title: pro-B_meninko_rep4

city: Hanover

first: Bin

middle: E

last: Li

state: New Hampshire

address: Remsen 725

department: Genetics

institute: Dartmouth College

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
Menin-deficient pro-B biological replicate 4

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Intensities were determined with Microarray Suite version 5.0 (Affymetrix), normalized using GCRMA (BRB-ArrayTools v4.2.1) and differentially-expressed probe sets were determined by class comparison using unfiltered expression values with fold-change cut-off of 1.2. A P-value cut-off of 0.001 was used to keep the FDR < 20%.

source_name: Menin-deficient pro-B

label_protocol: RNA was labeled with Biotin using BioArray HighYield RNA Transcript Labeling Kits (T7, Enzo Life Sciences)

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed and RNA was isolated using Qiagen RNeasy column and amplified using MessageAmp™II aRNA Amplification Kits (Ambion),

value: 2-3 weeks old

value: bone marrow

value: Fraction B cells B220+CD43+HSA+BP-1-

tag: genotype/variation

value: Menin-deficient


title: pro-B_meninko_rep2

status: Public on Aug 05 2013

type: RNA

country: USA

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
Menin-deficient pro-B biological replicate 2

label: biotin

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue

tag: cell type


title: pro-B_wt_rep3

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
control pro-B biological replicate 3

source_name: control pro-B

value: control


title: pro-B_wt_rep2

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
control pro-B biological replicate 2


title: pro-B_meninko_rep3

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
Menin-deficient pro-B biological replicate 3


title: pro-B_meninko_rep1

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
Menin-deficient pro-B biological replicate 1


title: DAY1KO biological replicate 4

city: Baltimore

first: Susan

middle: G

last: Dorsey

state: MD

address: 655 West Lombard Street

department: School of Nursing

institute: University of Maryland Baltimore

description:
Gene expression
D1KO38

hyb_protocol: Following fragmentation, 10ug cRNA was hybridized for 16hr at 45c

scan_protocol: Genechips were scanned per Affymetrix instructions

data_processing: The data were normalized by gcrma R package using GCRMA method.

source_name: Day 1 AFTER SCI

label_protocol: Biotinylated cRNA was prepared according to Affymetrix standard protocols from 1ug RNA

extract_protocol: Trizol extraction of total RNA performed according to manufacturer instructions

treatment_protocol: Sham or moderate contusion injury

tag: strain

value: C57BL/6J (greater than N20 generation)

value: Thoracic spinal cord

value: trkB.T1 KO

value: 8 - 12 weeks

tag: stress

value: SCI

tag: time

value: Day 1


title: DAY1WT biological replicate 5

description:
Gene expression
D1WT42

value: trkB.T1 WT


title: pro-B_wt_rep1

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
control pro-B biological replicate 1


title: DAY1KO biological replicate 1

description:
Gene expression
D1KO35


title: DGM-01774_M0_sm

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: gene expression

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Homo sapiens

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: nonsmoker


title: DGM-11113_M0_sm

description: gene expression

value: smoker

tag: cilia length


title: pro-B_wt_rep4

description:
Gene expression data from BM Fraction B cells B220+CD43+HSA+BP-1-
control pro-B biological replicate 4


title: DAY1WT biological replicate 3

description:
Gene expression
D1WT38


title: DGM-10986_M0_sm

description: gene expression


title: DGM-11021_M0_sm

description: gene expression


title: DAY1KO biological replicate 3

description:
Gene expression
D1KO37


title: DAY1WT biological replicate 4

description:
Gene expression
D1WT39


title: DGM-10704_M0_sm

description: gene expression


title: DAY1KO biological replicate 2

description:
Gene expression
D1KO36


title: SHAMKO biological replicate 2

description:
Gene expression
NavKO2

source_name: SHAM

value: baseline (sham)


title: DGM-11083_M0_sm

description: gene expression


title: DGM-10662_M0_sm

description: gene expression


title: DGM-10922_M0_sm

description: gene expression


title: SHAMKO biological replicate 4

description:
Gene expression
NavKO4


title: SHAMKO biological replicate 3

description:
Gene expression
NavKO3


title: DGM-10906_M0_sm

description: gene expression


title: DGM-11068_M0_sm

description: gene expression


title: DGM-10731_M0_sm

description: gene expression


title: DGM-10475_M0_sm

description: gene expression


title: SHAMKO biological replicate 1

description:
Gene expression
NavKO1


title: SHAMWT biological replicate 4

description:
Gene expression
NavWT4


title: DGM-10851_M0_sm

description: gene expression


title: DAY1WT biological replicate 2

description:
Gene expression
D1WT37


title: SHAMWT biological replicate 1

description:
Gene expression
NavWT1


title: SHAMWT biological replicate 2

description:
Gene expression
NavWT2


title: DAY7KO biological replicate 3

description:
Gene expression
D7KO29

source_name: Day 7 AFTER SCI

value: Day 7


title: Pulmonary fibroblasts_Usual Interstitial Pneumonia_ biological rep2

city: London

first: Carmel

last: Stock

address: 1b Manresa Road

department: Interstitial Lung Disease

country: United Kingdom

institute: National Heart and Lung Institute

description: Gene expression data from pulmonary fibroblasts in individuals with Usual Interstitial Pneumonia.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Homo sapiens U133A1. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 30007G scanner.

data_processing: The data were analyzed with dCHIP using the invariant set normalisation method.

label: Biotin

source_name: Primary pulmonary fibroblasts from Usual Interstitial Pneumonia patient 2

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

growth_protocol: Primary fibroblasts were cultured from lung biopsies as previously described (Abraham, D.J., et al. J.Biol.Chem 2000;275:15220-25).

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

treatment_protocol: Prior to RNA extraction confluent cultures were serum-deprived for 42 hours (media changed at 18 hours) in 0.1% bovine serum albumin.

value: Pulmonary fibroblasts

tag: disease status

value: Usual Interstitial Pneumonia


title: DAY7KO biological replicate 1

description:
Gene expression
D7KO27


title: DGM-10768_M0_sm

description: gene expression


title: DGM-10886_M0_sm

description: gene expression


title: DGM-10901_M0_sm

description: gene expression


title: SHAMWT biological replicate 3

description:
Gene expression
NavWT3


title: DAY7WT biological replicate 2

description:
Gene expression
D7WT29


title: DAY7WT biological replicate 3

description:
Gene expression
D7WT31


title: DGM-10500_M0_sm

description: gene expression


title: DAY7KO biological replicate 4

description:
Gene expression
D7KO30


title: Pulmonary fibroblasts_Usual Interstitial Pneumonia_ biological rep3

source_name: Primary pulmonary fibroblasts from Usual Interstitial Pneumonia patient 3


title: DAY7WT biological replicate 4

description:
Gene expression
D7WT43


title: DGM-10661_M0_sm

description: gene expression


title: DGM-10435_M0_sm

description: gene expression


title: DGM-10503_M0_sm

description: gene expression


title: DAY7KO biological replicate 2

description:
Gene expression
D7KO28


title: DGM-10573_M0_sm

description: gene expression


title: DAY1WT biological replicate 1

description:
Gene expression
D1WT36


title: DGM-10194_M0_sm

description: gene expression


title: DAY3KO biological replicate 4

description:
Gene expression
D3KO34

source_name: Day 3 AFTER SCI

value: Day 3


title: Pulmonary fibroblasts_control individual_ biological rep6

description: Gene expression data from pulmonary fibroblasts in individuals without lung disease.

source_name: Primary pulmonary fibroblasts from control individual 6

value: Control


title: DAY3KO biological replicate 1

description:
Gene expression
D3KO31


title: DAY3KO biological replicate 2

description:
Gene expression
D3KO32


title: HL60-undifferentiated

type: SAGE

anchor: NlaIII

city: Riaydh

first: Anason

last: Halees

department: Research Center

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

data_processing: Transformants were analyzed by colony PCR. Approximately 4000-5000 clones for each library were cycle sequenced using M13 forward primer and analyzed on Applied Biosystems DNA Sequencer. Approximately 20-25 individual tags were produced per clone. Sequences were analyzed using SAGE analysis software version 4.5 (Johns Hopkins University, Baltimore, MD, USA) and annotated using the downloadable reference sequence database SAGEmap.

molecule: polyA RNA

source_name: Acute promyelocytic lukemia HL-60 cell line (Catalog No.CCL-240)

growth_protocol: HL60 and KG1 cell were maintained in complete Iscoves Modified Medium (ATCC catalog No.30-2005) supplemented with 10% fetal bovine serum (ATCC catalog No. 30-2020), penicillin (100U/ml), and streptomycin (100µg/ml), at 37 degrees C and 5% CO2. Neutrophiles were maintained in Krebs-HEPES + BSA.

extract_protocol: Total cellular RNA was isolated from differentiated and from undifferentiated cell lines and human naïve neutrophils using tri-Reagent (MRC, Cincinati, OH) following manufacturer’s instructions. RNA integrity was routinely checked using 500 ng/ml of RNA on 1%  denaturing agarose gel. SAGE was performed according to the Serial Analysis of Gene Expression detailed Protocol Version C, with Nla III as the digestion enzyme, Mme as the tagging enzyme.

