title: HN5_HNSCC_rep1

description:
940CC0074-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: HSC2_HNSCC_rep2

status: Public on Oct 03 2017

type: RNA

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

description:
940CC0119-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: fRMA normalization and removal of date effect estimated with a limma linear model

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HNSCC cell line HSC2

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: cell type

value: HNSCC (head and neck squamous cell carcinoma)


title: CS6889 Replicate 2

city: Iizuka

first: Kazumasa

last: Shirai

state: Fukuoka

address: 680-4 Kawazu

department: Frontier Research Academy for Young Researchers

country: Japan

institute: Kyushu Institute of Technology

description: Gene expression of CS6889

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2505 BDNA microarray scanner (Agilent Technologies)

data_processing: Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies)

organism: Arabidopsis thaliana

source_name: Aerial parts of seedling

label_protocol: labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology), according to the manufacturer’s protocol.

growth_protocol: 18-days-old seedlings were growing on 1% agar plates containing Murashige and Skoog (MS)

extract_protocol: Approximately 500 μg total RNA was extracted from each sample using TRIzol (Invitrogen)

tag: accession

tag: age

tag: tissue

value: Aerial parts of seedling


title: CS6918 Replicate 1

description: Gene expression of CS6918


title: HO1u1_HNSCC_rep1

description:
940CC0086-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line HO1u1


title: UNC10_HNSCC_rep1

description:
940CC0122-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line UNC10


title: CS6891 Replicate 2

description: Gene expression of CS6891


title: CS6857 Replicate 2

description: Gene expression of CS6857


title: CS6889 Replicate 1

description: Gene expression of CS6889


title: CS6897 Replicate 1

description: Gene expression of CS6897


title: CS6850 Replicate 2

description: Gene expression of CS6850


title: CS6850 Replicate 1

description: Gene expression of CS6850


title: HSC2_HNSCC_rep1

description:
940CC0118-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: CS6839 Replicate 1

description: Gene expression of CS6839


title: CS6805 Replicate 2

description: Gene expression of CS6805


title: CS6839 Replicate 2

description: Gene expression of CS6839


title: CS6824 Replicate 2

description: Gene expression of CS6824


title: CS6826 Replicate 2

description: Gene expression of CS6826


title: CS6769 Replicate 1

description: Gene expression of CS6769


title: CS6736 Replicate 1

description: Gene expression of CS6736


title: JSQ3_HNSCC_rep1

description:
940CC0076-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line JSQ3


title: CS6826 Replicate 1

description: Gene expression of CS6826


title: CS6805 Replicate 1

description: Gene expression of CS6805


title: HO1u1_HNSCC_rep2

description:
940CC0087-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: CS6762 Replicate 2

description: Gene expression of CS6762


title: CS6824 Replicate 1

description: Gene expression of CS6824


title: CS6674 Replicate 1

description: Gene expression of CS6674


title: CS6769 Replicate 2

description: Gene expression of CS6769


title: CS6736 Replicate 2

description: Gene expression of CS6736


title: CS6693 Replicate 2

description: Gene expression of CS6693


title: CS6674 Replicate 2

description: Gene expression of CS6674


title: CS6706 Replicate 1

description: Gene expression of CS6706


title: CS6693 Replicate 1

description: Gene expression of CS6693


title: CS6706 Replicate 2

description: Gene expression of CS6706


title: CS6762 Replicate 1

description: Gene expression of CS6762


title: CS6688 Replicate 2

description: Gene expression of CS6688


title: CS28917 Replicate 2

description: Gene expression of CS28917


title: CS6660 Replicate 2

description: Gene expression of CS6660


title: CS28890 Replicate 2

description: Gene expression of CS28890


title: CS28917 Replicate 1

description: Gene expression of CS28917


title: CS6660 Replicate 1

description: Gene expression of CS6660


title: CS6688 Replicate 1

description: Gene expression of CS6688


title: Control

status: Public on Oct 02 2017

city: Bronx

first: Maureen

middle: J

last: Charron

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

description: RNA was extracted from the mouse liver exposure to a control diet in utero.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.see manufacturer's web site www.nimblegen.com

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.see manufacturer's web site www.nimblegen.com

data_processing: The raw data (.pair file) was analyzed the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Mus musculus

source_name: liver

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.see manufacturer's web site www.nimblegen.com

extract_protocol: Total RNA was extracted from 6 control and 7 HF liver using TRIzol Reagent (Invitrogen) then pooled. First and double strand cDNA was generated using SuperScript Double-Stranded cDNA synthesis Kit (Invitrogen).

tag: strain

value: Liver


title: CS28890 Replicate 1

description: Gene expression of CS28890


title: B2-3_SFTPC-pos-P5_rep1

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

hyb_protocol: 0.6 μg of labeled-cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent. Fragmentated samples were then hybridized to SurePrint G3 Human Gene Expression 8x60K v2 microarrays (Agilent technologies) for 17 hours at 65°C.

scan_protocol: The array slides were scanned using a microarray scanner (Agilent technologies, G2600D) with one color scan setting for 8x60k array slides..

data_processing: To obtain expression level, the scanned images were processed with Feature Extraction Software (Agilent technologies).

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P5, replicate 1

label_protocol: Cy3-labeled cRNA were generated from 0.1 µg of total RNA using the Low Input Quick Amp Labeling Kit (Agilent technologies) and purified by RNeasy column (Qiagen) according to the manufacture's protocol.

growth_protocol: CPMhigh progenitor cells were induced from iPSCs via ventralized anterior foregut andodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days, Step 2: SB431542 and Noggin for 4 days, Step 3: CHIR99021, BMP4 and ATRA, Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days.  P0 SFTPC+ cells were induced from CPMhigh progenitor cells by forming alveolar organoids (AO) via three-dimensional coculture with human fetal lung fibroblasts. P2 and P5 SFTPC+ cells were obtained from P2 and P5 AO which were derived from once and four-times passaged SFTPC+ cells by forming AO, respectively. PAECs were induced from VAFE cells under the treatment with CHIR99021 and FGF10 for 14 days followed by PneumaCult ALI medium with DAPT for 14 days in three-demensional culture.

extract_protocol: Total RNA was extracted by using the PureLink RNA Mini Kit (Life Technologies) according to manufacture's protocol. To digest genomic DNA, extracts was cleaned up by using the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel).

treatment_protocol: Adult AT2 cells were isolated from surgical human adult lung specimen by FACS-based sorting of EpCAMhighPDPN- population after enzymatic dissociation of non-tumor, non-pleural parenchyma.

value: B2-3 hiPSCs

tag: gender

value: female


title: 201B7_PAECs_rep3

source_name: Proximal airway epithelial cells derived from 201B7 hiPSCs, replicate 3

value: 201B7 hiPSCs


title: B2-3_SFTPC-pos-P2_rep1

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P2, replicate 1


title: 201B7_PAECs_rep2

source_name: Proximal airway epithelial cells derived from 201B7 hiPSCs, replicate 2


title: B2-3_SFTPC-pos-P0_rep2

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P0, replicate2


title: Adult-AT2_rep1

source_name: primary isolated alveolar epithelial type 2 cells, replicate 1

value: lung


title: B2-3_SFTPC-pos-P5_rep2

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P5, replicate 2


title: B2-3_SFTPC-pos-P5_rep3

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P5, replicate 3


title: HF

description: RNA was extracted from the mouse liver exposure to a high fat diet in utero.


title: Adult-AT2_rep3

source_name: primary isolated alveolar epithelial type 2 cells, replicate 3


title: Adult-AT2_rep2

source_name: primary isolated alveolar epithelial type 2 cells, replicate 2


title: B2-3_SFTPC-pos-P2_rep3

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P2, replicate 3


title: B2-3_SFTPC-pos-P0_rep1

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P0, replicate1


title: B2-3_CPM-high_rep2

source_name: CPM-high progenitor cells derived form B2-3 hiPSCs, replicate 2


title: B2-3_SFTPC-pos-P2_rep2

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P2, replicate 2


title: B2-3_SFTPC-pos-P0_rep3

source_name: SFTPC positive cells derived from B2-3 hiPSCs, P0, replicate3


title: B2-3_CPM-high_rep1

source_name: CPM-high progenitor cells derived form B2-3 hiPSCs, replicate 1


title: B2-3_SFTPC-neg_rep3

source_name: SFTPC negative cells derived from B2-3 iPSCs, replicate 3


title: B2-3_SFTPC-neg_rep1

source_name: SFTPC negative cells derived from B2-3 iPSCs, replicate 1


title: B2-3_SFTPC-neg_rep2

source_name: SFTPC negative cells derived from B2-3 iPSCs, replicate 2


title: B2-3_SFTPC-pos-P0_rep1


title: B2-3_CPM-high_rep3

source_name: CPM-high progenitor cells derived form B2-3 hiPSCs, replicate 3


title: B2-3_SFTPC-pos-P0_rep2


title: B2-3_CPM-high_rep1


title: ESC_P2_Rep2

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

description: SAMPLE 36

hyb_protocol: Purified and labeled cRNA was used for each hybridization reaction onto BeadChip Array Mouse WG-6 and MouseRef-8 v2.0 (Illumina, San Diego, CA, USA).

