: SAMPLE 72


title: Patient 25, Replicate 3

description: SAMPLE 78


title: Patient 23, Replicate 1

description: SAMPLE 70


title: Patient 22, Replicate 2

description: SAMPLE 68


title: RPMI8402 TD with control repl 2

first: Inge

last: Van de Walle

address: De Pintelaan 185, blokA 4th floor

institute: UGent

description: Gene expression of RMPI8402 transduced with control

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

source_name: RMPI8402 transduced with control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: RPMI8402 cells were transduced with lentivirus for control, shGATA3 or shTCF1. Cells were harvested 48 h after treatment to sort for EGFP+

tag: cell line

tag: transduction


title: RPMI8402 TD with shTCF1 repl 2

description: Gene expression of RMPI8402 transduced with shTCF1

source_name: RMPI8402 transduced with shTCF1


title: RPMI8402 TD with control repl 1


title: Patient 21, Replicate 3

description: SAMPLE 66


title: Patient 22, Replicate 1

description: SAMPLE 67


title: Patient 22, Replicate 3

description: SAMPLE 69


title: Patient 20, Replicate 3

description: SAMPLE 63


title: Patient 20, Replicate 2

description: SAMPLE 62


title: Patient 21, Replicate 2

description: SAMPLE 65


title: CKO_6707_rep3

first: M. David

last: Stewart

address: 4800 Calhoun Rd

institute: University of Houston

hyb_protocol: Phalanx Biotech One Array Plus protocol.  Each sample was hybridized in triplicate.

scan_protocol: Agilent 0.1 XDR protocol

data_processing: Normalization was performed using median scaling normalization method

source_name: left ventricle

label_protocol: 5 micrograms Cy5-labelled total RNA

extract_protocol: Free wall left ventricular tissues were dissected in PBS and flash frozen in liquid nitrogen.  RNA was extracted using Trizol reagent.

value: heart (free wall left ventricle)

value: 6-weeks old

tag: genotype

value: aMHC-cre Tg/+; Hira flox/-


title: CKO_6672_rep3


title: RPMI8402 TD with shTCF1 repl 1


title: Patient 20, Replicate 1

description: SAMPLE 61


title: CKO_6672_rep1


title: CT CD34+ TD with control replicate 3

description: Gene expression 48h cultured on OP9-DL1, transduced CT34+ with LIE

source_name: 34+ TD control repl3 48h

growth_protocol: Transduced cells were cocultured on OP9-DL1 for 48h supplemented with IL7, SCF and Flt3L

treatment_protocol: Primary cells were transduced with retovirus for control or GATA3, 24h after pre-culture. Cells were harvested 24 h after treatment to initiate cocultures.

value: primary cells

value: control repl 3


title: CKO_6707_rep2


title: CKO_6672_rep2


title: Patient 1 after one month of inductive therapy, Replicate 2

description: SAMPLE 59

source_name: Bone marrow stem cells, no complete remission after inductive therapy

value: one month of inductive therapy

value: no complete remission


title: Patient 1 after one month of inductive therapy, Replicate 3

description: SAMPLE 60


title: Patient 19, Replicate 2

description: SAMPLE 56


title: Patient 19, Replicate 3

description: SAMPLE 57


title: Patient 21, Replicate 1

description: SAMPLE 64


title: RPMI8402 TD with shGATA3 repl 1

description: Gene expression of RMPI8402 transduced with shGATA3

source_name: RMPI8402 transduced with shGATA3


title: CKO_6707_rep1


title: CT CD34+ TD with GATA3 replicate 2

description: Gene expression 48h cultured on OP9-DL1, transduced CT34+ with GATA3

source_name: 34+ TD G3 repl2 48h

value: GATA3 repl 2


title: CT CD34+ TD with GATA3 replicate 3

source_name: 34+ TD G3 repl3 48h

value: GATA3 repl 3


title: Patient 1 after one month of inductive therapy, Replicate 1

description: SAMPLE 58

value: adult

value: Colombian


title: Patient 19, Replicate 1

description: SAMPLE 55

value: bone marrow stem cells


title: RPMI8402 TD with shGATA3 repl 2


title: Patient 18, Replicate 3

description: SAMPLE 54

source_name: Bone marrow stem cells, complete remission after inductive therapy-BCR/ABL+