treatment_protocol: HL60 cells were differentiated with 1.3% DMSO (Sigma catalog No. D4540) in complete media for 6-8 days with media change every 3rd day. KG60 cells were differentiated with PMA (100ng/ml) for 5 days.

tag: cell line

value: Acute promyelocytic lukemia

tag: status

value: Undifferentiated


title: DAY7WT biological replicate 1

description:
Gene expression
D7WT28

value: C57BL/6J (greater than N20 generation)


title: DGM-10270_M0_sm

description: gene expression


title: HL60-DMSO_differentiated

value: Differentiated


title: DGM-10565_M0_sm

description: gene expression


title: KG1-undifferentiated

source_name: Acute mylogenous lukemia KG-1 cell line  (Catalog No.CCL-246)

value: Acute mylogenous lukemia


title: DGM-10380_M0_sm

description: gene expression


title: DGM-10213_M0_sm

description: gene expression


title: DGM-10288_M0_sm

description: gene expression


title: DAY3KO biological replicate 5

description:
Gene expression
D3KO39

value: Thoracic spinal cord

value: trkB.T1 KO

value: 8 - 12 weeks


title: Spleen, control diet fed for 1day, biological replicate 1

city: Nasushiobara

first: Yuichiro

last: Fukui

state: Tochigi

address: 17 Nishitomiyama

department: Nature & Wellness Research Department

country: Japan

institute: Research Institute, Kagome Co., Ltd.

hyb_protocol: After fragmenting, 12.5 µg aRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip mouse genome 430 2.0 array (Affymetrix) GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Robust Microarray Summarization (FARMS) algorithm, using the statistical language R and Bioconductor.

source_name: Spleen, fed control diet for 1day

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Tokyo, Japan)..

treatment_protocol: Spleens were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan) at 4˚C overnight.

tag: gender

value: Female

value: BALB/c

value: 9 weeks

value: Spleen

tag: diet

value: diet containing potato starch


title: Naiive_Netrophiles

source_name: Peripheral blood neutrophils

value: Neutrophils

value: Naiive


title: KG1-PMA_differentiated


title: DAY3WT biological replicate 4

description:
Gene expression
D3WT35

value: trkB.T1 WT

value: SCI

value: Day 3


title: DAY3KO biological replicate 3

description:
Gene expression
D3KO33


title: ATCC 17978 vs 17978hm Technical repeat

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

description: Technical repeat sample 3

hyb_protocol: The Ramaciotti Centre, UNSW, Sydney

scan_protocol: The Ramaciotti Centre, UNSW, Sydney

data_processing: The data obtained from replicate probes per gene was processed using Agilent Genespring GX version 9. The processed data was subseqeuntly analyzed using the Significance Analysis of Micrroarray data (Tusher et al. 2001) with a false discovery rate of less than 5%.

organism: Acinetobacter baumannii

source_name: Untreated cells

label_protocol: Cy3 and Cy5 labelling using Agilent Fairplay Microarray Labelling kit (Stratagene)

growth_protocol: 0.25% agar + Mueller-Hinton medium 8hrs

extract_protocol: Total RNA was purified using TriZol extraction followed by spin-column purification and on-column DNAseI treatment (all Invitrogen).

value: wild type

source_name: Motile cells

value: knockout derivative of strain ATCC17978

tag: phenotype

value: hyper-motile on semi-solid MH media


title: DGM-10254_M0_sm

description: gene expression

value: nonsmoker


title: DGM-10343_M0_sm

description: gene expression


title: DGM-10161_M0_sm

description: gene expression


title: DAY3WT biological replicate 2

description:
Gene expression
D3WT33

value: C57BL/6J (greater than N20 generation)

value: Thoracic spinal cord


title: CNT, biological rep. 3

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned  with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.

organism: Rattus norvegicus

source_name: Spinal cord dissociated cultures on CNT

label_protocol: A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.

growth_protocol: Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.

value: Sprague-Dawley

value: Spinal cord dissociated cultures


title: DAY3WT biological replicate 3

description:
Gene expression
D3WT34

value: 8 - 12 weeks


title: polyornithine, biological rep. 2

source_name: Spinal cord dissociated cultures on polyornithine


title: CNT, biological rep. 1


title: CNT, biological rep. 2


title: DAY3WT biological replicate 1

description:
Gene expression
D3WT32


title: DGM-10159_M0_sm

description: gene expression


title: polyornithine, biological rep. 3


title: ATCC 17978 vs 17978hm Replicate 1


title: polyornithine, biological rep. 1


title: ATCC 17978 vs 17978hm Replicate 2


title: EpiLCs, 48H, amp, rep2

status: Public on Aug 04 2013

city: Kyoto

first: Fumio

last: NAKAKI

address: Yoshidakonoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

description: Male, C57BL/6, Blimp1-mVenus, stella-ECFP

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

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

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings.

source_name: EpiLCs, 48H

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: Transfected ESCs were maintained under 2i+LIF condition and adapted to a feeder-free condition prior to induction. EpiLC differentiation was performed as reported previously (Hayashi et al., Cell, 2011).

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

treatment_protocol: After 36 hrs of differentiation, cells were harvested and cultured in a Lipidure-Coat 96-well plate (NOF) to be aggregated (started with 2,000 cells/well) in GK15 with 1.5 μg/ml of Dox (Clonetech) to induce TF-PGCLCs. Ck-PGCLCs were induced by BMP4 (500 ng/ml), BMP8A (500 ng/ml), SCF (100 ng/ml), LIF (1000 U/ml) and EGF (50 ng/ml) as previously described (Hayashi et al., Cell, 2011)

value: Male

tag: genetic background

tag: transgene

value: Blimp1-mVenus, stella-ECFP

value: EpiLCs


title: 2i+LIF ESCs, amp, rep2

source_name: 2i+LIF ESCs

value: 2i+LIF ESCs


title: Ck-PGCLCs, day6, amp, rep2

source_name: Ck-PGCLCs, day6

value: Ck-PGCLCs


title: Epiblast, E5.5, amp, rep2

description: unknown sex, C57BL/6

source_name: Epiblast, E5.5

value: unknown sex

value: unknown sex, C57BL/6

value: Epiblast


title: ATCC 17978 vs 17978hm Replicate 3

tag: genotype/variation

value: wild type


title: PGCs, E9.5, amp, rep2

description: unknown sex, C57BL/6, stella-EGFP

source_name: PGCs, E9.5

value: stella-EGFP

value: PGCs


title: EpiLCs, A (clone #8-2), 36H, rep1

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring V5-Tfap2c transgenes, differentiation time 36H

treatment_protocol: After 36 hrs of differentiation, cells were harvested and cultured in a Lipidure-Coat 96-well plate (NOF) to be aggregated (started with 2,000 cells/well) in GK15 with 1.5 μg/ml of Dox (Clonetech). After 24 hrs aggregation culture, whole cells from the aggregates were harvested.

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,


title: Epiblast, E5.5, amp, rep1

description: unknown sex, C57BL/6


title: BP14A (clone #3-3) +Doxycycline, day1, rep2

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1, 3xFLAG-Prdm14, V5-Tfap2c transgenes, cultured with doxycycline

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,


title: EpiLCs, P14 (clone #7-109), 36H, rep1

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring 3xFLAG-Prdm14 transgenes, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector


title: PGCs, E9.5, amp, rep1

description: unknown sex, C57BL/6, stella-EGFP


title: EpiLCs, Parental clone, 36H, rep1

source_name: EpiLCs induced from BVSCR26rtTA ESCs, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA


title: A (clone #8-2) +Doxycycline, day1, rep2

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring V5-Tfap2c transgenes, cultured with doxycycline


title: EpiLCs, BP14A (clone #3-3), 36H, rep1

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1, 3xFLAG-Prdm14, V5-Tfap2c transgenes, differentiation time 36H


title: EpiLCs, 48H, amp, rep1


title: DGM-10123_M0_sm

description: gene expression

source_name: small airway epithelium brushing

value: nonsmoker


title: Ck-PGCLCs, day6, amp, rep1


title: 2i+LIF BP14A-ESCs, amp, rep2

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,

source_name: BVSCR26rtTA BP14A ESCs under 2i+LIF condition

value: 2i+LIF BP14A-ESCs


title: BP14A-ESC+Dox, day2, SC+, amp, rep2

source_name: BVSCR26rtTA BP14A ESCs+Dox, day2, stella-ECFP positive cells

value: Male

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector


title: P14 (clone #7-109) +Doxycycline, day1, rep2

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring 3xFLAG-Prdm14 transgenes, cultured with doxycycline


title: Parental clone +Doxycycline, day1, rep2

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, cultured with doxycycline


title: EpiLCs, B (clone #2-4), 36H, rep1

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1 transgenes, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector


title: 2i+LIF ESCs, amp, rep1

value: Blimp1-mVenus, stella-ECFP

value: 2i+LIF ESCs


title: 2i+LIF BP14A-ESCs, amp, rep1


title: Ck-PGCLCs, Parental clone, day4, amp, rep1

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA

source_name: Ck-PGCLCs induced from BVSCR26rtTA ESCs, day4

value: Ck-PGCLCs


title: Parental clone +Doxycycline, day2, amp, rep2

source_name: BVSCR26rtTA ESCs +Doxycycline, day2

value: Parental ESCs clone


title: Ck-PGCLCs, Parental clone, day4, amp, rep2


title: BP14A-ESC+Dox, day2, SC+, amp, rep1


title: TF-PGCLCs, P14, day2, amp, rep2

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector

source_name: TF-PGCLCs induced from BVSCR26rtTA ESCs by Prdm14, day 2

value: TF-PGCLCs


title: Parental clone +Doxycycline, day2, amp, rep1


title: TF-PGCLCs, BP14, day2, amp, rep1

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector

source_name: TF-PGCLCs induced from BVSCR26rtTA ESCs by Blimp1 and Prdm14, day 2


title: TF-PGCLCs, P14, day2, amp, rep1


title: DGM-10869_M0_sm

description: gene expression

value: smoker


title: EpiLCs, Parental clone, 36H, amp, rep2

value: EpiLCs


title: 02_SRSF3si

city: Tokushima

first: Ken

last: Kurokawa

address: 3-18-15 Kuramoto

department: Health Biosciences

institute: The University of Tokushima Graduate School

hyb_protocol: Cy3-labeled cRNA was hybridized to whole human genome oligoDNA microarray (4x44k; Agilent) using GE Hybridization Kit (P/N 5188-5242) and and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) according to the manufacturer’s instructions.

scan_protocol: Microarray was scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent’s Feature Extraction software, version 10 (P/N G2567AA).

data_processing: Raw data output was imported into GeneSpring GX10 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization), and normalized each probe to the median expression of matched control intensity for that gene across all samples (per gene normalization).

label_protocol: For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Quick Amp Labeling Kit and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: Total RNA was extracted using a RNeasy mini kit (Qiagen, Valencia, CA). The quality of the purified RNA and its applicability for microarray analysis were assessed by the Agilent 2100 Bioanalyzer using a RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: treatment

value: SRSF3 siRNA


title: TF-PGCLCs, BP14, day2, amp, rep2

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector


title: TF-PGCLCs, BP14A, day4, amp, rep1

source_name: TF-PGCLCs induced from BVSCR26rtTA ESCs by Blimp1, Prdm14, and Tfap2c, day 4


title: TF-PGCLCs, P14A, day2, amp, rep1

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector

source_name: TF-PGCLCs induced from BVSCR26rtTA ESCs by Prdm14 and Tfap2c, day 2


title: EpiLCs, Parental clone, 36H, amp, rep1


title: TF-PGCLCs, P14A, day2, amp, rep2

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector


title: 01_Controlsi

value: control siRNA


title: TF-PGCLCs, BP14A, day2, amp, rep2

source_name: TF-PGCLCs induced from BVSCR26rtTA ESCs by Blimp1, Prdm14, and Tfap2c, day 2


title: Pancreatic Cancer PBMC Sample 3

status: Public on Aug 03 2013

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression data from PBMC sample of pancreatic cancer patient.

hyb_protocol: The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

data_processing: The data was analysed using Partek Genomics Suite version 6.6. CEL files were imported into Partek with GCRMA background correction, quantile normalisation and log2 transformation.

source_name: PBMC sample from pancreatic cancer patient

label_protocol: Five micrograms of total RNA were reverse-transcribed and labeled with biotin.

growth_protocol: Patients with primary pancreatic, gastric or HCC were recruited at diagnosis. Informed consent was obtained from all subjects before blood samples were collected. A total of 10 ml of blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

extract_protocol: Total RNA was extracted from PBMC and WBC using TRIzol reagent (Invitrogen, USA) according to the manufacturer's protocol.

treatment_protocol: Within 6 hours of collection, blood was processed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Sweden). Residual red blood cells were lysed and washed with phosphate-buffered saline (PBS). The isolated peripheral blood mononuclear cells (PBMCs) were stored at -80 oC.

value: peripheral blood mononuclear cell (PBMC)

value: pancreatic cancer


title: Pancreatic Cancer PBMC Sample 2


title: Normal PBMC Sample 9

description: Gene expression data from PBMC sample of healthy patient.

source_name: PBMC sample from healthy patient

value: healthy


title: Pancreatic Cancer PBMC Sample 1


title: TF-PGCLCs, BP14A, day4, amp, rep2

value: Male


title: Normal PBMC Sample 10


title: TF-PGCLCs, BP14A, day2, amp, rep1

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,


title: Normal PBMC Sample 7


title: Jmjd1aKO_Male_rep2

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

institute: RIKEN BioResource Research Center

description: Gene expression in gonadal somatic cells purified from single mouse embryo at E11.5.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo DNA Microarray 4 x 44 K (G4122F) for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images of microarray slides were processed using Feature Extraction software (Agilent Technologies). All raw data were loaded into Gene Spring GX 12 (Agilent Technologies) and transformed by quantile normalization. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: male, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 2

label_protocol: Low input Quick Amp Labelig kit (Agilent Technologies) was used for the linear amplification and Cy3-labeling of RNAs, followed by RNAeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using RNA 6000 Nano kits (Agilent Technologies).

extract_protocol: RNA was purified from bipotential gonadal somatic cells purified from single embryo at 11.5dpc with Trizol (Life technologies) following the manufacturer's instructions. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Single cell suspension was prepared by trypsinizing gonads and mesonephroi isolated from embryos carrying the Nr5a1/CD271-transgene. Immunomagnetic isolation of CD271-expressing cells was performed according to the standard protocols (Miltenyi Biotech). Typically, ~2×10^5 cells were collected from one pair of E11.5 gonads and methonephroi and ~4×10^4 cells were immunomagnetically purified from them.

tag: tissue

value: purified gonadal somatic cells

tag: developmental stage

tag: jmjd1a mutant allele

value: homozygous


title: Jmjd1aKO_Male_rep1

source_name: male, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 1


title: Jmjd1aKO_Male_rep3

source_name: male, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 3


title: Normal PBMC Sample 4

tag: cell type


title: Jmjd1aKO_Female_rep2

source_name: female, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 2

value: Female


title: Normal PBMC Sample 8


title: Normal PBMC Sample 6


title: Normal PBMC Sample 3


title: Control_Male_rep1

source_name: male, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 1

value: heterozygous


title: Normal PBMC Sample 5


title: Jmjd1aKO_Female_rep1

source_name: female, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 1


title: Normal PBMC Sample 2


title: Control_Female_rep2

source_name: female, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 2


title: Control_Male_rep3

source_name: male, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 3


title: Jmjd1aKO_Female_rep3

source_name: female, Jmjd1a_null, gonadal somatic cells purified from single embryo, E11.5, replicate 3


title: Control_Female_rep3

source_name: female, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 3


title: JK02520-Dde_3000-minimal

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Quantile normalized the probe intensities to match G20 lactate sulfate media, averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.

label: Alexa fluor 555

organism: Oleidesulfovibrio alaskensis G20

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK02520, minimal media

label_protocol: Prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen).

growth_protocol: We collected expression data of Desulfovibrio alaskensis str. G20 wildtype, 10 mutants of G20 with transposon insertions in regulator proteins and one mutant with a transposon insertion in a pilus assembly protein on 60 mM lactate/30mM Sulfate in minimal media under anaerobic conditions at 30C. Cells were collected in mid-log growth. Basal salts - 8mM MgCl2, 20mM NH4Cl, 2mM K2PO4(dibasic), .6mM CaCl2, 30mM Tris-HCl. Thauer's vitamins and trace elements.

extract_protocol: Isolated total RNA with RNeasy mini kit (Qiagen).

treatment_protocol: Different strains including G20 were collected under similar conditions.

value: Dde_3000-gene disrupted by a transposon

tag: carbon source

value: lactate (60 mM)

tag: electron acceptor

value: sulfate (50 mM)

tag: stressor

value: mid-log


title: Control_Female_rep1

source_name: female, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 1


title: Control_Male_rep2

source_name: male, Jmjd1a heterozygous control, gonadal somatic cells purified from single embryo, E11.5, replicate 2


title: HCC PBMC Sample 9

description: Gene expression data from PBMC sample of hepatocellular carcinoma patient.

source_name: PBMC sample from hepatocellular carcinoma patient

tag: disease status

value: hepatocellular carcinoma (HCC)


title: HCC PBMC Sample 8


title: JK07841-Dde_3127_minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK07841, minimal media

value: Dde_3127-gene disrupted by a transposon


title: JK02209-Dde_2365-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK02209, minimal media

value: Dde_2365-gene disrupted by a transposon


title: JK04660-Dde_3135_SahR-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK04660, minimal media

value: Dde_3135-gene disrupted by a transposon


title: G20-minimal

data_processing: Quantile normalized the probe intensities to match G20, averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.