scan_protocol: Scanning was performed using the iScan reader (Illumina, San Diego, CA, USA). The raw signal intensities of regular and control probes were extracted from Illumina® GenomeStudio software

data_processing:
RAW expression values were extracted from Illumina GenomeStudio, and were background corrected and quantile normalized by “neqc” function of the R/Bioconductor package “limma” [PMID: 25605792]. Differentially expressed genes were identified by the Empirical Bayesian method of the package limma.
The genes with a minimum absolute log2 fold-change of 1 and Benjamini-Hochberg adjusted p-value of 0.01 were considered significant. Subsequent analysis was performed using custom scripts in R programming language

label: Biotin

source_name: ESC_passage 2

label_protocol: RNA samples (RIN > 9) were subjected to a two-round amplification performed using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre) according to the manufacturer’s instructions.

growth_protocol: For ICM isolation, the E3.5 blastocysts were submitted to zona removal using acidic Tyrode’s solution (pH=2.2), then placed in a mouse trophoblast antibody for 40 min. Next, blastocysts were treated by guinea pig complement in 50 μl droplets under oil for 10 min. After bubbling and lysis of the trophectoderm cells, they were removed by pipetting. The isolated ICMs were washed in PBS twice before they were picked for microarray analysis. Mouse ES cells were derived by transferring the zona-free E3.5 blastocyst/isolated ICM on gelatin coated plates (0.1%, Sigma-Aldrich) that contained N2B27 defined medium supplemented with R2i (which included 1µM PD0325901 (Stemgent) and 10µM SB431542 (Sigma-Aldrich)) as well as 1000 U/ml LIF (ESGRO, Millipore). The time when the E3.5 blastocysts/isolated ICMs were transferred into ES cell culture was designated as day 0.

extract_protocol: Total RNA was isolated using the AllPrep DNA/RNA Micro Kit (Qiagen). Integrity and quality of RNA samples was checked using a RNA 2100 Bioanalyzer (Agilent).

treatment_protocol: For the first microarray analysis, ICM-outgrowths were collected on days-3, -5, -7, and -9 from seeded E3.5 blastocysts as well as from isolated ICMs and ES cells, in three biological replicates. Between 20 to 30 ICM-outgrowths were picked and pooled for each biological replicate.  For the second microarray analysis, we collected new samples in a time resolution experiment that included ICM outgrowths on days-0.5, -1, -2, -3, -5 and ES cells that were in passages -2, -4, and-15. In addition, we collected ICM-outgrowths cultivated in N2B27 supplemented with SB431542 on days -1 (D1-SB) and -3 (D3-SB) as the negative control. Between 30 to 40 ICM-outgrowths were picked and pooled in two biological replicates.

tag: lineage

value: Hybrid_B6 x C3H

tag: culture condition

value: R2i (PD+SB)


title: ICM_Balbc_Rep1

description: SAMPLE 41


title: ICM_Balbc_Rep2

description: SAMPLE 42


title: B2-3_SFTPC-pos-P0_rep3


title: ESC_P15_Rep1

description: SAMPLE 39

source_name: ESC_passage 15


title: ESC_P15_Rep2

description: SAMPLE 40


title: ESC_P4_Rep2

description: SAMPLE 38

source_name: ESC_passage 4


title: B2-3_CPM-high_rep2


title: ESC_P4_Rep1

description: SAMPLE 37


title: 201B7_PAECs_rep1

source_name: Proximal airway epithelial cells derived from 201B7 hiPSCs, replicate 1


title: SBIO_D1_Rep2

description: SAMPLE 32

source_name: ICM outgrowth, Day1, SB Condition

value: SB


title: ESC_P2_Rep1

description: SAMPLE 35


title: SBIO_D1_Rep1

description: SAMPLE 31


title: SBIO_D3_Rep1

description: SAMPLE 33

source_name: ICM outgrowth, Day3, SB Condition


title: IO_D5_Rep1

description: SAMPLE 29

source_name: ICM outgrowth, Day5


title: ESC_Balbc_Rep3

description: SAMPLE 18

value: Balbc


title: IO_D3_Rep2

description: SAMPLE 28

source_name: ICM outgrowth, Day3


title: B2-3_CPM-high_rep3


title: IO_D3_Rep1

description: SAMPLE 27


title: ESC_Balbc_Rep2

description: SAMPLE 17


title: IO_D0.5_Rep2

description: SAMPLE 22

source_name: ICM outgrowth, Day0.5


title: IO_D5_Rep2

description: SAMPLE 30


title: IO_D2_Rep2

description: SAMPLE 26

source_name: ICM outgrowth, Day2


title: IO_D0.5_Rep1

description: SAMPLE 21


title: ESC_Balbc_Rep1

description: SAMPLE 16


title: IO_D2_Rep1

description: SAMPLE 25


title: SBIO_D3_Rep2

description: SAMPLE 34


title: IO_D1_Rep2

description: SAMPLE 24

source_name: ICM outgrowth, Day1


title: BO_D9_Rep2

description: SAMPLE 14

source_name: Blastocyst outgrowth, Day9


title: BO_D9_Rep1

description: SAMPLE 13


title: IO_D1_Rep1

description: SAMPLE 23


title: BO_D7_Rep3

description: SAMPLE 12

source_name: Blastocyst outgrowth, Day7


title: ICM_Hyb_Rep2

description: SAMPLE 20

value: Embryo_Hybrid_B6 x C3H


title: BO_D7_Rep1

description: SAMPLE 10


title: BO_D9_Rep3

description: SAMPLE 15


title: BO_D5_Rep3

description: SAMPLE 9

source_name: Blastocyst outgrowth, Day5


title: BO_D7_Rep2

description: SAMPLE 11


title: ICM_Hyb_Rep1

description: SAMPLE 19


title: BO_D5_Rep1

description: SAMPLE 7


title: BO_D5_Rep2

description: SAMPLE 8


title: ICM_Balbc_Rep2

description: SAMPLE 2


title: BO_D3_Rep2

description: SAMPLE 5

source_name: Blastocyst outgrowth, Day3


title: ICM_Balbc_Rep1

description: SAMPLE 1


title: BO_D3_Rep3

description: SAMPLE 6


title: HH1811_SPA70+TO90137_rep1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

hyb_protocol: Microarray hybridization was performed at 65°C for 18 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 3μm resolution, and the array data was extracted with Agilent feature extraction software using the GE1_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used along with LOWESS normalization

label_protocol: 100ng of total RNA were labeled (Cy3) according to Agilent's labeling protocol

growth_protocol: HPPs were cultured in Williams’ Medium E containing Hepatocyte Maintenance Supplement Pack  at 37°C, 5% CO2

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: HPPs were treated with DMSO, 1 μM rifampicin,  100 nM SR12813, and 30 nM TO90137 without and with 2.5 μM SPA70 for 48 hours in 6-well plates.

value: primary human hepatocytes

tag: treatment

value: 48hr treatment of 30 nM TO90137 with 2.5 μM SPA70


title: HH1811_SPA70_rep3

value: 48hr treatment of 2.5 μM SPA70


title: HH1811_SPA70+SR12813_rep3

value: 48hr treatment of 100 nM SR12813 with 2.5 μM SPA70


title: HH1811_SPA70+Rifampicin_rep1

value: 48hr treatment of 1 μM rifampicin with 2.5 μM SPA70


title: HH1811_SPA70+Rifampicin_rep2


title: HH1811_SPA70_rep2


title: HH1811_SPA70+Rifampicin_rep3


title: Control2

type: genomic

description: DNA was extracted from the mouse exposure to a control diet in utero.