title: Patient 18, Replicate 1

description: SAMPLE 52


title: CKO_6499_rep3


title: CT CD34+ TD with control replicate 2

source_name: 34+ TD control repl2 48h

value: control repl 2


title: Patient 17, Replicate 3

description: SAMPLE 51


title: Patient 17, Replicate 1

description: SAMPLE 49


title: Patient 17, Replicate 2

description: SAMPLE 50


title: Patient 16, Replicate 3

description: SAMPLE 48


title: CKO_6499_rep1


title: Patient 16, Replicate 1

description: SAMPLE 46


title: CT CD34+ TD with GATA3 replicate 1

source_name: 34+ TD G3 repl1 48h

value: GATA3 repl 1


title: CT CD34+ TD control replicate 1

source_name: 34+ TD control repl1 48h

value: control repl 1


title: CKO_6499_rep2


title: Patient 16, Replicate 2

description: SAMPLE 47

value: B-acute lymphoblastic leukemia (B-ALL)

value: inductive therapy


title: WFB_fibro

city: John Radcliffe hospital

first: Jenny

last: Wilding

state: Headington, Oxford

address: Weatherall institute of molecular medicine

department: oncology

institute: University of Oxford

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Partek® Genomic suite® software was used to generate normalized fluorescent intensities(log base 2)  using default software settings.

source_name: human skin fibroblast cell line

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

value: human skin fibroblast cell line

tag: source

value: skin fibroblast cell line


title: Patient 18, Replicate 2

description: SAMPLE 53

value: complete remission


title: JB_Fibro


title: CKO_6300_rep1

tag: strain

value: heart (free wall left ventricle)

value: 6-weeks old

value: aMHC-cre Tg/+; Hira flox/-


title: H_SKIN_fibro


title: Patient 15, Replicate 3

description: SAMPLE 45


title: Patient 15, Replicate 1

description: SAMPLE 43


title: Patient 15, Replicate 2

description: SAMPLE 44


title: Patient 14, Replicate 1

description: SAMPLE 40


title: Patient 14, Replicate 3

description: SAMPLE 42


title: H_F_Fibro

source_name: human foreskin fibroblast cell line

value: human foreskin fibroblast cell line

value: foreskin fibroblast cell line


title: Patient 14, Replicate 2

description: SAMPLE 41


title: control_6497_rep3

value: aMHC-cre Tg/+; Hira flox/+


title: Myo6024

source_name: human colonic myofibroblast primary culture

value: derived from macroscopically normal colon tissue


title: CKO_6300_rep2


title: CKO_6300_rep3


title: Patient 13, Replicate 3

description: SAMPLE 39

value: adult

value: Colombian


title: Patient 13, Replicate 2

description: SAMPLE 38

value: bone marrow stem cells


title: control_6497_rep2


title: control_6497_rep1


title: Patient 12, Replicate 3

description: SAMPLE 36


title: Patient 13, Replicate 1

description: SAMPLE 37


title: CCD18CO

value: human colonic myofibroblast primary culture


title: control_6675_rep3


title: Myo2020

value: derived from colorectal cancer


title: Patient 11, Replicate 2

description: SAMPLE 32

value: B-acute lymphoblastic leukemia (B-ALL)

value: no complete remission


title: Patient 12, Replicate 2

description: SAMPLE 35

value: inductive therapy


title: control_6675_rep1


title: MYO1998


title: Patient 10, Replicate 2

description: SAMPLE 29


title: Patient 12, Replicate 1

description: SAMPLE 34


title: Patient 11, Replicate 1

description: SAMPLE 31


title: Patient 11, Replicate 3

description: SAMPLE 33


title: Patient 10, Replicate 3

description: SAMPLE 30


title: Myo2156


title: control_6675_rep2


title: Patient 10, Replicate 1

description: SAMPLE 28


title: control_6299_rep3


title: Patient 9, Replicate 3

description: SAMPLE 27


title: Patient 9, Replicate 2

description: SAMPLE 26


title: xenograft tumor expressing PREX2 Q1430STOP replicate 3

first: Lynda

last: Chin

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: MD Anderson Cancer Center

description: gene expression experiment from xenograft tumors from primary melanocytes expressing mutant NRAS and respectively shown proteins