source_name: Desulfovibrio alaskensis str. G20, minimal

label_protocol: Prepared first-strand labeled cDNA with SuperScript III Plus Indirect cDNA Labeling Module Alexa 555 (Invitrogen).

growth_protocol: We collected expression data of Desulfovibrio alaskensis str. G20 and 7 mutants of G20 with transposon insertions in a regulator protein on 60 mM lactate/50mM sulfate in minimal media under anaerobic conditions at 30C. Cells were collected from mid-log to late-log growth phase. Basal salts - 8mM MgCl2,20mM NH4Cl, 2.2 mM K2PO4(dibasic), .6mM CaCl, 30mM PIPES. Thauers vitamins and trace minerals.

value: wild-type

tag: growth phase


title: JK08988-Dde_2676-Fur-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK08988, minimal

value: transposon insertion in Dde_2676


title: JK00494-Dde_3327-phnF-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK00494, minimal media

value: Dde_3327-gene disrupted by a transposon


title: Normal PBMC Sample 1

source_name: PBMC sample from healthy patient

value: peripheral blood mononuclear cell (PBMC)

value: healthy


title: HCC PBMC Sample 10


title: HCC PBMC Sample 5


title: B (clone #2-4) +Doxycycline, day1, rep2

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1 transgenes, cultured with doxycycline

value: Male

tag: strain

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector


title: JK12035-Dde_1283-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK12035, minimal media

value: Dde_1283-gene disrupted by a transposon


title: JK03973-Dde_2702-Rex-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK03973, minimal

value: transposon insertion in Dde_2702


title: HCC PBMC Sample 4


title: HCC PBMC Sample 6


title: JK08886-Dde_0289-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK08886, minimal media

value: Dde_0289-gene disrupted by a transposon


title: JK05252-Dde_2226-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05252, minimal media

value: Dde_2226-gene disrupted by a transposon

value: lactate (60 mM)


title: JK05953-Dde_3135-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05953, minimal media

value: sulfate (50 mM)

value: mid-log


title: Case 2

type: genomic

city: Fitzroy

first: Ruth

middle: N

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

institute: St Vincent's Hospital (Melbourne)

hyb_protocol: Illumina Infinium Assay Ultra.

scan_protocol: Illumina BeadArray Reader.

data_processing: Karyostudio v1.2, default settings.

molecule: genomic DNA

source_name: acute myeloid leukaemia

label_protocol: Illumina Infinium Assay Ultra.

growth_protocol: None: specimen from bone marrow biopsy.

extract_protocol: Qiagen DNeasy Cell and Tissue kit.

treatment_protocol: Stored at 4 degrees Celsius for 33 days (R4, Case 1) or 2 days (R13, Case 2), then -80 degrees Celsius; thawed before DNA extraction.

value: bone marrow

tag: primary tumor

value: acute myeloid leukaemia

tag: tumor type

value: therapy-related acute myeloid leukaemia after treatment for breast cancer

tag: gender

value: female

tag: lineage

value: myeloid


title: Thalassiosira_pseudonana_CCMP1335_under_phosphorus_limitation

city: Woods Hole

first: Sonya

last: Dyhrman

state: MA

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing: Tag sequences and counts were generated using a tag-seq profiling approach by Illumina Inc.   Illumina library construction included a polyA selection and digestion with NlaIII.  This resulted in the 18 bp sequence reads reported here which are called tags and should map to the most 3’ NlaIII site in each transcript.  Tags were sequenced and counted by Illumina on their genome analyzer, and reported in a look up table of unique tag sequences and their observed frequency in a given sample.

organism: Thalassiosira pseudonana CCMP1335

source_name: Phosphorus limited T. pseudonana CCMP1335 culture

extract_protocol: Transcriptome profiling was completed using a tag-seq profiling approach by Illumina Inc. Briefly, equal volumes from replicate P-replete cultures, and triplicate P-deficient cultures were pooled prior to filtration.  RNA was extracted from 5.40 x 10^8 cells and 3.51 x 10^8 cells, from the P-replete and P-deficient samples, respectively, using Qiagen’s RNeasy Midi kit according to the manufacturer’s instructions with the following exceptions; cells were lysed using 0.5 mm zirconia/silica beads (BioSpec) along with the lysis buffer solution and vortexed until the solution looked homogenous (2-3 min).  The lysis solution was then put over Qiashredder columns (Qiagen) to aid in the removal of any large cell wall material that could clog the spin columns.  To aid in the removal of DNA, an on-column DNase digestion was performed during the extraction using the RNase-free DNase Set (Qiagen) according to the manufacturer’s instructions.  Roughly 11 μg of P-replete and 8 μg of P-deficient total RNA was sent to Illumina and converted to cDNA. Illumina library construction included a polyA selection and digestion with NlaIII.  This resulted in 21 bp sequence reads called tags that should map to the most 3’ NlaIII site in each transcript.

tag: nutrient conditions

value: phosphorus-limitation with otherwise environmentally relevant conditions


title: JK11239-Dde_2226-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK11239, minimal media

tag: genotype/variation


title: JK03141-Dde_3327-phnF-minimal

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK03141, minimal media

value: Dde_3327-gene disrupted by a transposon


title: Case 1

value: male


title: JK01512-Dde_3674-PerR-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK01512, minimal

value: transposon insertion in Dde_3674


title: JK07841-Dde_3127-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK07841, minimal

value: transposon insertion in Dde_3127


title: JK05162-Dde_2665-LysX-rich

description: lysXrich

data_processing: Quantile normalized the probe intensities to match the G20 rich lactate/sulfate media, averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05162, rich media

growth_protocol: We collected expression data of Desulfovibrio alaskensis str. G20 and 2 mutants with transposon insertions in regulator proteins. We grew the cultures in minimal 60 mM lactate/ 30mM sulfate media in an anaerobic chamber at 30C until cells reached early stationary phase. Basal salts - 8mM MgCl2, 20mM NH4Cl, 2mM K2PO4 (dibasic), .6mM CaCl2, 30mM Tris-HCl. Thauer's vitamins and trace elements.

treatment_protocol: We transferred pellets to new media, resuspended the pellets, waited one hour, then collected the pellets and stored them in -80C until RNA extraction. The choline mutant was transferred to a 30 mM choline/ 30 mM sulfate media and a lactate/sulfate media. The lysX mutant was transferred to minimal media with .3 mM lysine and to rich media (.1% Yeast extract). G20 was transferred to choline/sulfate media, a lactate/sulfate media, a lactate/choline/sulfate media, a rich lactate/sulfate media, a minimal lactate/sulfate media with lysine.

value: Dde_2665 gene disrupted by a transposon

value: sulfate (30 mM)

tag: added nutrient

value: yeast extract (.1%)

value: early stationary


title: JK03191-Dde2644-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK03191, minimal

value: transposon insertion in Dde_2644

value: lactate (60 mM)


title: JK00442-Dde_3511-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK08886, minimal

value: transposon insertion in Dde_3511

value: sulfate (50 mM)

value: mid-log


title: Thalassiosira_pseudonana_CCMP1335_under_nutrient_replete_conditions

source_name: Nutrient replete T. pseudonana CCMP1335 culture

value: nutrient replete with otherwise environmentally relevant conditions


title: G20-lactatesulfate-minimal, rep2

description: wtLSb

source_name: Desulfovibrio alaskensis str. G20, lactate/sulfate minimal media

value: wild-type


title: JK05048-Dde_3291-lactatesulfate-minimal

description: cholLS

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05048, lactate/sulfate minimal media

value: Dde_3291 gene disrupted by a transposon


title: JK05162-Dde_2665-Lysx-lysine

description: lysXlys

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05162, minimal media with lysine

value: lysine (.3mM)


title: JK05048-Dde_3291-cholinesulfate-minimal

description: cholCS

source_name: Desulfovibrio alaskensis str. G20 mutant str. JK05048, choline/sulfate minimal media

value: choline (30 mM)


title: G20-lactatesulfate-rich

description: wtRich

source_name: Desulfovibrio alaskensis str. G20, rich media


title: JK05162-Dde_2665_lysX-minimal

source_name: Desulfovibrio alaskensis str. G20 str. JK05162, minimal

value: transposon insertion in Dde_2665


title: G20-lactatecholinesulfate-minimal

description: wtLCS

source_name: Desulfovibrio alaskensis str. G20, lactate/choline/sulfate minimal media

value: lactate (60 mM)/ choline(30 mM)


title: G20-cholinesulfate-minimal

description: wtCS

source_name: Desulfovibrio alaskensis str. G20, choline/sulfate minimal media


title: BM_High density culture_15Days_rep2

city: Shanghai

first: Yang

last: Lu

address: 639 Zhi Zao Ju Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression after 15days high density culture of rat bone marrow cells

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After Quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0).

source_name: endothelial progenitor cells (EPCs)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: After 15 days of culture at regular or high density, total RNA was extracted from the cells with Trizol (Invitrogen).