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

scan_protocol: see manufacturer's web site www.nimblegen.com

data_processing: Data analysis was performed using our published pipeline (Thompson, Reimers, Khulan, Gissot, Richmond, Chen, Zheng, Kim and Greally 2008), an open source resource available through BioConductor (HELP package)

molecule: genomic DNA

source_name: LM-PCR products from HpaII digested DNA

label_protocol: The samples were labeled for microarray analysis as described previously [Selzer, Genes Chromosomes Cancer 44:305–319] using Cy3 or Cy5-conjugated oligonucleotides and random primers.

extract_protocol: High molecular weight genomic DNA was extracted from liver in mouse exposure to a control or high fat (HF) diet in utero

tag: genotype

value: wild type

tag: fraction

value: HpaII digested DNA

source_name: LM-PCR products from MspI digested DNA

value: MspI digested DNA


title: HH1811_TO90137_rep2

value: Liver

value: 48hr treatment of 30 nM TO90137


title: HH1811_SPA70_rep1


title: HH1811_SPA70+SR12813_rep1


title: ICM_Balbc_Rep3

description: SAMPLE 3


title: HH1811_SPA70+SR12813_rep2


title: HH1811_SPA70+TO90137_rep2


title: HH1811_TO90137_rep3


title: HF3

description: DNA was extracted from the mouse exposure to a high fat diet in utero.


title: Control3


title: HH1811_SPA70+TO90137_rep3


title: HH1811_TO90137_rep1


title: HF2


title: HH1811_SR12813_rep3

value: 48hr treatment of 100 nM SR12813


title: HF1


title: Patient HN75

city: Aviano

first: Francesca

last: Citron

state: PN

address: Via F.Gallini 2

department: Molecular Oncology

country: Italy

institute: C.R.O. of Aviano - National Cancer Institute

hyb_protocol: tagged miRNA preparation were hybridated with target-specific probes pair for each miR. The Reporter probe carries the fluorescent signal and the Capture Probe allows the complex to be immortalized for data collection.

scan_protocol: After the hybridization, excess probes are removed and probe/target complex are analyzed in a nCounter Cartridge using nCounter Digital Analyzer for data collection

data_processing:
After samples preparation and detection, nCounter Analysis system was used to obtain miRs expression data
Raw Data was normalized to internal postive spike control present in each reaction to account for minor different hybridization and purification efficiencies. This normalized data was also normalized for housekeeping gene for the account of starting RNA quantity.

label: tags specific to their target miRs

source_name: primary HNSCC

label_protocol: 100 ng of RNA samples were prepared following a multiplex annealing of specific tags to their target miRs, a ligation reaction and an enzymatic purification step to remove unligated material

extract_protocol: total RNA was extracted using Tryzol Solution (Invitrogen) from frozen (-80°C)  primary HNSCC tumors

value: primary HNSCC

tag: recurrence status after 2 years

value: no


title: Patient HN78


title: HH1811_SR12813_rep1


title: Patient HN74


title: Patient HN76


title: Patient HN73


title: HH1811_SR12813_rep2


title: Control1


title: HH1811_Rifampicin_rep3

value: 48hr treatment of 1 μM rifampicin


title: Patient HN69


title: Patient HN66

value: yes


title: Patient HN65


title: HH1811_DMSO_rep3

value: 48hr treatment of DMSO


title: HH1811_Rifampicin_rep2


title: HH1811_DMSO_rep2


title: HH1811_Rifampicin_rep1


title: Patient HN62


title: Patient HN63


title: Patient HN61


title: HH1811_DMSO_rep1


title: Patient HN72


title: Patient HN55


title: Patient HN52


title: Patient HN50


title: Patient HN49


title: Patient HN46


title: HUVEC FOXO1 SI.2

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

hyb_protocol: Samples were hybridized onto beadchips according to gene expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed.

source_name: HUVEC

label_protocol: Samples were labeled according to gene expression profiling protocol from Illumina

growth_protocol: HUVECs grown in EGM-2 (Lonza)

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Transfected with siRNAs (Stealth siRNA, Invitrogen) for 72 hours

value: HUVEC

tag: genotype/variation

value: FOXO1 knockdown


title: Patient HN45


title: Patient HN44


title: Patient HN42


title: HUVEC FOXO1 SI.1


title: Patient HN40


title: Patient HN34


title: Patient HN37


title: Patient HN33


title: Patient HN56


title: Patient HN25


title: Patient HN23


title: Patient HN24


title: Patient HN36


title: Patient HN21


title: Patient HN20


title: Patient HN31


title: Patient HN19


title: Patient HN32


title: Patient HN15


title: Patient HN26


title: Patient HN8


title: Patient HN18


title: Patient HN7


title: Patient HN4


title: Patient HN22


title: Patient HN2


title: Patient HN1


title: Sample 1A

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

country: Germany

institute: Bundeswehr Institute for Radiobiology

hyb_protocol: Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; SurePrint G3 Human Genome CGH Microarray 2x400K, 5.3 kb spacing).

scan_protocol: Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.3 March 2014; Agilent® G2505C; Scan Control Version A.8.1.3; resolution 3 µm; 16 bit TIFF; no XDR; Images were quantified using Agilent Feature Extraction Software (version 12.0).

data_processing: Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.

label_protocol: Samples were labeled with Cy3 and reference DNA (GM12878) was labeled Cy5 according to manufactures protocol (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).

growth_protocol:
samples were mechanically grinded in liquid nitrogen; we added a digestion step with 1 µg RNAse A at 37°C for 30 minutes, samples were washed in 200µl 1xTE-buffer
controls (suspension cells) were washed in PBS twice and centrifuged at 6000g. Afterward controls were treated same as samples

extract_protocol: Genomic DNA was extracted from tissue samples with Quiagen Genomic DNA Isolation Kit Mini for Blood and Tissue (Version 04/12).

value: basal cell carcinoma

tag: tag

value: IV


title: Sample 2


title: Sample II


title: Sample 1


title: GIC7, control shRNA, rep 2

status: Public on Oct 01 2017

city: Barcelona

first: Nuria

last: de la Iglesia

address: Rossello 153

country: Spain

institute: IDIBAPS

description:
GIC-CTRL_02
gene expession of control glioma initiating cells in serum-free neural stem cell medium

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (Agilent-039494) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data normalization was carried out using GeneSpring GX version 11.5 (Agilent Technologies).

source_name: proneural glioma stem-like cell_shRNA control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Patient-derived GICs were cultured under adherent conditions on laminin in serum-free neural stem cell medium (in the presence of bFGF and EGF) at 37°C, 5% CO2 and 5% oxygen.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality control was monitored in a 2100 Bioanalyzer (Agilent Technologies). In all cases, the RNA integrity number was >7.

treatment_protocol: Control- and GPR56 knockdown-GICs were obtained by infection with lentiviruses expressing either a non-mammalian shRNA control or a shRNA targeting GPR56, followed by puromycin selection.

tag: tumor type

value: Glioblastoma

value: Patient-derived CD44low glioma stem-like initiating cell (GICs)

value: control


title: BO_D3_Rep1

description: SAMPLE 4

value: Balbc

value: R2i (PD+SB)


title: GIC7, GPR56 shRNA, rep 1

description:
GIC-SH5_05
gene expession of GPR56 knockdown glioma initiating cells in serum-free neural stem cell medium

source_name: proneural glioma stem-like cell_GPR56 shRNA

value: GPR56 knockdown


title: GIC2, GPR56 shRNA, rep 2

description:
GIC-SH5_08
gene expession of GPR56 knockdown glioma initiating cells in serum-free neural stem cell medium


title: GIC2, control shRNA, rep 2

description:
GIC-CTRL_04
gene expession of control glioma initiating cells in serum-free neural stem cell medium


title: Sample 3


title: GIC7, GPR56 shRNA, rep 2

description:
GIC-SH5_06
gene expession of GPR56 knockdown glioma initiating cells in serum-free neural stem cell medium


title: GIC2, control shRNA, rep 1

description:
GIC-CTRL_03
gene expession of control glioma initiating cells in serum-free neural stem cell medium


title: GIC2, GPR56 shRNA, rep 1

description:
GIC-SH5_07
gene expession of GPR56 knockdown glioma initiating cells in serum-free neural stem cell medium


title: CtrlsiRNA + LPS 3

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description: Gene expression after Ctrl-siRNA treat for 24h plus LPS 4h