hyb_protocol: Performed according to Affymetrix protocols. Affmetrix GeneChip Human Genome U133 plus 2 arrays containing probe sets for >45,000 characterized genes and expressed sequence tags, were used. Approximately 12.5 μg of fragmented cRNA was used in a 250-μl hybridization mixture containing herring-sperm DNA (0.1 mg/ml; Promega), plus bacterial and phage cRNA controls (1.5 pM BioB, 5 pM BioC, 25 pM BioD, and 100 pM Cre) to serve as internal controls for hybridization efficiency. Aliquots (200 μl) of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin– phycoerythrin (Life Technologies) and amplified with biotinylated anti-streptavidin antibody (Vector Laboratories) on the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Performed according to Affymetrix protocols. Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities.

data_processing: Signal intensity and presence call data were derived with the MAS5 (Affymetrix) algorithm.

source_name: xenograft tumors

label_protocol: Performed according to Affymetrix protocols. Briefly, double-stranded cDNA was synthesized from total RNA with GeneChip 3’ IVT express kit (Affmetrix), with a T7 RNA polymerase promoter site added to its 3′ end (Genset, La Jolla, CA). Biotinylated cRNAs were generated from cDNAs in vitro and amplified by using GeneChip 3’ IVT express kit. After purification of cRNAs by the RNeasy mini kit (Qiagen, Hilden, Germany), 15 μg of cRNA was fragmented at 94°C for 35 min.

extract_protocol: Total RNA isolation was performed with the Qiagen RNeasy kit, according to the manufacturer’s instructions.

treatment_protocol: primary immortalized melanocytes harboring the indicated constructs were injected subcutaneously in ncr-nude mice. Tumors were harvested before 1.5cm growth reached.

value: primary xenograft tumor


title: xenograft tumor expressing PREX2 E824STOP replicate 3


title: Patient 9, Replicate 1

description: SAMPLE 25


title: control_6299_rep1


title: control_6706_rep3


title: Patient 8, Replicate 3

description: SAMPLE 24

source_name: Bone marrow stem cells, complete remission after inductive therapy

value: complete remission


title: xenograft tumor expressing PREX2 Q1430STOP replicate 2


title: control_6299_rep2

value: heart (free wall left ventricle)


title: control_6706_rep2

value: 6-weeks old


title: Patient 7, Replicate 3

description: SAMPLE 21


title: xenograft tumor expressing PREX2 Q1430STOP replicate 1


title: Patient 7, Replicate 1

description: SAMPLE 19


title: Patient 8, Replicate 1

description: SAMPLE 22


title: Patient 7, Replicate 2

description: SAMPLE 20


title: Patient 8, Replicate 2

description: SAMPLE 23


title: Patient 6, Replicate 3

description: SAMPLE 18


title: xenograft tumor expressing PREX2 E824STOP replicate 1


title: control_6706_rep1


title: xenograft tumor expressing PREX2 K278STOP replicate 3


title: xenograft tumor expressing PREX2 E824STOP replicate 2


title: ΔspdR x WT- rep4

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: Agilent protocol  Agilent protocol  Agilent protocol  Agilent protocol

scan_protocol: Agilent protocol  Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excell and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: WT- stationary phase

label_protocol: standard Cy3-dCTP and Cy5-dCTP incorporations  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation

growth_protocol: Overnight cultures were diluted in fresh complex medium to OD= 0.1