tag: background strain

value: Wistar

tag: tissue type

value: bone marrow

tag: age

value: 6 weeks


title: Gastric Cancer PBMC Sample 3

description: Gene expression data from PBMC sample of gastric cancer patient.

source_name: PBMC sample from gastric cancer patient

tag: cell type

value: peripheral blood mononuclear cell (PBMC)

value: gastric cancer


title: HCC PBMC Sample 2

source_name: PBMC sample from hepatocellular carcinoma patient

value: hepatocellular carcinoma (HCC)


title: Gastric Cancer PBMC Sample 2


title: G20-lactatesulfate-minimal, rep1

description: wtLS

tag: carbon source

value: lactate (60 mM)

value: sulfate (30 mM)

value: early stationary


title: BM_High density culture_15Days_rep1


title: HCC PBMC Sample 3


title: BM_Regular density culture_15Days_rep2

description: Gene expression after 15days regular density culture of rat bone marrow cells


title: wt-2

city: Los Angeles

first: Jae U

last: Jung

state: CA

address: 1450 Biggy Street

department: Department of Molecular Microbiology and Immunology

institute: University of Southern California, Keck School of Medicine

description: KSHV infected PEL

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

scan_protocol: Genechip was scanned using GeneChip Scanner 300

data_processing: The data was RMA normalized by GeneSpring GX 10.0.2 software. Comparisons are made with a fold change of 2.

source_name: KSHV_vIRF4-BCBL-1, No treatment of Doxycyline, rep2

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

growth_protocol: TREx/BCBL-1 vIRF4 cell lines were cultured with RPMI media+ 10% FBS+ P/S +100mg/ml

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

treatment_protocol: In order to induce vIRF4 gene expression, we treated 1mg/ml of doxycycline into TREx/BCBL-1 vIRF4 cell lines

tag: cell line

value: BCBL-1 (PEL derived cell line)

tag: phenotype

value: vIRF4 not expressed


title: HCC PBMC Sample 1

tag: disease status


title: wt+2

description: KSHV infected PEL

source_name: KSHV_vIRF4-BCBL-1, 24 h treatment of Doxycyline, rep2

value: vIRF4 overexpression


title: G20-lysine

description: wtLYS

source_name: Desulfovibrio alaskensis str. G20, minimal media with lysine

value: wild-type

tag: electron acceptor


title: Gastric Cancer PBMC Sample 1


title: wt-1

description: KSHV infected PEL

source_name: KSHV_vIRF4-BCBL-1, No treatment of Doxycyline, rep1


title: G20_wildtype-minimal

description: WT

source_name: Desulfovibrio alaskensis str. G20, minimal media

value: sulfate (50 mM)

tag: stressor

value: mid-log


title: BM_Regular density culture_15Days_rep1


title: HCC PBMC Sample 7


title: NATURI_67_Nasal mucosa_AsmNoEx_day 6

status: Public on Aug 02 2013

city: Chicago

first: Peter

last: McErlean

state: Illinois

address: 240 E. Huron, McGaw M-530h

department: Allergy Immunology

institute: Northwestern University

description:
NATURI_67
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).

data_processing: Processed data are presented in one data matrix with the 36,866 Agilent Probe IDs (out of possible 41108 and 36926, respectively), which are represented in both platform records. This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al Bioinformatics. 2003 Jan 22;19(2):185-93. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: Nasal mucosa from asthmatic without exacerbation at day 6 of cold symptoms

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)

growth_protocol: In vivo sampling of nasal mucosa of the course of naturally occuring colds.

extract_protocol: Total RNA was extracted from nasal mucosa samples using RNeasy Mini Kit (QIAGEN) with the addition of a DNAse treatment (1U/mL fro 1hr at 37C; Promega) and re-purification phase. Extracted RNA was further purified using the RNA Clean and Concentrator (ZYMO Research) and quality assesed by Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Nasal mucosa was sampled using Rhinoprobe and stored in RLT lysis buffer (QIAGEN) at -80C

tag: group

value: Asthmatic_no exacerbation

value: female

value: 19 yrs

tag: time point (visit)

value: Day 6 (V2)

tag: tissue

value: Nasal mucosa


title: NATURI_59_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_59
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic without exacerbation at day 2 of cold symptoms

tag: gender

value: Day 2 (V1)


title: NATURI_78_Nasal mucosa_AsmEx_baseline

description:
NATURI_78
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.

source_name: Nasal mucosa from asthmatic with exacerbation baseline after cold

value: 41 yrs

value: Baseline (V3)


title: NATURI_37_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_37
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

source_name: Nasal mucosa from asthmatic without exacerbation baseline after cold


title: NATURI_54_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_54
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_81_Nasal mucosa_AsmEx_baseline

description:
NATURI_81
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.

value: male

value: 39 yrs


title: NATURI_65_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_65
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: 51 yrs


title: NATURI_53_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_53
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_49_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_49
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: 37 yrs


title: NATURI_43_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_43
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: 49 yrs


title: wt+1

description: KSHV infected PEL

source_name: KSHV_vIRF4-BCBL-1, 24 h treatment of Doxycyline, rep1

value: BCBL-1 (PEL derived cell line)

value: vIRF4 overexpression


title: NATURI_51_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_51
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: 26 yrs


title: NATURI_68_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_68
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms


title: NATURI_60_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_60
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_50_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_50
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_34_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_34
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.


title: NATURI_87_Nasal mucosa_AsmEx_day 2

description:
NATURI_87
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic with exacerbation at day 2 of cold symptoms


title: NATURI_84_Nasal mucosa_AsmEx_day 2

description:
NATURI_84
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_91_Nasal mucosa_AsmEx_day 6

description:
NATURI_91
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, six days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic with exacerbation at day 6 of cold symptoms


title: NATURI_90_Nasal mucosa_AsmEx_day 6

description:
NATURI_90
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, six days after the onset of cold symptoms


title: NATURI_73_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_73
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms


title: NATURI_25_Nasal mucosa_Allrg Rhin_day 6

description:
NATURI_25
Gene expression in the nasal mucosa of an individual with allergic rhinitis six days after the onset of cold symptoms

source_name: Nasal mucosa from allergic rhinitis at day 6 of cold symptoms

value: Allergic Rhinitis

value: 47 yrs


title: NATURI_36_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_36
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: Asthmatic_no exacerbation

value: female


title: NATURI_32_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_32
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.


title: NATURI_18_Nasal mucosa_Allrg Rhin_baseline

description:
NATURI_18
Gene expression in the nasal mucosa of an individual with allergic rhinitis following a cold.

source_name: Nasal mucosa from allergic rhinitis baseline after cold


title: NATURI_42_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_42
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: 19 yrs


title: NATURI_64_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_64
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: Day 6 (V2)

value: Nasal mucosa


title: NATURI_21_Nasal mucosa_Allrg Rhin_day 2

description:
NATURI_21
Gene expression in the nasal mucosa of an individual with allergic rhinitis two days after the onset of cold symptoms

source_name: Nasal mucosa from allergic rhinitis at day 2 of cold symptoms

value: Day 2 (V1)


title: NATURI_23_Nasal mucosa_Allrg Rhin_day 2

description:
NATURI_23
Gene expression in the nasal mucosa of an individual with allergic rhinitis two days after the onset of cold symptoms

value: 31 yrs


title: NATURI_13_Nasal mucosa_Healthy_day 6

description:
NATURI_13
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms

source_name: Nasal mucosa from healthy at day 6 of cold symptoms

value: healthy (no underlying respiratory disease)

value: 18 yrs


title: NATURI_33_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_33
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: 51 yrs

value: Baseline (V3)


title: NATURI_12_Nasal mucosa_Healthy_day 6

description:
NATURI_12
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms


title: NATURI_11_Nasal mucosa_Healthy_day 2

description:
NATURI_11
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms

source_name: Nasal mucosa from healthy at day 2 of cold symptoms

value: male


title: NATURI_15_Nasal mucosa_Healthy_day 6

description:
NATURI_15
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms

value: 30 yrs


title: NATURI_14_Nasal mucosa_Healthy_day 6

description:
NATURI_14
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms

value: 29 yrs


title: NATURI_02_Nasal mucosa_Healthy_baseline

description:
NATURI_02
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease following a cold.

source_name: Nasal mucosa from healthy baseline after cold


title: NATURI_09_Nasal mucosa_Healthy_day 2

description:
NATURI_09
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms


title: NATURI_05_Nasal mucosa_Healthy_baseline

description:
NATURI_05
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease following a cold.

value: 26 yrs


title: NATURI_08_Nasal mucosa_Healthy_day 2

description:
NATURI_08
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms


title: NATURI_17_Nasal mucosa_Healthy_day 6

description:
NATURI_17
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms


title: NATURI_06_Nasal mucosa_Healthy_day 2

description:
NATURI_06
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms


title: NATURI_01_Nasal mucosa_Healthy_baseline

description:
NATURI_01
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease following a cold.