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A

scan_protocol: A total of 2 µg RNA from each sample was then labeled with the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). After hybridization, the slides were scanned with the Agilent Microarray Scanner (Agilent p/n G2505C),

data_processing: Quantified signals were extracted and analyzed by using the Agilent Feature Extraction Software, in accordance with MIAME guidelines

source_name: RAW264.7 mouse macrophage cells

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The RAW264.7 mouse macrophage cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplied with 10% fetal bovine serum and antibiotics (100 IU/ml of penicillin and 100 µg/ml of streptomycin). Atmosphere: air, 95%; carbon dioxide (CO2), 5% ; Temperature: 37°C

treatment_protocol: The RAW264.7 mouse macrophage cells were grown to 80% confluence for four groups: the siRNA control (Group A, cells treated with a non-specific scrambied siRNA control), the LPS-stimulated (Group B, cells treated with the siRNA control plus LPS stimulation), lincRNA-Tnfaip3 siRNA (Group C, cells treated with an siRNA to lincRNA-Tnfaip3), and lincRNA-Tnfaip3 siRNA/LPS stimulated (Group D, cells treated with the lincRNA-Tnfaip3 plus LPS stimulation). Cells were treated with the siRNAs for 24h, followed by additional culture for 4h in the presence or absence of LPS (E. coli LPS, 1 µg/ml). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: macrophage


title: LOG fold changes: C13 line, Hypoxia 24h - C13 line, Control 24h

city: Helsinki

first: Olga

last: Blokhina

address: Viikinkaari 1

department: Biosciences

country: Finland

institute: University of Helsinki

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
Analysis used  RNA from 16d old + 24 hours untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 24 hours of hypoxia.

hyb_protocol: Each microarray field was used to hybridise  (for 16 h at 65oC) three samples labelled with three different dyes.

scan_protocol: Signal intensities were processed with GenePix Pro 6.1

data_processing: Data normalization was performed by R language and BioConductor Packages. First the data was normalized using quantile normalization and in-house modified version of COMBAT software.

label: HyPer5, Cy3, Alexa 488

label_protocol: Reverse transcription of tRNA (500 ng), second strand cDNA synthesis, in vitro transcription and synthesis of amino allyl-modified RNA were carried out with Amino AllylMessageAMPTMaRNA Amplification kit (Ambion). Individual samples were randomly labelled with three dyes: Cy3, HyPer5 (GE Healthcare) and Alexa Fluor 488 (Invitrogen). Each microarray field was used to hybridise three samples

growth_protocol: Seeds were sterilized in 70% ethanol supplemented with 2% TRITON X-100 for 5 min, and imbibed for 72 h at +4oC in the dark. Plants were grown for 16 d on vertical square 10x10 cm agar plates (½ MS; 1% sucrose; 0.7% agar, pH 5.7). Before plating the agar layer was covered with sterile 100 μm polypropylene mesh (Nitex 03- 100/47, Sefar) to facilitate post-treatment harvesting of plant material and to prevent root growth into agar. All plants were grown under short day conditions with 10 h/14 h light/dark, at 22-24oC and light intensity100 μeinstein m-2 s-1.

extract_protocol: After the hypoxic and DETA treatments shoots were harvested in a timed manner (less than 1 min/plate) and immediately frozen in liquid N2. Total RNA was extracted from 25-35 mg of frozen pulverized shoots using Sigma Spectrum Plant total RNA kit according to manufacturer’s instructions.

treatment_protocol: Hypoxic stress was created by sealing plates with seedlings for 2 and 24 h in Oxoid AnaeroGen Compact kit AnaeroGen W-zip bags with oxygen-consuming sachet and controlled with O2 indicators (Oxoid, Thermo Fisher Scientific, UK). NO donor DETA treatment was initiated by dilution of stable stock solution of DETA to a final concentration 500uM. Two ml of 500uM DETA was applied per plate in a timed manner. During the incubation plants were kept in the growth chamber with the settings described, and were able to photosynthesize.

tag: organ

value: shoot

source_name: C13 plants grown under normal conditions for 16d + 24 h, C13 Control 24h


title: LOG fold changes: Mt62 line, Hypoxia 24h - Mt62 line, Control 24h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old + 24 hours untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 24 hours of hypoxia

source_name: Mt62 plants grown under normal conditions for 16d + 24 h, Mt62 Control 24h


title: LincTnfaip3siRNA + LPS 3

description: Gene expression after Linc-Tnfaip3-siRNA  treat for 24h plus LPS 4h

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

tag: cell line


title: CtrlsiRNA + LPS 2

tag: cell type


title: LincTnfaip3siRNA 2

description: Gene expression after Linc-Tnfaip3-siRNA  treat for 24h


title: LincTnfaip3siRNA 1


title: Sample I


title: CtrlsiRNA + LPS 1


title: LincTnfaip3siRNA + LPS 2


title: LOG fold changes: WT, Hypoxia 24h -  WT, Control 24h

description:
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
Analysis used  RNA from 16d old + 24 hours untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 24 hours of hypoxia

source_name: WT plants grown under normal conditions for 16d + 24 h, WT Control 24h


title: LincTnfaip3siRNA 3


title: GIC7, control shRNA, rep 1

description:
GIC-CTRL_01
gene expession of control glioma initiating cells in serum-free neural stem cell medium


title: CtrlsiRNA 3

description: Gene expression after Ctrl-siRNA treat for 24h


title: CtrlsiRNA 2


title: LincTnfaip3siRNA + LPS 1


title: CtrlsiRNA 1


title: LOG fold changes: C13 line, Hypoxia 2h- C13 line, Control 2h

description:
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911603_A7F4_Hy5  C13 c 2h _Cy 3  Wt DETA 24h  _ Al C13 H2h
lost
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911603_A7F4_Hy5  C13 c 2h _Cy 3  Wt DETA 24h  _ Al C13 H2h
Analysis used  RNA from 16d old + 2hours untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 2 hours of hypoxia

source_name: C13 plants grown under normal conditions for 16d + 2 h, C13 Control 2h


title: LOG fold changes: Mt62 line, Hypoxia 2h-Mt62 line, Control 2h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used  RNA from 16d old + 2hours untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 2 hours of hypoxia.

source_name: Mt62 plants grown under normal conditions for 16d + 2 h, Mt62 Control 2h


title: Patient HN38

value: primary HNSCC


title: LOG fold changes: WT, Hypoxia 2h - WT Control 2h

description:
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
Analysis used  RNA from 16d + 2 hours old untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 2 hours of hypoxia.

source_name: WT plants grown under normal conditions for 16d + 2 h, WT Control 2h


title: LOG fold changes: C13 line, DETA treatment 24h- C13 line, Control 24h

description:
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
Analysis used  RNA from 16d old + 24 hours untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 24 hours of DETA treatment.


title: LOG fold changes: Mt62 line, DETA treatment 24h - Mt62 line, Control 24h

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old + 24 hours untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 24 hours of DETA treatment.


title: LOG fold changes: C13 line, DETA treatment 2h - C13 line, Control 2h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911603_A7F4_Hy5  C13 c 2h _Cy 3  Wt DETA 24h  _ Al C13 H2h
Analysis used  RNA from 16d old + 2hours untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 2 hours of DETA treatment.


title: LOG fold changes: WT, DETA treatment 2h - WT,  Control 2h

description:
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
lost
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
Analysis used  RNA from 16d old + 2hours untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 2 hours of DETA treatment.


title: LOG fold changes: WT, DETA treatment 24h - WT,  Control 0h

description:
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 24 hours of DETA treatment.

source_name: WT plants grown under normal conditions for 16d, Control 0h


title: LOG fold changes: WT, DETA treatment 24h - WT, Control 24h

description:
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
Analysis used  RNA from 16d old + 24 hours untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 24 hours of DETA treatment


title: LOG fold changes: Mt62 line, DETA treatment 2h - Mt62 line, Control 2h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used  RNA from 16d old + 2hours untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 2 hours of DETA treatment.