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

treatment_protocol: Cultures were grown for 24h after dilution

tag: sample type

value: NA1000 cells at stationary phase

value: WT

source_name: ΔspdR- stationary phase

value: ΔspdR

value: spdR mutant at stationary phase


title: xenograft tumor expressing PREX2 K278STOP replicate 2


title: Patient 5, Replicate 3

description: SAMPLE 15


title: Patient 5, Replicate 1

description: SAMPLE 13


title: ΔspdR x WT- rep2


title: xenograft tumor expressing PREX2 K278STOP replicate 1


title: Patient 3, Replicate 3

description: SAMPLE 9


title: Patient 4, Replicate 1

description: SAMPLE 10


title: xenograft tumor expressing PREX2 wt replicate 1


title: Patient 3, Replicate 1

description: SAMPLE 7


title: Patient 4, Replicate 3

description: SAMPLE 12


title: xenograft tumor expressing PREX2 wt replicate 3


title: ΔspdR x WT- rep3


title: Patient 2, Replicate 1

description: SAMPLE 4


title: Patient 6, Replicate 2

description: SAMPLE 17


title: Patient 2, Replicate 2

description: SAMPLE 5


title: Patient 1, Replicate 2

description: SAMPLE 2


title: xenograft tumor expressing GFP replicate 3


title: ΔspdR x WT- rep1


title: Patient 1, Replicate 3

description: SAMPLE 3


title: Patient 5, Replicate 2

description: SAMPLE 14


title: Patient 1, Replicate 1

description: SAMPLE 1


title: Patient 6, Replicate 1

description: SAMPLE 16


title: Patient 4, Replicate 2

description: SAMPLE 11


title: xenograft tumor expressing GFP replicate 1


title: Patient 3, Replicate 2

description: SAMPLE 8


title: xenograft tumor expressing PREX2 wt replicate 2


title: GB tissue 2

city: Geneva

first: Thanos

last: Halazonetis

state: GE

address: Sciences III, 30, quai Ernest-Ansermet

department: IDepartment of Molecular Biology

institute: University of Geneva

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) following the standard protocol of the manufacturer.

scan_protocol: Standard Affymetrix.

data_processing: RMA Probes to Import: Interrogating Probes, Probe filtering: skip,Algorithm: RMA,Background Correction: RMA Background Correction,Normalization: Quantile Normalization,Log Probes using Base: 2,Probeset Summarization: Median Polish

source_name: GB tissue

label_protocol: 5.5 ug of ds cDNA were fragmented and labeled using the GeneChip WT DNA terminal labeling kit.

growth_protocol: Organoids were cultured in Matrigel with tissue culture media based on AdDMEM/F12 (Life Technologies) and supplemented with B27, N2 (Life Technologies) and 1.25 uM N-Acetylcysteine (Sigma-Aldrich). The following growth factors were also added: 50 ng/mL murine recombinant EGF (Life Technologies), 50 ng/mL murine recombinant FGF10 (R&D system), 10 mM nicotinamide (Sigma-Aldrich), 50 ng/mL murine recombinant HGF (Peprotech) and R-spondin 1 and noggin home-made conditioned media (prepared as in Sato et al., Nature 459: 262-265, 2009).

extract_protocol: RNA was extracted from liver, gallbladder or small intestine tissues, and liver, gallbladder or small intestine organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).

treatment_protocol: Differentiated gallbladder organoids were obtained by culturing the organoids in media lacking R-spondin 1, noggin and nicotinamide for two weeks.

tag: tissue/cell type

value: GB tissue


title: xenograft tumor expressing GFP replicate 2


title: wild type in larval stage, biological rep2

city: Shanghai

first: Yan

last: Zhang

address: 294 Tai Yuan Road Shanghai, 200031 P.R.China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

hyb_protocol: Array hybridization and wash was performed using a GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#000331-220V, Affymetrix, Santa Clara, CA, US) and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned using a GeneChip Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Drosophila melanogaster

source_name: larva

label_protocol: Total RNA from fruit flies was amplified, labeled and purified by using a GeneChip 3 0 IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Fruit flies were raised at 25 1C and 60% relative humidity on cornmeal–yeast food.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: wild type

tag: developmental stage

value: larval stage


title: liver tissue 1

source_name: liver tissue

value: liver tissue


title: liver organoids 2

source_name: liver organoids

value: liver organoids


title: liver tissue 2


title: GB tissue 1


title: wild type in larval stage, biological rep1

tag: genotype/variation


title: intestine organoids 2

source_name: intestine organoids

value: intestine organoids


title: intestine organoids 1


title: intestine tissue 2

source_name: intestine tissue

value: intestine tissue


title: SPS2 knockdown in larval stage, biological rep2

value: SPS2 knockdown


title: SPS2 knockdown in larval stage, biological rep3


title: SPS2 knockdown in larval stage, biological rep1


title: wild type in adult stage, biological rep3

source_name: adult

value: adult stage


title: differentiated gallbladder organoid 1

source_name: differentiated gallbladder organoid

value: differentiated gallbladder organoid


title: gallbladder organoid 2

source_name: gallbladder organoid

value: gallbladder organoid


title: liver organoids 1


title: gallbladder organoid 1


title: wild type in adult stage, biological rep2


title: wild type in adult stage, biological rep1


title: 133A_Human Peripheral blood NK cells CD56Bright CD16-  Donor B

description: Corresponds to sample 14 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p5 Dim.