title: NATURI_03_Nasal mucosa_Healthy_baseline

description:
NATURI_03
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease following a cold.


title: NATURI_27_Nasal mucosa_Allrg Rhin_day 6

description:
NATURI_27
Gene expression in the nasal mucosa of an individual with allergic rhinitis six days after the onset of cold symptoms

value: Allergic Rhinitis


title: NATURI_07_Nasal mucosa_Healthy_day 2

description:
NATURI_07
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms


title: NOA-SCOS-1

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: Paracrine-autocrine project

hyb_protocol: Array hybridization, washing, and scanning were performed according to manufacturer’s recommendations by using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays scanned using Affymetrix 3000 Scanner according to the instructions of the manufacturer

data_processing: Raw data were normalized with RMA method using Affymetrix software delivered to the scanner.

source_name: testicular biopsy with nonobstructive azoospermia

label_protocol: The sense-strand cDNA was fragmentized and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Not applicable, total RNA extracted from testicular biopsy cells

extract_protocol: Tri-Reagent (Sigma-Aldrich, St. Louis, USA)  and post-purification using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Not applicable, samples extracted from untreated patients with various stages of azoospermia

tag: Sex

tag: condition

value: NOA

value: testis

tag: testis region

value: right

tag: age (yrs)

tag: histopatological desription

value: Sertoli Cell Only-Syndrome

tag: fertility status

value: infertile


title: NOA-SCOS-4

description: Paracrine-autocrine project

value: left


title: NOA-SCOS-5

description: Paracrine-autocrine project


title: NOA-SCOS-6

description: Paracrine-autocrine project


title: NOA-MEI-6

description: Paracrine-autocrine project

value: meiotic arrest


title: NOA-MEI-1

description: Paracrine-autocrine project


title: NOA-MEI-2

description: Paracrine-autocrine project


title: NOA-POST-6

description: Paracrine-autocrine project

value: postmeiotic arrest


title: control-3

description: Paracrine-autocrine project

source_name: commercially available total RNA

extract_protocol: commercial available total RNA

value: control

value: full spermatogenesis


title: NOA-POST-7

description: Paracrine-autocrine project


title: NOA-POST-11

description: Paracrine-autocrine project

value: pulled-right and left


title: NOA-SCOS-7

description: Paracrine-autocrine project


title: NOA-MEI-7

description: Paracrine-autocrine project


title: NOA-POST-10

description: Paracrine-autocrine project


title: control-2

description: Paracrine-autocrine project


title: NOA-POST-5

description: Paracrine-autocrine project


title: NOA-POST-2

description: Paracrine-autocrine project


title: control-4

description: Paracrine-autocrine project


title: PP2Ac_Tg_0_Rep

city: Boston

first: Jose

middle: C

last: Crispin

address: 330 Brookline Ave, CLS-928

department: Medicine

institute: Beth Israel Deaconess Medical Center

hyb_protocol: The cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

scan_protocol: The chips were transferred to a fluidics instrument that performs washes to remove cDNA that was not hybridized to its complementary oligonucleotide probe. The bound cDNA was fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) and additional fluors were added using biotinylated anti-streptavidin antibody and additional SAPE. Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: Raw data were background-corrected and normalized using RMAExpress. Data were analyzed with R.

source_name: Naïve CD4 T cells from PP2Ac transgenic mice, unstimulated

label_protocol: cDNA was end-labeled with a biotinylated nucleotide analog.

growth_protocol: RPMI 10% FCS

extract_protocol: TRIZOL followed by RNA purification using Qiagen RNA columns

treatment_protocol: T cells were stimulated with plate bound goat anti-hamster antibodies and soluble anti-CD3 (0.25 ug/mL, Clone 145-2C11) and anti-CD28 (0.5 ug/mL, Clone 37.51)

tag: strain


title: WT_0_Rep

source_name: Naïve CD4 T cells from WT transgenic mice, unstimulated


title: PP2Ac_Tg_24_Rep

source_name: Naïve CD4 T cells from PP2Ac transgenic mice, stimulated 24 hours with anti-CD3 and anti-CD28


title: WT_24_Rep

source_name: Naïve CD4 T cells from WT transgenic mice, stimulated 24 hours with anti-CD3 and anti-CD28


title: WT_6

source_name: Naïve CD4 T cells from WT transgenic mice, stimulated 6 hours with anti-CD3 and anti-CD28


title: WT_6_Rep


title: PP2Ac_Tg_6_Rep

source_name: Naïve CD4 T cells from PP2Ac transgenic mice, stimulated 6 hours with anti-CD3 and anti-CD28


title: PP2Ac_Tg_0


title: Lymphocytes,female_GF,rep2

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

description: NOD/ShiLtJ

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed with GenomeStudio using Illumina default analysis settings.

source_name: Lymphocytes isolated from pancreatic lymph nodes (PLNs)

label_protocol: Total RNA was processed using the Illumina Totalprep kit (Ambion, Life Technologies, Carlsbad, CA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using guanidinium cesium chloride gradient ultracentrifugation (Chirgwin et al., 1979).

value: female

tag: microbiota

value: germ-free (GF)

value: NOD/ShiLtJ

tag: cell type


title: PP2Ac_Tg_6


title: WT_0


title: Lymphocytes,male_SPF,rep1

description: NOD/ShiLtJ

value: male

value: specific-pathogen free (SPF)

value: Lymphocytes isolated from pancreatic lymph nodes (PLNs)


title: PP2Ac_Tg_24


title: NOA-POST-3

description: Paracrine-autocrine project

value: NOA


title: WT_24


title: Lymphocytes,female_SPF,rep2

description: NOD/ShiLtJ


title: Lymphocytes,male_GF,rep1

description: NOD/ShiLtJ


title: Lymphocytes,female_SPF,rep3

description: NOD/ShiLtJ


title: Lymphocytes,male_GF,rep3

description: NOD/ShiLtJ


title: Lymphocytes,male_SPF,rep2

description: NOD/ShiLtJ


title: control-1

description: Paracrine-autocrine project

value: testis


title: Lymphocytes,male_SPF,rep3

description: NOD/ShiLtJ


title: Lymphocytes,female_GF,rep3

description: NOD/ShiLtJ


title: Lymphocytes,female_SPF,rep1

description: NOD/ShiLtJ


title: Lymphocytes,male_GF,rep2

description: NOD/ShiLtJ


title: Lymphocytes,female_GF,rep1

description: NOD/ShiLtJ


title: Day-42 triple 3

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

institute: MCG

description: triple 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Model Base Background Correction (MBCB)

label: biotin-UTP

source_name: one-phase culture

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPre RNA amplification kit with T-7 RNA polymerase IVT for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by quality check using the BioRad Experion system

value: one-phase culture

tag: days in culture

value: CD34 cells from umbilical cord blood


title: Day-49 triple 1

description: triple 1


title: Day-42 triple 2

description: triple 2


title: Day-56 triple 3

description: triple 3


title: Day-56 triple 2

description: triple 2


title: Day-42 triple 1

description: triple 1


title: Day-21 triple 1

description: triple 1


title: Day-21 triple 2

description: triple 2


title: Day-49 triple 3

description: triple 3


title: Day-56 triple 1

description: triple 1


title: Day-49 triple 2

description: triple 2


title: Day-21 triple 3

description: triple 3


title: lymphoblast T-ALL sample #48

city: New York

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: sample collected in human clinical trial E2993 (Marks et al., 2009)

hyb_protocol: 500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion) and hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina)

data_processing: Gene expression profiling data from 53 adult T-ALL patients were transfomed to log2 scale and normalized using quantile normalization without background subtraction

source_name: lymphoblast TALL patient 103

label_protocol: 10ng of RNA from each T-cell subset was amplified using the Ovation® PicoSL WTA System (Nugen), labeled by the EncoreTM BiotinIL Module (Nugen)

extract_protocol: RNA isolation from lymphoblast obtained from adult T-ALL patient samples was achieved using the RNeasy plus mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Leukemic DNA and cryopreserved lymphoblast samples were provided by the Eastern Cooperative Oncology Group (ECOG). All samples were collected in clinical trial E2993(Marks et al., 2009) and informed consent to use leftover material for research purposes was obtained from all the patients at trial entry according to the declaration of Helsinki. T-cell phenotype was confirmed by flow cytometry

value: cryopreserved lymphoblast

tag: subtype

value: early immature


title: lymphoblast T-ALL sample #42

source_name: lymphoblast TALL patient 54

value: cortical/mature


title: lymphoblast T-ALL sample #53

source_name: lymphoblast TALL patient 108


title: MDAPca2b_p48_untreated_control_rep2

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

hyb_protocol: 4.5 µg of fragmented Biotin-Labeled aRNA was hybridized on a HT Human Genome U219 96-Array plate (Affymetrix, Santa Clara, USA). The 96-Array plat was, washed, stained and scanned with the GeneTitan Instrument (Affymetrix, Santa Clara, USA).