title: LOG fold changes: C13 line, DETA treatment 2h  - WT, DETA treatment 2h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
lost
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used  RNA from WT plants subjected to 2 hours of DETA treatment  as control samples for comparison to the experimental C13 plants subjected to 2 hours of DETA treatment


title: LOG fold changes: Mt62 line, Hypoxia 24h - WT, Hypoxia 24h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
Analysis used RNA from WT plants after 24 h of hypoxia as control samples for comparison to the experimental Mt62 plants after 24 h of hypoxia

source_name: Mt62 plants subjected to 24 hours of  hypoxia

source_name: WT plants subjected to 24 hours of  hypoxia


title: LOG fold changes: Mt62 line,  DETA treatment 2h - WT, DETA treatment 2h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
lost
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used  RNA from WT plants subjected to 2 hours of DETA treatment  as control samples for comparison to the experimental Mt62 plants subjected to 2 hours of DETA treatment


title: LOG fold changes: C13 line, DETA treatment 24h - C13 line, Control 0h

description:
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 24 hours of DETA treatment.

source_name: C13 plants grown under normal conditions for 16 d, Control 0 h


title: LOG fold changes: WT, DETA treatment 2h - WT, Control 0h

description:
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
lost
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 2 hours of DETA treatment


title: LOG fold changes: Mt62 line, DETA treatment 24h - Mt62 line, Control 0h

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
lost
Analysis used  RNA from 16d old untreated Mt62 plants   as control samples for comparison to the experimental MT62 plants subjected to 24 hours of DETA treatment.

source_name: Mt62 plants subjected to 24 hours of DETA treatment

source_name: Mt62 plants grown under normal conditions for 16 d, Control 0 h


title: LOG fold changes: Mt62 line, DETA treatment 24h - WT, DETA treatment 24h

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
Analysis used  RNA from WT plants subjected to 24 hours of DETA treatment  as control samples for comparison to the experimental Mt62 plants subjected to 24 hours of DETA treatment


title: LOG fold changes: Mt62 line, DETA treatment 2h - Mt62 line, Control 0h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
lost
Analysis used  RNA from 16d old untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 2 hours of DETA treatment.


title: LOG fold changes: C13 line, Hypoxia 24h  -  WT, Hypoxia 24h

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
Analysis used RNA from WT plants after 24 h of hypoxia as control samples for comparison to the experimental C13 plants after 24 h of hypoxia

source_name: C13 plants subjected to 24 hours of  hypoxia


title: LOG fold changes: C13 line, DETA treatment 24h -WT, DETA treatment 24h

description:
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911603_A7F3_Hy5  M62 DETA 2h _Cy 3  Wt c 2h _ Al C13 DETA 24h
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
Analysis used  RNA from WT plants subjected to 24 hours of DETA treatment  as control samples for comparison to the experimental C13 plants subjected to 24 hours of DETA treatment


title: LOG fold changes: C13 line, Hypoxia 24h - C13 line, Control 0h

description:
2521116911605_A1F4_ Hy5 Wt c24h_Cy3 M62 DETA 24h_Al C13 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911598_A4F3_Hy5 Wt DETA 2h_Cy3 C13 H24h_Al Wt DETA 24h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911602_A6F3_Hy5  C13 c 0h _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 24 hours of hypoxia.


title: LOG fold changes: Mt62 line Hypoxia 24h - Mt62 line, Control 0h

description:
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911604_A2F4_Hy5 C13 DETA 24h_Wt c 24h_Al M62 H24h
252116911597_A3F3_Hy5 C13 H24h_Cy3 M62 H24h_Al M62 c 2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
lost
Analysis used  RNA from 16d old untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 24 hours of hypoxia.

source_name: Mt62  plants grown under normal conditions for 16 d, Control 0 h


title: LOG fold changes: WT, Hypoxia 24h - WT, Control 0h

description:
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911598_A4F2_Hy5 C13 c 2h_Cy3 Wt H24h _Al Mt62 DETA 2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 24 hours of hypoxia.


title: LOG fold changes: C13 line, DETA treatment 2h -C13 line,  Control 0h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911601_A5F1_Hy5 C13 DETA 2h_Cy3 Wt c 2h_ Al Wt H24h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
252116911603_A7F1_Hy5  Wt c 24h_Cy 3  Wt DETA 24h_ Al C13 DETA 2h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 2 hours of DETA treatment.


title: LOG fold changes: WT, Hypoxia 2h - WT, Control 0h

description:
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the experimental WT plants subjected to 2 hours of hypoxia


title: LOG fold changes: Mt62 line, Hypoxia 2h - WT, Hypoxia 2h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used RNA from WT plants after 2h of hypoxia as control samples for comparison to the experimental  Mt62 plants after 2 h of hypoxia

source_name: Mt62 plants subjected to 2 hours of  hypoxia

source_name: WT plants subjected to 2 hours of hypoxia


title: LOG fold changes: C13 line, Hypoxia 2h - C13  line, Control 0h

description:
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911603_A7F4_Hy5  C13 c 2h _Cy 3  Wt DETA 24h  _ Al C13 H2h
lost
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911602_A6F3_Hy5  C13 c 0h _Cy3  C13 DETA 2h _Al  M62 c 24h
Analysis used  RNA from 16d old untreated C13 plants   as control samples for comparison to the experimental C13 plants subjected to 2 hours of hypoxia.


title: LOG fold changes: C13 line, Hypoxia 2h - WT, Hypoxia 2h

description:
252116911604_A2F3_Hy5 Wt DETA 24h_Cy3 M62 c 2h_Al C13 H2h
252116911602_A6F1_Hy5 M62 H24h_Cy3 C13 H2h_Al Wt c 2h
252116911603_A7F4_Hy5  C13 c 2h _Cy 3  Wt DETA 24h  _ Al C13 H2h
lost
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911601_A5F3_Hy5 Wt H2h_Cy3 M62 c 24h_ Al C13 H24h
252116911602_A6F4_Hy5 M62 c 2h_Cy3 Wt H2h _Al Wt DETA 2h
Analysis used RNA from WT plants after 2h of hypoxia as control samples for comparison to the experimental C13 plants after 2 h of hypoxia

source_name: C13 plants subjected to 2 hours of  hypoxia


title: LOG fold changes: Mt62 line, Hypoxia 2h - Mt62 line, Control 0h

description:
2521116911605_A1F3_ Hy5 M62 c2h_Cy3 C13 DETA 2h_Al M62 H2h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911598_A4F1_Hy5 Wt c 2h_Cy3 M62 H2h_Al C13 c 24h
252116911601_A5F2 _Hy5 M62 DETA 24h_Cy3 C13 c 2h_ Al  M62 H2h
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
lost
Analysis used  RNA from 16d old untreated Mt62 plants   as control samples for comparison to the experimental Mt62 plants subjected to 2 hours of hypoxia.


title: LOG fold changes: Mt62 line, Control 0h -  WT, Control 0h

description:
252116911597_A3F4_Hy5 M62 c 0h_Cy3 Wt c 24h_Al C13 DETA 24h
252116911598_A4F4_Hy5 M62 c 24h_Cy3 M62 c 0h_Al WT H2h
252116911603_A7F2_Hy5 C13 c 24h _Cy 3  M62 c 0h_ Al M62 DETA 24h
lost
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the 16d old untreated experimental samples  expressing Vitreoscilla Hb at 0h.


title: L. Garvieae 21881, Linoleic acid rep1

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

description: Biological replicate 1 of 3. L. Garvieae str.21881 grown in media with linoleic acid

hyb_protocol: Hybridization protocol followed was that suggested by Agilent´s according to the Two-color microarray-based prokaryote analysis protocol

scan_protocol: Image acquisition and scanning was done following Agilent's instruction and protocols (GE2_107_Sep09) on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS Normalization was done using BRB Array Express software

organism: Lactococcus garvieae 21881

source_name: L. Garvieae 21881, Linoleic acid

label_protocol: A total of 5 ug of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III labeling kit (Agilent ) and according to the two color microarray-based prokaryote analysis protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). The yield and the specific activity of each labelling reaction were determined in a NanoDrop 1000 spectrophotometer.

growth_protocol: L. garvieae 21881 was grown aerobically in MRS broth under different stress conditions (4% NaCl, 0.001% Linoleic Acid, 42 ºC) and harvested at the mid-log phase (OD600 ~ 0.9) for RNA extraction. For the reference sample, L. garvieae strains 21881 and 8831 were grown aerobically in MRS broth al 29 ºC.

extract_protocol: Total RNA from L. garvieae strains 21881 and 8831 was isolated from three independent biological replicates of each temperature condition by using RNeasy protect bacteria mini kit (Qiagen) according to the manufacturer’s protocol. The quality and concentration of RNA was determined by using the RNA 6000 NanoKit on the Bioanalyzer 2100 (Agilent). Only high- quality RNA samples (RIN > 9) were used for labeling and hybridization.