hyb_protocol: cRNA were hybridized on GeneChip Human HG-U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  D-chip software was used to analyze the data for the manuscript but the D-chip output was lost due to hard drive damage.

source_name: Human Peripheral blood NK cells CD56Bright CD16-  Donor B - Single donor

label_protocol: Fragmented and biotinylated cRNA hybridized and eluted from HGU95Av2 arrays ( Koopman et al JEM 2003) were kept frozen at -80C for 16 monrths and hybridized to HG-U133B arrays, the eluted material was frozen and hybridized 4 days later to HG-U133A arrays

extract_protocol: Trizol extraction as described in Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12

treatment_protocol: Ex vivo Decidual NK cells were extracted from 1st trimester decidual samples by DNAse-Collagenase digestion  and Flow Cytometry sorted as CD3- CD56Bright CD16- cells, Peripheral blood NK cells were isolated from leucopack  by enrichment with negatrive enrichment  antibody cocktail Rosette Sep NK ( Milteny Biotech) followed by flow cytometry sorting as CD3- CD56Bright CD16- cells (Peripheral blood NK cells CD56Bright CD16-) or CD3- CD56Dim CD16+ cells (Peripheral blood NK cells CD56Dim CD16+). For detailed methods see Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12.

value: NK cells

value: peripheral blood

tag: cell markers

value: CD56[Bright], CD16-


title: 133A_Human Peripheral blood NK cells CD56Dim CD16+  Donor B

description: Corresponds to sample 19 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample  p6 Bright.

source_name: Human Peripheral blood NK cells CD56Dim CD16+  Donor B - Single donor


title: SPS2 knockdown in adult stage, biological rep3


title: intestine tissue 1


title: 133A_Human Peripheral blood NK cells CD56Dim CD16+  pooled from 3 donors

description: Corresponds to sample18 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12).  Donors are the same as sample  p3p Bright.


title: 133A_Human Peripheral blood NK cells CD56Bright CD16-  pooled from 3 donors

description: Corresponds to sample 13 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donors are the same as sample p1p Dim.


title: differentiated gallbladder organoid 2


title: 133A_Human Peripheral blood NK cells CD56Bright CD16-  Donor A

description: Corresponds to sample 12 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p10Dim.

source_name: Human Peripheral blood NK cells CD56Bright CD16-  Donor A - Single donor


title: 133A_Human Peripheral blood NK cells CD56Dim CD16+  Donor A

description: Corresponds to sample 17 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p11Bright.

source_name: Human Peripheral blood NK cells CD56Dim CD16+  Donor A - Single donor


title: optA1_gpt_360 (High Dilution) Rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from optA1 gpt strain w/o hypoxanthine 360 min at high dilution protocol

hyb_protocol: 1 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

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

label_protocol: Total RNA was amplified as directed in the Affymetrix Prokaryotic Target Labeling Assay protocol.

growth_protocol: The strains were grown exponentially (after initiation by a 1,000-fold dilution from overnight cultures) for ~5 generations at 37°C in Vogel-Bonner (VB) minimal medium supplemented with glucose (0.4%), pantothenic acid (5 µg/ml), casamino acids (Becton-Dickenson) (1%), and hypoxanthine (50 µg/ml).

extract_protocol: At each time point, 15 ml of each culture was mixed with 30 ml of RNAprotect Bacteria Reagent (Qiagen), vortexed for 5s, incubated for 5 min at room temperature, and centrifuged for 10 min at 5000g.  The pellet was processed using a Qiagen RNeasy Midi kit with on-column DNase digestion using Qiagen DNase.  The final elution of RNA from the column was with 160 μl RNase-free water.