data_processing: The microarray data was normalised with RMA (Irizarry et al., 2003)  and summarised with the hthgu133pluspmhsentrezgcdf_15.0.0 CDF (Dai et al., 2005). Genes that show little expression variation across the samples are filtered out based on I/NI calls (Talloen et al., 2007), leaving us with 5934 out of the 18837.

source_name: MDA Pca 2b (p48) untreated

label_protocol: Biotin-Labeled aRNA was synthesized from 200 ng of total RNA using the 3’IVT Express Kit (Affymetrix, Santa Clara, USA). The aRNA was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc., Indianapolis,USA) on the BioMek Fx Workstation (Beckman Coulter Inc., Indianapolis ,USA). Biotin-Labeled aRNA was fragmented using the 3’IVT Express Kit (Affymetrix, Santa Clara, USA).

growth_protocol: LNCaP and MDA PCa 2b cells were seeded in 12 wells. Both cell lines were seeded in triplicates. 2 biological replicates were performed.

extract_protocol: Cells were lysed using RLT buffer (Qiagen, Hilden, Germany) and homogenized using the QIAshredder spin column (Qiagen, Hilden, Germany). RNA was isolated using the miRNeasy 96 kit by following the manufacturer's instructions (Qiagen, Hilden, Germany). During RNA isolation an on-plate DNase digestion was performed. The RNA concentration of the samples was determined on a Nanodrop-8000 UV-Vis Spectrophotometer (Thermo Scientific, Vienna, Austria). RNA quality was determined with the RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, USA).

treatment_protocol: The cells were starved for 24 h and then treated with 5 ng/ml IL-6 for 18 h.

tag: cellline

value: MDA Pca 2b

tag: passage

tag: treatment

value: untreated

tag: duration


title: lymphoblast T-ALL sample #40

source_name: lymphoblast TALL patient 50

tag: tissue


title: lymphoblast T-ALL sample #35

source_name: lymphoblast TALL patient 40


title: lymphoblast T-ALL sample #32

source_name: lymphoblast TALL patient 37


title: MDAPca2b_p48_5ng/mlIL6_18h_rep3

scan_protocol: GeneTitan Instrument (Affymetrix, Santa Clara, USA)

source_name: MDA Pca 2b (p48) treated with 5 ng/ml IL6 for 18h

value: 5 ng/ml IL6


title: lymphoblast T-ALL sample #45

source_name: lymphoblast TALL patient 57


title: lymphoblast T-ALL sample #43

source_name: lymphoblast TALL patient 55


title: lymphoblast T-ALL sample #50

source_name: lymphoblast TALL patient 105


title: MDAPca2b_p48_untreated_control_rep3

value: control


title: lymphoblast T-ALL sample #52

source_name: lymphoblast TALL patient 107


title: lymphoblast T-ALL sample #44

source_name: lymphoblast TALL patient 56


title: lymphoblast T-ALL sample #41

source_name: lymphoblast TALL patient 51


title: lymphoblast T-ALL sample #28

source_name: lymphoblast TALL patient 33


title: lymphoblast T-ALL sample #37

source_name: lymphoblast TALL patient 42


title: lymphoblast T-ALL sample #51

source_name: lymphoblast TALL patient 106


title: lymphoblast T-ALL sample #38

source_name: lymphoblast TALL patient 43


title: lymphoblast T-ALL sample #49

source_name: lymphoblast TALL patient 104


title: lymphoblast T-ALL sample #31

source_name: lymphoblast TALL patient 36


title: lymphoblast T-ALL sample #47

source_name: lymphoblast TALL patient 102


title: lymphoblast T-ALL sample #34

source_name: lymphoblast TALL patient 39


title: lymphoblast T-ALL sample #33

source_name: lymphoblast TALL patient 38


title: MDAPca2b_p48_untreated_control_rep1

source_name: MDA Pca 2b (p48) untreated


title: lymphoblast T-ALL sample #46

source_name: lymphoblast TALL patient 101


title: lymphoblast T-ALL sample #39

source_name: lymphoblast TALL patient 46


title: lymphoblast T-ALL sample #30

source_name: lymphoblast TALL patient 35


title: lymphoblast T-ALL sample #29

source_name: lymphoblast TALL patient 34


title: lymphoblast T-ALL sample #36

source_name: lymphoblast TALL patient 41


title: LNCaP_p43_untreated_control_rep1

source_name: LNCaP (p43) untreated

value: LNCaP


title: lymphoblast T-ALL sample #27

source_name: lymphoblast TALL patient 32


title: LNCaP_p43_5ng/mlIL6_18h_rep3

source_name: LNCaP (p43) treated with 5 ng/ml IL6 for 18h


title: MDAPca2b_p48_5ng/mlIL6_18h_rep1

source_name: MDA Pca 2b (p48) treated with 5 ng/ml IL6 for 18h


title: LNCaP_p43_5ng/mlIL6_18h_rep2


title: lymphoblast T-ALL sample #17

source_name: lymphoblast TALL patient 20


title: lymphoblast T-ALL sample #26

source_name: lymphoblast TALL patient 31


title: MDAPca2b_p48_5ng/mlIL6_18h_rep2


title: LNCaP_p43_5ng/mlIL6_18h_rep1


title: lymphoblast T-ALL sample #23

source_name: lymphoblast TALL patient 26


title: lymphoblast T-ALL sample #24

source_name: lymphoblast TALL patient 27


title: MDAPca2b_p46_5ng/mlIL6_18h_rep3

source_name: MDA Pca 2b (p46) treated with 5 ng/ml IL6 for 18h


title: MDAPca2b_p46_untreated_control_rep3

source_name: MDA Pca 2b (p46) untreated


title: lymphoblast T-ALL sample #20

source_name: lymphoblast TALL patient 23


title: MDAPca2b_p46_untreated_control_rep1


title: lymphoblast T-ALL sample #25

source_name: lymphoblast TALL patient 29


title: lymphoblast T-ALL sample #21

source_name: lymphoblast TALL patient 24


title: lymphoblast T-ALL sample #22

source_name: lymphoblast TALL patient 25


title: lymphoblast T-ALL sample #16

source_name: lymphoblast TALL patient 19


title: lymphoblast T-ALL sample #19

source_name: lymphoblast TALL patient 22


title: lymphoblast T-ALL sample #18

source_name: lymphoblast TALL patient 21


title: LNCaP_p43_untreated_control_rep3

source_name: LNCaP (p43) untreated


title: MDAPca2b_p46_untreated_control_rep2


title: MDAPca2b_p46_5ng/mlIL6_18h_rep2


title: lymphoblast T-ALL sample #15

source_name: lymphoblast TALL patient 18


title: peripheral blood T-cells miRNA control11

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: gene expression data from T-cell

hyb_protocol: Samples were hybridized for 16 hr at 45C on miRNA 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Robust Multi-array Analysis (RMA) with quantile normailization using the Affymetrix software expression console.

source_name: peripheral blood T-cell

label_protocol: 1000 ng RNA from T-cells were biotin labeled using the FlashTag Biotin HSR kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions

extract_protocol: Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))

treatment_protocol: Cells were snap frozen in -80 C

tag: disease state

value: Control

value: peripheral blood T-cells


title: peripheral blood T-cells miRNA control8

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA control10

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #13

source_name: lymphoblast TALL patient 16


title: peripheral blood T-cells miRNA control6

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA control1

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA control4

description: gene expression data from T-cell


title: MDAPca2b_p46_5ng/mlIL6_18h_rep1


title: peripheral blood T-cells miRNA control3

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA control2

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA Patient10

description: gene expression data from T-cell

value: multiple sclerosis


title: peripheral blood T-cells miRNA Patient7

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #10

source_name: lymphoblast TALL patient 10


title: LNCaP_p40_5ng/mlIL6_18h_rep2

source_name: LNCaP (p40) treated with 5 ng/ml IL6 for 18h


title: peripheral blood T-cells miRNA Patient8

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA Patient9

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA Patient11

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA control7

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #12

source_name: lymphoblast TALL patient 14


title: lymphoblast T-ALL sample #14

source_name: lymphoblast TALL patient 17


title: LNCaP_p40_untreated_control_rep1

source_name: LNCaP (p40) untreated


title: LNCaP_p40_untreated_control_rep3


title: lymphoblast T-ALL sample #9

source_name: lymphoblast TALL patient 9


title: lymphoblast T-ALL sample #11

source_name: lymphoblast TALL patient 13


title: LNCaP_p43_untreated_control_rep2


title: peripheral blood T-cells miRNA Patient6

description: gene expression data from T-cell


title: peripheral blood T-cells miRNA Patient4

description: gene expression data from T-cell


title: LNCaP_p40_5ng/mlIL6_18h_rep1


title: peripheral blood T-cells miRNA Patient5

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #8

source_name: lymphoblast TALL patient 8


title: LNCaP_p40_untreated_control_rep2


title: LNCaP_p40_5ng/mlIL6_18h_rep3


title: lymphoblast T-ALL sample #6

source_name: lymphoblast TALL patient 6


title: peripheral blood T-cells miRNA Patient1

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #5

source_name: lymphoblast TALL patient 5


title: NATURI_89_Nasal mucosa_AsmEx_day 6

description:
NATURI_89
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, six days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic with exacerbation at day 6 of cold symptoms

tag: group

tag: gender

value: female

tag: age

value: 26 yrs

tag: time point (visit)

value: Day 6 (V2)

value: Nasal mucosa


title: lymphoblast T-ALL sample #3

source_name: lymphoblast TALL patient 3


title: lymphoblast T-ALL sample #1

source_name: lymphoblast TALL patient 1


title: NATURI_86_Nasal mucosa_AsmEx_day 2

description:
NATURI_86
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic with exacerbation at day 2 of cold symptoms

value: Day 2 (V1)


title: NATURI_79_Nasal mucosa_AsmEx_baseline

description:
NATURI_79
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.