tag: temperature

value: Linoleic acid

organism:
Lactococcus garvieae 8831
Lactococcus garvieae 21881

source_name: Reference control

tag: reference

value: Equimolar mixture of 21881 & 8831 strains at 29C


title: LOG fold changes: C13  line, Control 0 h - WT, Control 0h

description:
2521116911605_A1F2_ Hy5 C13 c0h_Cy3 Wt DETA 2h_Al Wt H2h_A
252116911604_A2F2_Hy5 M62 DETA 2h_Cy3 C13 c 0h_Al M62 H24h
252116911597_A3F2_Hy5 Wt H24h_Cy3 C13 c 24h_Al C13 c 0h
252116911602_A6F3_Hy5  C13 c 0h  _Cy3  C13 DETA 2h _Al  M62 c 24h
2521116911605_A1F1_Hy5 WT c0h_Cy3 M62 c24h_Al C13 DETA 24h
252116911604_A2F1_Hy5 C13 c 24h_Cy3 Wt c 0h_Al Wt H24 h
252116911597_A3F1_Hy5 M62 H2h_Cy3 M62 DETA 2h_Al Wt c 0h
252116911602_A6F2_Hy5 Wt c 0h _Cy3  M62 DETA 24h_Al C13 c 2h
Analysis used  RNA from 16d old untreated WT plants   as control samples for comparison to the 16d old untreated experimental samples  expressing Vitreoscilla Hb at 0h.


title: L. Garvieae 21881, Linoleic acid rep2

description: Biological replicate 2 of 3. L. Garvieae str.21881 grown in media with linoleic acid


title: L. Garvieae 21881, 42C rep1

description: Biological replicate 1 of 3. L. Garvieae str.21881 grown at 42 degrees celsius

source_name: L. Garvieae 21881, 42C

value: 42 degrees Celsius


title: L. Garvieae 21881, High Salt rep2

description: Biological replicate 2 of 3. L. Garvieae str.21881 grown in high salt content media

source_name: L. Garvieae 21881, High Salt

value: High salt


title: L. Garvieae 21881, High Salt rep3

description: Biological replicate 3 of 3. L. Garvieae str.21881 grown in high salt content media


title: resting memory (CD4+CD45RO+CD38-)

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: primary cells

hyb_protocol: Samples were hybridised as per Affymetrix standard protocols

scan_protocol: Samples were scanned as per Affymetrix standard protocols

data_processing: RMA normalised using the Affy package in R and only the ‘main’ probes were used.

label_protocol: Samples were labelled as per Affymetrix standard protocols

growth_protocol: A healthy individual was recruited from university staff undergoing routine inoculation with vaccinia virus as required by local occupational health and safety regulations. The vaccinia virus was administered into the left or right deltoid region. PBMC was collected at baseline and day 13 post-inoculation. Day 13 PBMCs were sorted by FAC.

extract_protocol: Total mRNA extracted  using TriZol® Reagent (Invitrogen, 15596-018) followed by chloroform extraction (Sigma, C2432) and precipitation with isopropanol.


title: L. Garvieae 21881, Linoleic acid rep3

description: Biological replicate 3 of 3. L. Garvieae str.21881 grown in media with linoleic acid


title: Polysome-bound RNA from naive spinal cord, biological replicate 1

city: Heidelberg

first: Ana

last: Martin-Villalba

address: In Neuenheimer Feld 581

department: Molecular Neurobiology

institute: German Cancer Research Centre

description: Polysome-bound RNA

hyb_protocol: 15μg fragmented cRNA was hybridized on GeneChip Mouse Genome 430A 2.0 Array for 16 hours at 45°C with 60rpm in the rotisserie oven. For washing and staining the probe arrays, the Affymetrix GeneChip Fluidics Station 400 was used

scan_protocol: GeneChips were scanned using the Affymetrix HP GeneArray scanner

data_processing: The data were normalized with the vsn package (R/Bioconductor) using the vsnrma function with parameter lts.quantile=0.5

source_name: Polysome-bound RNA from mouse spinal cord after sham operation

label_protocol: Biotinylated cRNA were prepared using GeneChip One-Cycle Target Labeling and Control Reagents according to manufacturer's protocol, from 5µg of total RNA or 3µg of polysome-bound RNA

growth_protocol: Wild-type female C57BL/6 mice of 10 weeks of age

extract_protocol: Spinal cords were lyzed with a Dounce homogenizer. A small aliquit was taken to isolate total RNA. The rest underwent sucrose gradient fractionation to isolate polysome-bound RNA. Detailed protocols are as in (Lou et al., Jove, 2014)

treatment_protocol: Spinal cords were exposed by laminectomy and an 80% transectional cut was performed with irridectomy scissors. Naïve mice were subjected only to laminectomy. Nine hours after the operation, 2.5 cm of spinal cord tissue centering on the lesion site was extracted. Procedures were conducted in accordance with the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

tag: tissue

value: spinal cord

value: female

tag: age

value: 10 weeks


title: L. Garvieae 21881, 42C rep2

description: Biological replicate 2 of 3. L. Garvieae str.21881 grown at 42 degrees celsius


title: Total RNA from injured spinal cord, biological replicate 2

description: Total RNA

source_name: Total RNA from mouse spinal cord after transection injury

tag: gender


title: Polysome-bound RNA from injured spinal cord, biological replicate 2

description: Polysome-bound RNA

source_name: Polysome-bound RNA from mouse spinal cord after transection injury


title: activated memory (CD4+CD45RO+CD38+)

description: primary cells


title: Polysome-bound RNA from naive spinal cord, biological replicate 3

description: Polysome-bound RNA


title: Total RNA from naive spinal cord, biological replicate 2

description: Total RNA

source_name: Total RNA from mouse spinal cord after sham operation


title: Total RNA from injured spinal cord, biological replicate 3

description: Total RNA


title: L. Garvieae 21881, High Salt rep1

description: Biological replicate 1 of 3. L. Garvieae str.21881 grown in high salt content media


title: Polysome-bound RNA from injured spinal cord, biological replicate 1

description: Polysome-bound RNA


title: Polysome-bound RNA from injured spinal cord, biological replicate 3

description: Polysome-bound RNA


title: Senescent_rep 4

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Dox treated cells after culturing in fresh medium for 8 days

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent  scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: Images were quantified using Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using GeneSpring GX  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: Senescent

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: U2OS control cells were cultured in 10% FBS. For quiescence, U2OS cells were cultured in 0.1% serum for 96 h and then the G0 (quiescent) cells were sorted using FACS.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit  following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For senescence, U2OS cells were treated with doxorubicin (1μM) for 2 h, then cells were recultured in fresh medium for 8 days.

tag: growth phase

value: Growth arrested

value: Dox treated

tag: cell state

value: Senescent


title: Quiescent_rep 4

description: Sorted G0 cells cultured in 0.1% FBS for 96 h

source_name: Quiescent

tag: treatment

value: G0 sorted cells

value: Quiescent


title: Total RNA from injured spinal cord, biological replicate 1

description: Total RNA

tag: genotype


title: Total RNA from naive spinal cord, biological replicate 1

description: Total RNA


title: Polysome-bound RNA from naive spinal cord, biological replicate 2

description: Polysome-bound RNA


title: Control_rep 4

description: U2OS cells cultured in 10% FBS

source_name: Control

value: Proliferating

value: Control


title: L. Garvieae 21881, 42C rep3

description: Biological replicate 3 of 3. L. Garvieae str.21881 grown at 42 degrees celsius


title: Total RNA from naive spinal cord, biological replicate 3

description: Total RNA


title: naïve (CD4+CD45RO-CD38dim),

description: primary cells


title: Control_rep 3

description: U2OS cells cultured in 10% FBS


title: Senescent_rep 3


title: Parental cell lines

city: Osaka

first: Kazuko

last: Sakai

address: 377-2, Osaka-sayama

department: Dept. of Genome Biology

institute: Kindai University Faculty of Medicine

description: Gene expression data from parental NCI-N87 cell lines

hyb_protocol: Samples were hybridized using Affymetrix hybridization, Wash and Stain kit.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix) according to manufacturer guidelines.

data_processing: Raw data (CEL files) were analyzed using Affymetrix Expression Console™ Software (version 1.4).