treatment_protocol: At OD630nm = 0.1, the cultures were filtered through 47-mm diameter polycarbonate membrane filter (0.4 µm pore size; Millipore), washed with the same medium without hypoxanthine (Hx), and then resuspended at the same cell density (OD630 = 0.1) in the medium without Hx, and growth was continued as before.  The OD630 was followed closely during the next two hours, and the cells were periodically diluted with fresh, pre-warmed medium without Hx to keep OD between values 0.1 and 0.3 (low-dilution protocol).  Samples were taken for microarray analysis (see below) at 0, 15, 30, 45, 60 and 120 minutes.  In a parallel procedure, the optA1 gpt double mutant was also followed in a near-identical manner using a more highly diluted culture over a six-hour incubation period in the absence of hypoxanthine (high-dilution protocol).  The effectiveness of the latter treatment was followed microscopically by observing the extensive cellular filamentation associated with dGTP starvation.


title: optA1_gpt_120 (Low Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 120 min at low dilution protocol


title: optA1_gpt_60 (Low Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 60 min at low dilution protocol


title: optA1_gpt_300 (High Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 300 min at high dilution protocol


title: 133A_Human Decidual NK cells sample 7

description: Corresponds to sample 8 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 6 weeks + 2 days pregnancy Single donor

value: Decidual NK cells

value: uterine endometrium


title: optA1_gpt_180 (High Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 180 min at high dilution protocol


title: SPS2 knockdown in adult stage, biological rep2


title: optA1_gpt_240 (High Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 240 min at high dilution protocol


title: optA1_gpt_45 (Low Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 45 min at low dilution protocol


title: 133A_Human Decidual NK cells sample 3

description: Corresponds to sample 5 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 7 weeks + 5 days pregnancy Single donor


title: 133A_Human Decidual NK cells sample 4

description: Corresponds to sample 6 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 7 weeks + 1 day pregnancy Single donor


title: optA1_gpt_180 (High Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 180 min at high dilution protocol


title: optA1_gpt_360 (Low Dilution) Rep2

description: Gene expression from optA1 gpt strain w/o hypoxanthine 360 min at low dilution protocol


title: optA1_gpt_45 (Low Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 45 min at low dilution protocol


title: optA1_gpt_0_Hx Rep3

description: Gene expression from optA1 gpt strain with hypoxanthine

source_name: optA1 gpt strain with hypoxanthine


title: optA1_gpt_360 (High Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 360 min at high dilution protocol


title: optA1_gpt_240 (High Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 240 min at high dilution protocol


title: optA1_gpt_120 (High Dilution) Rep2

description: Gene expression from optA1 gpt strain w/o hypoxanthine 120 min at high dilution protocol


title: optA1_gpt_120 (Low Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 120 min at low dilution protocol


title: optA1_gpt_120 (High Dilution) Rep3

source_name: optA1 gpt strain w/o hypoxanthine 120 min at high dilution protocol


title: optA1_gpt_30 (Low Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 30 min at low dilution protocol


title: optA1_gpt_15 (Low Dilution) Rep3

description: Gene expression from optA1 gpt strain w/o hypoxanthine 15 min at low dilution protocol


title: 133A_Human Decidual NK cells sample 8

description: Corresponds to sample 9 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 5 to 6  weeks  Single donor


title: optA1_gpt_300 (High Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 300 min at high dilution protocol


title: optA1_gpt_30 (Low Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 30 min at low dilution protocol


title: SPS2 knockdown in adult stage, biological rep1

source_name: adult


title: optA1_gpt_60 (Low Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 60 min at low dilution protocol


title: optA1_gpt_300 (High Dilution) Rep1


title: optA1_gpt_360 (High Dilution) Rep1


title: optA1_gpt_0_Hx Rep2


title: optA1_gpt_15 (Low Dilution) Rep2

source_name: optA1 gpt strain w/o hypoxanthine 15 min at low dilution protocol


title: optA1_gpt_360 (Low Dilution) Rep1

source_name: optA1 gpt strain w/o hypoxanthine 360 min at low dilution protocol


title: optA1_gpt_240 (High Dilution) Rep1


title: 2/3PH 6H (s01m76)

first: Zhikun

last: Liu

address: Qingchun Road 79#

institute: Zhejiang University

hyb_protocol: Each slide was hybridized with 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit in hybridization Oven (Agilent Technologies) at 55°C, 20rpm for 20 hours according to the manufacturer’s instructions for hybridization.