source_name: Nasal mucosa from asthmatic with exacerbation baseline after cold

value: 29 yrs

value: Baseline (V3)


title: NATURI_77_Nasal mucosa_AsmEx_baseline

description:
NATURI_77
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.


title: NATURI_85_Nasal mucosa_AsmEx_day 2

description:
NATURI_85
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms


title: NATURI_75_Nasal mucosa_AsmEx_baseline

description:
NATURI_75
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.

value: 24 yrs


title: peripheral blood T-cells miRNA Patient3

description: gene expression data from T-cell

source_name: peripheral blood T-cell


title: NATURI_80_Nasal mucosa_AsmEx_baseline

description:
NATURI_80
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.


title: NATURI_82_Nasal mucosa_AsmEx_day 2

description:
NATURI_82
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms

value: 46 yrs


title: NATURI_83_Nasal mucosa_AsmEx_day 2

description:
NATURI_83
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, two days after the onset of cold symptoms


title: lymphoblast T-ALL sample #2

source_name: lymphoblast TALL patient 2

value: cryopreserved lymphoblast

value: cortical/mature


title: peripheral blood T-cells miRNA Patient2

description: gene expression data from T-cell


title: lymphoblast T-ALL sample #7

source_name: lymphoblast TALL patient 7


title: NATURI_76_Nasal mucosa_AsmEx_baseline

description:
NATURI_76
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, following a cold.


title: NATURI_74_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_74
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic without exacerbation at day 6 of cold symptoms

value: Asthmatic_no exacerbation

value: 53 yrs


title: NATURI_88_Nasal mucosa_AsmEx_day 6

description:
NATURI_88
Gene expression in the nasal mucosa of an individual with asthma, who did experience an episode of exacerbation, six days after the onset of cold symptoms


title: NCH644 Glioma Cells_CD133 POS

city: Charlottesville

first: Roger

last: Abounader

state: Virginia

department: Microbiology

institute: University of Virginia

description: RNA was extracted using a protocol for small RNAs and hybridized to the Agilent human miRNA Version 2 microarray

hyb_protocol: established Beckman Coulter procedure for Eukaryotic DNA: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.  The hybridized array was then washed  protocol:Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.  The hybridized array was then washed and scanned

data_processing: data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

source_name: primary brain cancer

label_protocol: established Beckman Coulter procedure for Eukaryotic DNA: 100ng of RNA was labeled with Cyanine-3-pCp (Cy 3) using the miRNA Complete Labeling Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s  protocol.

growth_protocol: cells were passaged for no more than 20 passages before total RNA was harvested; normal cells were assessed for chromosomal abnormalities and expression markers.

extract_protocol: total RNA was extracted using the Qiagen miRNeasy mini kit

value: NCH644 Glioma Cells CD133 POS

tag: cell line

value: primary brain cancer

tag: tumor stage

value: IV


title: NCH441 Glioma Cells_CD133 POS

scan_protocol: established Beckman Coulter procedure for Eukaryotic DNA

value: NCH441 Glioma Cells CD133 POS


title: NATURI_71_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_71
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: female

value: 30 yrs


title: NATURI_69_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_69
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: male

value: 43 yrs

value: Day 6 (V2)


title: NATURI_70_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_70
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: 25 yrs

value: Nasal mucosa


title: BLV4 Neural Precursor Cells_CD133 NEG

source_name: normal brain tissue

value: BLV4 Neural Precursor Cells CD133 NEG

value: normal brain tissue

value: normal tissue


title: B4 Glioma Cells_CD133 NEG

value: B4 Glioma Cells CD133 NEG


title: BLV4 Neural Precursor Cells_CD133 POS

value: BLV4 Neural Precursor Cells CD133 POS


title: NATURI_72_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_72
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: Asthmatic_no exacerbation

value: 51 yrs


title: B4 Glioma Cells_CD133 POS

value: B4 Glioma Cells CD133 POS

value: primary brain cancer


title: NATURI_62_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_62
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: 28 yrs


title: NATURI_66_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_66
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: female

value: 36 yrs


title: NATURI_58_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_58
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic without exacerbation at day 2 of cold symptoms

value: Day 2 (V1)


title: NATURI_63_Nasal mucosa_AsmNoEx_day 6

description:
NATURI_63
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, six days after the onset of cold symptoms

value: 33 yrs


title: Leaf_CC_rep2

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

country: Spain

institute: Mision Biologica de Galicia (CSIC)

hyb_protocol: Fifteen µg of cRNA per sample were hybridized using Affymetrix standard procedures

scan_protocol: Fluorescence signaling was scanned using a GeneChip® 3000 scanner followinfg Affymetrix standard procedures

data_processing: Data analysis was performed using the Robust Multichip Average (RMA) tool included in the Affymetrix Expression Console software. Genes with an expression ratio (CL vs. CC) ≤ 0.5 or ≥ 2 were considered down and up-regulated respectively. To identify genes differentially expressed between treatments, a Benjamini-Hochberg multi-test adjusted FDR was calculated between log2-transformed expression ratios from CL and CC sections using the LIMMA software. Genes with a FDR ≤ 0.05 were considered as differentially expressed

organism: Zea mays

source_name: Leaf tissue

label_protocol: Two hundred and fifty ng of total RNA were labeled with the GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA) following manufacturer’s instructions

growth_protocol: Maize seeds were grown on sterilized peat in phytotron under fluorescent light (228 µmol m-2 s-1) in a 14 h light/10 h dark light regime and watered as needed

extract_protocol: Sample tissues were ground in liquid nitrogen and the RNA was extracted using the RiboPureTM kit following manufacturer´s instructions

treatment_protocol: Plants were grown under cold conditions (15 ºC) for three weeks and then exposed to control temperatures (25 ºC) for one extra week. After this period the third leaf showed two well defined sections: distal (chlorophyll-less; CL) and proximal (chlorophyll-containing; CC) sections. Two centimeters of the distal (chlorophyll-less; CL) and proximal (chlorophyll-containing; CC) sections closest to the transition zone were collected from three biological replicates

tag: line

tag: leaf sections

value: Chlorophyll-Containing (CC) section


title: NATURI_61_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_61
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: 53 yrs


title: NATURI_56_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_56
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: male

value: 25 yrs

value: Nasal mucosa


title: NATURI_57_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_57
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: 30 yrs


title: Leaf_CC_rep1


title: NATURI_48_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_48
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: Leaf_CC_rep3


title: NATURI_55_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_55
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: 43 yrs


title: NATURI_52_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_52
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms


title: lymphoblast T-ALL sample #4

description: sample collected in human clinical trial E2993 (Marks et al., 2009)

source_name: lymphoblast TALL patient 4

value: cryopreserved lymphoblast

value: cortical/mature


title: Leaf_CL_rep2

value: Chlorophyll-Less (CL) section


title: NATURI_47_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_47
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: Asthmatic_no exacerbation


title: mid log, D-xylose minimal media, replicate 2

city: La Jolla

first: Haythem

last: Latif

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

organism: Thermotoga maritima MSB8

source_name: Thermotoga maritima MSB8 (ATCC: 43589) wild type

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

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown anoxically at 80 °C in 500 mL serum bottles containing 200 mL of minimal media{Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85} supplemented with the carbon source associated with the condition listed above. This carbon source was the sole carbon source provided to the cells.

extract_protocol: RNA isolation was performed using the RNeasy mini kit (Qiagen) protocol with DNaseI treatment. Total RNA yields were measured by using a NanoDrop (Thermo) at wavelength of 260 nm and quality was checked on an agarose gel.  cDNA synthesis was conducted as described in {Qiu et al., 2010, Genome Res, 20, 1304-11}. In short, 10 μg of purified total RNA sample was reversed transcribed to cDNA with amino-allyl dUTP. The amino-allyl labeled cDNA samples were then coupled with Cy5 Monoreactive dyes (Amersham). Cy5 labeled cDNA samples were fragmented to 50-300 bp range with DNase I (Epicentre). High-density four-plex oligonucleotide tiling arrays consisting of 4 x 71,423 probes of variable length spaced across the whole Thermotoga maritima genome were used (Roche Nimblegen). Hybridization, wash and scan were performed according to the manufacturer’s instructions.

tag: genotype

value: Wild Type

tag: accession

tag: growth media

value: D-xylose minimal media