source_name: Parental NCI-N87 cells

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

growth_protocol: Tumor cells cultured in medium and incubated at 37˚C with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Untreated parental cancer cell line and TDM-1 resistant cancer cell line

value: gastric carcinoma cell


title: Senescent_rep 2


title: TDM-1 resistant cell lines

description: Gene expression data from TDM-1 resistant cancer cell line

source_name: TDM-1 resistant cell lines


title: Control_rep 2

description: U2OS cells cultured in 10% FBS


title: Quiescent_rep 3


title: Control_rep 1

description: U2OS cells cultured in 10% FBS


title: Quiescent_rep 1


title: Senescent_rep 1


title: Quiescent_rep 2


title: Gansu Alpine Merino (SAMPLE 20)

city: Lanzhou

first: quanwei

last: zhang

state: Gansu

address: Anning District of Lanzhou

country: China

institute: Gansu Agriculture University

description: Genomic DNA extracted from sheep was genotyped using IlluminaOvineSNP 50 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Reader (Illumina).

data_processing: Genomic DNA extracted from blood was genotyped using Infinium OvineSNP50 Beadchip (Illumina).

label: C-Bio and A-DNP

organism: Ovis aries

source_name: blood

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: In order to better adapt to these climates and environments, the Gansu Morden sheep breed was hybridized with Dorper, Poll Dorset and Small-Tail Han sheep. The resulting hybrids, which contain 75.0% foreign high-quality sheep genetics, were selected for planned crossbreeding. This new breed and other sheep breeds were selected and used for the present analysis of copy number variations by SNP50 BeadChip array, with the aim of generating a fuller understanding of sheep genetic resources.

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

treatment_protocol: Genomic DNA samples were obtained from eight sheep breeding no special treatment.

tag: breed

value: Gansu Alpine Merino

value: Male

value: blood


title: Gansu Morden sheep breed (SAMPLE 24)

value: Gansu Morden


title: South African Mutton Merino (SAMPLE 15)

value: South African Mutton Merino


title: Gansu Morden sheep breed (SAMPLE 22)


title: Borderdale (SAMPLE 18)

value: Borderdale


title: Gansu Alpine Merino (SAMPLE 19)


title: Gansu Alpine Merino (SAMPLE 21)


title: Borderdale (SAMPLE 17)


title: Columbia-0 (Wild type), 3 hr

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

institute: Guizhou University

description: Gene expression data from 2-week-old seedlings of the wild-type(col) grown on 1/2 MS medium containing 2% sucrose at 4˚C treatment for 3hour

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis ATH1 Genome  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Genesystem Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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: seedlings of the wild-type and lcbk1-2grown on 1/2 MS medium containing 2% sucrose at 22˚C  or 4˚C treatment 3hr and 24hr under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1.

extract_protocol: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany)

treatment_protocol: transient chilling temperature treatment(4˚C treatment）

value: the whole plant

value: wild-type

tag: ecotype

value: 2-week-old seedlings


title: Borderdale (SAMPLE 16)


title: South African Mutton Merino (SAMPLE 13)


title: South African Mutton Merino (SAMPLE 14)


title: Gansu Morden sheep breed (SAMPLE 23)


title: lcbk1-2 (mutant), 3 hr

description: Gene expression data from 2-week-old seedlings of the lcbk1-2 grown on 1/2 MS medium containing 2% sucrose at 4˚C treatment for 3hour

tag: genotype/variation


title: lcbk1-2 (mutant), 24 hr

description: Gene expression data from 2-week-old seedlings of the lcbk1-2 grown on 1/2 MS medium containing 2% sucrose at 4˚C treatment for 24hr


title: Suffolk (SAMPLE 11)

value: Suffolk


title: lcbk1-2 (mutant), 0 hr

description: Gene expression data from 2-week-old seedlings of the lcbk1-2 grown on 1/2 MS medium containing 2% sucrose at 22˚C


title: Suffolk (SAMPLE 12)


title: Suffolk (SAMPLE 10)


title: Texel (SAMPLE 9)

value: Texel


title: Texel (SAMPLE 8)


title: Columbia-0 (Wild type), 0 hr

description: Gene expression data from 2-week-old seedlings of the wild-type(col) grown on 1/2 MS medium containing 2% sucrose at 22˚C


title: Texel (SAMPLE 7)


title: Poll Dorset (SAMPLE 4)

value: Poll Dorset


title: Columbia-0 (Wild type), 24 hr

description: Gene expression data from 2-week-old seedlings of the wild-type(col) grown on 1/2 MS medium containing 2% sucrose at 4˚C treatment for 24hr


title: Poll Dorset (SAMPLE 6)


title: Poll Dorset (SAMPLE 5)


title: spleen_Hmgn1-/-n2-/-_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: SAMPLE 54

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

value: male

value: double knock out_Hmgn1-/-n2-/-

value: 21 weeks

tag: mouse id

value: spleen


title: thymus_Hmgn1-/-n2-/-_rep2

description: SAMPLE 62

value: thymus


title: thymus_wt_F_rep2

description: SAMPLE 58

value: wild type


title: Dorper (SAMPLE 1)

value: Dorper

value: Male


title: Dorper (SAMPLE 3)

value: blood


title: thymus_Hmgn1-/-n2-/-_rep1

description: SAMPLE 61


title: thymus_wt_E_rep1

description: SAMPLE 57


title: thymus_wt_G_rep3

description: SAMPLE 59


title: Dorper (SAMPLE 2)


title: thymus_wt_H_rep4

description: SAMPLE 60


title: spleen_wt_G_rep3

description: SAMPLE 51


title: liver_Hmgn1-/-n2-/-_rep2

description: SAMPLE 46

value: liver


title: thymus_Hmgn1-/-n2-/-_rep4

description: SAMPLE 64


title: thymus_Hmgn1-/-n2-/-_rep3

description: SAMPLE 63


title: spleen_wt_E_rep1

description: SAMPLE 49


title: liver_Hmgn1-/-n2-/-_rep1

description: SAMPLE 45


title: spleen_Hmgn1-/-n2-/-_rep1

description: SAMPLE 53


title: spleen_wt_H_rep4

description: SAMPLE 52


title: spleen_Hmgn1-/-n2-/-_rep4

description: SAMPLE 56


title: liver_Hmgn1-/-n2-/-_rep4

description: SAMPLE 48


title: liver_Hmgn1-/-n2-/-_rep3

description: SAMPLE 47


title: spleen_wt_F_rep2

description: SAMPLE 50


title: spleen_Hmgn1-/-n2-/-_rep3

description: SAMPLE 55


title: liver_wt_E_rep1

description: SAMPLE 41


title: brain_Hmgn1-/-n2-/-_rep2

description: SAMPLE 38

value: brain


title: liver_wt_G_rep3

description: SAMPLE 43


title: brain_Hmgn1-/-n2-/-_rep3

description: SAMPLE 39


title: brain_Hmgn1-/-n2-/-_rep4

description: SAMPLE 40


title: liver_wt_H_rep4

description: SAMPLE 44


title: brain_wt_G_rep3

description: SAMPLE 35


title: thymus_Hmgn2-/-_rep3

description: SAMPLE 31

value: homozygous Hmgn2-/-


title: brain_wt_F_rep2

description: SAMPLE 34


title: thymus_wt_B_rep2

description: SAMPLE 26


title: brain_wt_E_rep1

description: SAMPLE 33


title: brain_Hmgn1-/-n2-/-_rep1

description: SAMPLE 37


title: thymus_Hmgn2-/-_rep1

description: SAMPLE 29


title: spleen_Hmgn2-/-_rep2

description: SAMPLE 22


title: thymus_wt_C_rep3

description: SAMPLE 27


title: thymus_wt_A_rep1

description: SAMPLE 25


title: brain_wt_H_rep4

description: SAMPLE 36


title: thymus_Hmgn2-/-_rep4

description: SAMPLE 32


title: thymus_Hmgn2-/-_rep2

description: SAMPLE 30


title: spleen_wt_B_rep2

description: SAMPLE 18


title: spleen_wt_A_rep1

description: SAMPLE 17


title: thymus_wt_D_rep4

description: SAMPLE 28


title: spleen_Hmgn2-/-_rep3

description: SAMPLE 23


title: spleen_Hmgn2-/-_rep4

description: SAMPLE 24


title: liver_Hmgn2-/-_rep3

description: SAMPLE 15


title: spleen_wt_C_rep3

description: SAMPLE 19


title: spleen_Hmgn2-/-_rep1

description: SAMPLE 21


title: spleen_wt_D_rep4

description: SAMPLE 20


title: liver_Hmgn2-/-_rep4

description: SAMPLE 16


title: liver_wt_C_rep3

description: SAMPLE 11


title: liver_Hmgn2-/-_rep2

description: SAMPLE 14


title: brain_Hmgn2-/-_rep3

description: SAMPLE 7


title: liver_wt_B_rep2

description: SAMPLE 10


title: brain_Hmgn2-/-_rep1

description: SAMPLE 5


title: liver_Hmgn2-/-_rep1

description: SAMPLE 13


title: brain_wt_D_rep4

description: SAMPLE 4


title: glioma subclone J3T-1

city: Okayama

first: Yoshihiro

last: Otani

address: 2-5-1 Shikata, kita-ku

department: Neurological Surgery

institute: Okayama University

description: Gene expression data from J3T-1

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

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

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method.