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent Technologies), and Feature Extraction software 10.7 (Agilent Technologies) was used with the default settings.

data_processing: Raw data were normalized against the Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies).

organism: Rattus norvegicus

source_name: 2/3PH 6H remnant liver

label_protocol: The molecular miRNA within the total RNA was labeled by the miRNA Complete Labeling and Hyb Kit (Agilent Technologies) followed the manufacturer’s instructions for labeling.

growth_protocol: remnant liver after partial hepatectomy

extract_protocol: Total RNA was extracted and purified using the mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions and was confirmed for the RIN number to inspect RNA integration using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The left lateral lobe, which accounts for 30% of the total liver mass, was removed for 1/3 PH. In addition, 2/3 PH surgeries were performed as originally described. The regenerating lobes (right lobes) were harvested 6, 12, 24, or 36 hours after surgery. The right lobes of 3 rats without PH were also harvested as the normal controls. To avoid differences related to circadian rhythms in miRNA expression, liver harvest was performed between 8 a.m. and 12 p.m.

tag: gender

value: male

tag: protocol

tag: time

value: 6 hours after surgery

value: liver


title: 1/3PH 12H (s02m2)

source_name: 1/3PH 12H remnant liver

value: 12 hours after surgery


title: 2/3PH 12H (s02m3)

source_name: 2/3PH 12H remnant liver


title: 1/3PH 12H (s02m5m)


title: 2/3PH 6H (s01m70B)


title: optA1_gpt_120 (Low Dilution) Rep1


title: 1/3PH 12H (s02m6)


title: optA1_gpt_180 (High Dilution) Rep1

source_name: optA1 gpt strain w/o hypoxanthine 180 min at high dilution protocol


title: optA1_gpt_360 (Low Dilution) Rep3


title: 2/3PH 6H (s01m67)


title: optA1_gpt_30 (Low Dilution) Rep1


title: gpt_60 (Low Dilution) Rep3

description: Gene expression from gpt strain w/o hypoxanthine 60 min at low dilution protocol


title: optA1_gpt_15 (Low Dilution) Rep1


title: optA1_gpt_0_Hx Rep1


title: optA1_gpt_60 (Low Dilution) Rep1


title: gpt_45 (Low Dilution) Rep3

description: Gene expression from gpt strain w/o hypoxanthine 45 min at low dilution protocol


title: gpt_120 (Low Dilution) Rep3

description: Gene expression from gpt strain w/o hypoxanthine 120 min at low dilution protocol


title: gpt_30 (Low Dilution) Rep3

description: Gene expression from gpt strain w/o hypoxanthine 30 min at low dilution protocol


title: optA1_gpt_120 (High Dilution) Rep1


title: 1/3PH 6H (s01m64)

source_name: 1/3PH 6H remnant liver


title: 1/3PH 6H (s01m62)


title: gpt_15 (Low Dilution) Rep3

description: Gene expression from gpt strain w/o hypoxanthine 15 min at low dilution protocol


title: normal 3

source_name: normal liver

value: sham

value: control


title: optA1_gpt_45 (Low Dilution) Rep1

source_name: optA1 gpt strain w/o hypoxanthine 45 min at low dilution protocol


title: gpt_0_Hx Rep3

description: Gene expression from gpt strain with hypoxanthine

source_name: gpt strain with hypoxanthine


title: gpt_120 (Low Dilution) Rep2

source_name: gpt strain w/o hypoxanthine 120 min at low dilution protocol


title: 1/3PH 36H (s04m47)

source_name: 1/3PH 38H remnant liver

value: 36 hours after surgery


title: gpt_60 (Low Dilution) Rep2

source_name: gpt strain w/o hypoxanthine 60 min at low dilution protocol


title: gpt_0_Hx Rep2


title: 2/3PH 36H (s04m39B)

source_name: 2/3PH 37H remnant liver


title: normal 1


title: 2/3PH 36H (s04m37B)

source_name: 2/3PH 36H remnant liver


title: 2/3PH 36H (s04m40)

source_name: 2/3PH 38H remnant liver


title: gpt_45 (Low Dilution) Rep2

source_name: gpt strain w/o hypoxanthine 45 min at low dilution protocol


title: gpt_120 (Low Dilution) Rep1


title: 2/3PH 24H (s03m31B)

source_name: 2/3PH 26H remnant liver

value: 24 hours after surgery


title: 2/3PH 24H (s03m29B)