organism: Canis lupus familiaris

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit from 250 ng total RNA according to the manufacturer's instructions.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum and 100U penicillin and 0.1mg ml-1 storeptomycin.

extract_protocol: Total RNA of J3T-1 and J3T-2 were isolated using RNeasy kit according to the manufacturer's instructions.

value: glioma


title: glioma subclone J3T-2

description: Gene expression data from J3T-2


title: Dye swap Cdk6-/-

first: Florian

last: Bellutti

address: Veterinärplatz 1

country: Austria

institute: University of Veterinary Medicine

description: BCR-ABL+ colonies

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on a G2505C DNA microarray scanner (Agilent). Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation, background subtraction

data_processing: Loes Normalization and linear model fitting was done using the FlexArray Software (Version 1.6.3)

source_name: Pool wt2+wt3+wt4+wt5

label_protocol: Commercial "Two-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling" kit (version 6.7, Agilent) was used to amplify and label 100 ng of sample by following manufacturer instructions.

growth_protocol: Bone marrow cells from 6 weeks old donor mice were transduced with retroviral supernatents (incl. Polybrene). After 24h cells were harvested and equal numbers of cells were embedded into growth factor-free methylcellulose (MethoCult™).  After 10 days, colonies were counted and isolated for RNA extraction.

extract_protocol: Total RNA was isolated from individual colonies picked from methylcellulose. The RNA was extracted using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Colony formation in growth factor-free methylcellulose, no additional treatment

value: bone marrow


title: Dye swap K43M

description: BCR-ABL+ colonies


title: brain_wt_A_rep1

description: SAMPLE 1


title: brain_Hmgn2-/-_rep2

description: SAMPLE 6


title: brain_Hmgn2-/-_rep4

description: SAMPLE 8


title: liver_wt_D_rep4

description: SAMPLE 12


title: brain_wt_B_rep2

description: SAMPLE 2


title: liver_wt_A_rep1

description: SAMPLE 9


title: brain_wt_C_rep3

description: SAMPLE 3


title: Human Serum Day 23, biological rep B

city: Edmonton

first: Rineke

last: Steenbergen

state: Alberta

address: 6-0096 Katz Building

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description:
Gene expression data from Huh7.5 cells 23 days after transferring from fetal bovine to human serum.
HS_D23_B

hyb_protocol: 300ng of each total RNA was labeled using the Affymetrix GeneChip  3’ IVT Express Kit ( P/N 901229) and the Affymetrix GeneChip 3’ IVT Express kit manual. Poly A controls were added to each sample at the beginning of the labeling. 10ug of fragmented, biotin-modified aRNA  was hybridized to the  Affymetrix PrimeView Human microarray (Ref 901838) in the Affymetrix GeneChip Hybridization Oven 645 at 45 deg. C. with 60rpm for 16 hours. Hybridization controls were added to each sample before the arrays were hybridized.  The arrays were washed and stained with  Affymetrix GeneChip  Wash and Stain Kit (P/N 900720) on the Affymetrix GeneChip Fluidics Station 450

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 7G and the cel files (raw data ) were  generated .

data_processing: Data were processed with R/Bioconductor, using the “affy” package. RMA was used as the normalization method.

source_name: Huh7.5 cells, 23 days after switch to human serum

label_protocol: Standard Affymetrix protocol

growth_protocol: Huh7.5 cells were maintained in DMEM/10% FBS/penicillin/streptomycin. After approximately 20-30 passages, cells were discarded, and a new vial was thawed.

extract_protocol: Total RNA from cells was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: At the time of transfer to human serum cells were trypsinized, trypsin was inactivated with DMEM/10% FBS/penicillin/streptomycin and cells were centrifuged at 300g. Cell pellets were then resuspended in DMEM/2% HS/penicillin/streptomycin, and plated at a density of 30-50%. At confluency cells were trypsinized once more, plated at a density of 50%, and then left to form confluent layers of undividing cells.

tag: culture conditions

value: cultured in FBS, then switched to human serum

tag: time

value: 23 days after switch


title: Human Serum Day 23, biological rep A

description:
Gene expression data from Huh7.5 cells 23 days after transferring from fetal bovine to human serum.
HS_D23_A

tag: cell line


title: Human Serum Day 23, biological rep C

description:
Gene expression data from Huh7.5 cells 23 days after transferring from fetal bovine to human serum.
HS_D23_C


title: liver_wt_F_rep2

description: SAMPLE 42


title: Human Serum Day 15, biological rep A

description:
Gene expression data from Huh7.5 cells 15 days after transferring from fetal bovine to human serum.
HS_D15_A

source_name: Huh7.5 cells, 15 days after switch to human serum

value: 15 days after switch


title: Human Serum Day 15, biological rep B

description:
Gene expression data from Huh7.5 cells 15 days after transferring from fetal bovine to human serum.
HS_D15_B


title: Human Serum Day 15, biological rep C

description:
Gene expression data from Huh7.5 cells 15 days after transferring from fetal bovine to human serum.
HS_D15_C


title: Human Serum Day 8, biological rep A

description:
Gene expression data from Huh7.5 cells 8 days after transferring from fetal bovine to human serum.
HS_D8_A

source_name: Huh7.5 cells, 8 days after switch to human serum

value: 8 days after switch


title: Human Serum Day 8, biological rep C

description:
Gene expression data from Huh7.5 cells 8 days after transferring from fetal bovine to human serum.
HS_D8_C


title: K43M Replicate 4

description: BCR-ABL+ colonies


title: Human Serum Day 8, biological rep B

description:
Gene expression data from Huh7.5 cells 8 days after transferring from fetal bovine to human serum.
HS_D8_B


title: Fetal Bovine Serum, biological rep A

description:
Gene expression data from Huh7.5 cells cultured in fetal bovine serum.
FBS_A

source_name: Huh7.5 cells, cultured in fetal bovine serum

value: cultured in FBS

value: control


title: K43M Replicate 3

description: BCR-ABL+ colonies


title: Fetal Bovine Serum, biological rep C

description:
Gene expression data from Huh7.5 cells cultured in fetal bovine serum.
FBS_C


title: Fetal Bovine Serum, biological rep B

description:
Gene expression data from Huh7.5 cells cultured in fetal bovine serum.
FBS_B


title: Cdk6-/- Replicate 4

description: BCR-ABL+ colonies


title: K43M Replicate 2

description: BCR-ABL+ colonies


title: K43M Replicate 1

description: BCR-ABL+ colonies


title: Cdk6-/- Replicate 1

description: BCR-ABL+ colonies


title: Cdk6-/- Replicate 2

description: BCR-ABL+ colonies


title: Cdk6-/- Replicate 3

description: BCR-ABL+ colonies


title: Stress induced-2

description: Stress induced-2

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent Microarray Gene expression 8x15k Array (AMADID: 019439). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift .Gene based analysis was performed.

organism: Escherichia coli

source_name: BLR

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: E.coli cells (BLR and 4FR clones in BLR) were grown till late expression phase from overnight culture. One percent of overnight culture was transferred to 10 ml of LB and incubated at 37C. Samples were harvested at 0.6-0.7 OD at 600nm. Finally, pelleted at 4000rpm for 10 min. and pellets were washed with water (thrice) and pelleted again. All samples were prepared in triplicate.

extract_protocol: RNA Extraction was perforemd using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: PCR amplified linear fragments with overhang regions for homologous recombination were transformed into BLR by electroporation (treated BLR-4FR).

value: RecA deleted


title: Stress induced-3

description: Stress induced-3