source_name: 2/3PH 25H remnant liver


title: 1/3PH 36H (s04m45B)

source_name: 1/3PH 36H remnant liver


title: gpt_15 (Low Dilution) Rep2

source_name: gpt strain w/o hypoxanthine 15 min at low dilution protocol


title: gpt_30 (Low Dilution) Rep1

source_name: gpt strain w/o hypoxanthine 30 min at low dilution protocol


title: 2/3PH 24H (s03m26)

source_name: 2/3PH 24H remnant liver


title: normal 2


title: gpt_60 (Low Dilution) Rep1


title: gpt_15 (Low Dilution) Rep1


title: 1/3PH 24H (s03m24)

source_name: 1/3PH 26H remnant liver


title: wild type in larval stage, biological rep3

source_name: larva

value: wild type

value: larval stage


title: Patient 2, Replicate 3

description: SAMPLE 6

source_name: Bone marrow stem cells, complete remission after inductive therapy

tag: disease state

value: B-acute lymphoblastic leukemia (B-ALL)

tag: age

value: adult

tag: population

value: Colombian

value: bone marrow stem cells

tag: treatment

value: inductive therapy

value: complete remission

tag: patient identifier


title: hypoxia ketamine replicate 4

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

description: SAMPLE 16; HK4

hyb_protocol: This was performed following protocols from Agilent. Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and  hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida. Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis, resulting in 9301 data rows.

data_processing: Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays.  To identify the genes that were differentially regulated (DR) between groups, the normalized and transformed intensities were analyzed by moderated t-test using empirical Bayes method for small sample size per group (p<0.05).   Analyses were carried out using Bioconductor's Limma Package for R software v. 2.15.1.

organism: Ovis aries

source_name: fetal cerebral cortex 24 hrs after onset of 30 min hypoxia and intravenous injection of ketamine

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.4 to 14.4 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the cerebral cortex using Trizol (Invitrogen, Carlsbad, CA) , followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA).The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.  RNA Integrity Number (RIN) values ranged from 7.7 to 9.2.

treatment_protocol: Chronically catheterized late gestation fetal sheep were subjected to transient (30 min) maternal ventilatory hypoxia without (n=5) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) or to normoxia without (n=3) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) followed by 23.5 h normoxia.  Fetal frontal cerebral cortex was collected at the end of normoxia recovery period.

value: late gestation fetal sheep

tag: pretreated with

value: ketamine (3 mg/kg, iv)

tag: subjected to

tag: time point

value: 24 hours after onset of 30 min hypoxia

tag: tissue

value: fetal frontal cerebral cortex


title: optA1_120 (Low Dilution) Rep3

description: Gene expression from optA1 strain w/o hypoxanthine 120 min at low dilution protocol

tag: strain


title: gpt_0_Hx Rep1

source_name: gpt strain with hypoxanthine


title: hypoxia ketamine replicate 3

description: SAMPLE 15; HK3

value: transient (30 min) maternal ventilatory hypoxia


title: 1/3PH 24H (s03m23)

source_name: 1/3PH 25H remnant liver

value: male

value: liver


title: gpt_45 (Low Dilution) Rep1


title: 1/3PH 24H (s03m20)

source_name: 1/3PH 24H remnant liver


title: optA1_60 (Low Dilution) Rep3

description: Gene expression from optA1 strain w/o hypoxanthine 60 min at low dilution protocol


title: 2/3PH 12H (s02m12B)

source_name: 2/3PH 14H remnant liver

value: 12 hours after surgery


title: 2/3PH 12H (s02m7)

source_name: 2/3PH 13H remnant liver


title: optA1_15 (Low Dilution) Rep3

description: Gene expression from optA1 strain w/o hypoxanthine 15 min at low dilution protocol


title: optA1_30 (Low Dilution) Rep3

description: Gene expression from optA1 strain w/o hypoxanthine 30 min at low dilution protocol


title: optA1_120 (Low Dilution) Rep2

source_name: optA1 strain w/o hypoxanthine 120 min at low dilution protocol


title: hypoxia control (no ketamine) replicate 3

description: SAMPLE 10; HC3

source_name: fetal cerebral cortex 24 hrs after onset of 30 min hypoxia