title: 102261-24_germ cell tumor_DG

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: Further processing was carried out in R using the LUMI package [1] according to [2, 3]. Briefly, poorly performing probes (detection p<0.01 in > 95% of the samples), cross hybridizing probes and probes with a SNP at or within 10 bp of the target CpG (allele frequency >= 0.05) were excluded [3]. 44,540 probes were discarded, leaving 437,881 valid, methylation related (cgXXXXXXXX) probes for processing and analysis. No batch effects were observed. Finally, color adjustment, quantile normalization and correction for probe type bias (Infinium I vs II) were performed (BMIQ) [1, 2, 4].  1. Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8.  2. Marabita, F., et al., An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics, 2013. 8(3): p. 333-46.  3. Chen, Y.A., et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013. 8(2): p. 203-9.  4. Teschendorff, A.E., et al., A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics, 2013. 29(2): p. 189-96.

source_name: DG

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research).

growth_protocol:
(TUMOR SAMPLES) Samples were extracted at the Department of Pathology, Erasmus MC, Rotterdam, the Netherlands. Use of tissue samples for scientific reasons was approved by an institutional review board (MEC 02.981 and CCR2041). Samples were used according to the “Code for Proper Secondary Use of Human Tissue in The Netherlands” developed by the Dutch Federation of Medical Scientific Societies (FMWV (Version 2002, update 2011).Samples were extracted at the Department of Pathology, Erasmus MC, Rotterdam, the Netherlands. Use of tissue samples for scientific reasons was approved by an institutional review board (MEC 02.981 and CCR2041). Samples were used according to the “Code for Proper Secondary Use of Human Tissue in The Netherlands” developed by the Dutch Federation of Medical Scientific Societies (FMWV (Version 2002, update 2011).
(CELL LINES) TCam-2, 2102EP, NCCIT and NT2 were grown in T75 cm2 flasks to 75-90% confluence in RPMI1640 (#61870-010, Thermo Fisher Scientific / Life Technologies, Carlsbad, CA, USA), DMEM/F12 (#12634-010, Thermo Fisher Scientific / Life Technologies), DMEM/F12 and DMEM high glucose (#31966-021, Thermo Fisher Scientific / Life Technologies) respectively, each with the addition of 10% Fetal Calf Serum (#CH30160.03, FCS, GE Healthcare Life Sciences, HyClone Laboratories, Utah, USA) and 1/100 Penicillin/Streptomycin (#15140, , Thermo Fisher Scientific / Life Technologies).

extract_protocol: DNA was isolated as described earlier [1].   1. Nettersheim, D., et al., NANOG promoter methylation and expression correlation during normal and malignant human germ cell development. Epigenetics, 2011. 6(1): p. 114-22.

treatment_protocol: n/a, cell lines were analyzed as wild type

value: germ cell tumor (GCT)

tag: histology

value: DG

tag: subtype

value: type II GCT


title: 102261-23_germ cell tumor_DG

status: Public on Feb 26 2015

type: genomic

department: Pathology

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: NASH [0599_SEN_252185017049_S01_CGH_107_Sep09_1_2]

city: kuala lumpur

first: shamsul mohd

last: zain

address: jalan lembah pantai

department: department of pharmacology

country: Malaysia

institute: univeristy of malaya

description: Normalised ratios between patients and controls were used for CNV calls

hyb_protocol: Hybridization mix was prepared. The target was denatured and the mixture was incubated. The Agilent SureHyb Gasket was placed into an Agilent Chamber base. Immediately, hybridisation mix was pipetted onto the gasket slide. OGT array was placed onto the Gasket slide. The hybridisation chamber was placed in the hybridisation oven and hybridised. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data were extracted using Feature Extraction Software (version 10.7.3.1) and uploaded into the CytoSure™ Interpret software (version 4.2.5), normalized and converted into .cgh files. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm.

source_name: NAFLD

label_protocol: Reaction tubes were prepared as a mixture of 18 μL of genomic DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy5-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.

extract_protocol: Genomic DNA were extracted using Qiagen as recommended by the manufacturer

tag: Stage

value: NASH

tag: blood

value: lymphocytes

tag: age

tag: gender

value: Female

source_name: Control


title: NASH [0599_SEN_252185017050_S01_CGH_107_Sep09_1_2]


title: 102261-22_germ cell tumor_DG


title: NASH [0599_SEN_252185017047_S01_CGH_107_Sep09_1_2]


title: Simple steatosis [0599_SEN_252185017048_S01_CGH_107_Sep09_1_1]

value: Simple steatosis


title: NASH [0599_SEN_252185017030_S01_CGH_107_Sep09_1_2]

value: Male


title: Simple steatosis [0599_SEN_252185017046_S01_CGH_107_Sep09_1_1]


title: 102261-19_germ cell tumor_I.TE.o

value: type I teratoma


title: 102261-21_germ cell tumor_DG


title: Simple steatosis [0599_SEN_252185017030_S01_CGH_107_Sep09_1_1]


title: NASH [0599_SEN_252185017048_S01_CGH_107_Sep09_1_2]


title: Simple steatosis [0599_SEN_252185017049_S01_CGH_107_Sep09_1_1]


title: 102261-20_germ cell tumor_I.TE.o


title: NASH [0599_SEN_252185017029_S01_CGH_107_Sep09_1_2]


title: NASH [0599_SEN_252185017028_S01_CGH_107_Sep09_1_2]


title: Simple steatosis [0599_SEN_252185017029_S01_CGH_107_Sep09_1_1]


title: Simple steatosis [0599_SEN_252185017028_S01_CGH_107_Sep09_1_1]


title: Simple steatosis [0599_SEN_252185017047_S01_CGH_107_Sep09_1_1]


title: 102261-17_germ cell tumor_I.TE.o


title: 102261-05_germ cell tumor_I.TE.s.f


title: Simple steatosis [0599_SEN_252185017027_S01_CGH_107_Sep09_1_1]


title: 102261-11_germ cell tumor_DC

source_name: DC

value: DC

value: type IV GCT


title: 102261-12_germ cell tumor_DC


title: 102261-15_germ cell tumor_II.TE.t

value: type II teratoma


title: 102261-18_germ cell tumor_I.TE.o


title: Simple steatosis [0599_SEN_252185017026_S01_CGH_107_Sep09_1_1]


title: 102261-06_germ cell tumor_I.TE.s.f


title: 102261-04_germ cell tumor_I.TE.s.f


title: 102261-14_germ cell tumor_II.TE.t


title: 102261-16_germ cell tumor_II.TE.t


title: 102261-13_germ cell tumor_DC


title: NASH [0599_SEN_252185017027_S01_CGH_107_Sep09_1_2]


title: 102261-03_germ cell tumor_I.TE.s.m


title: 102261-09_germ cell tumor_I.TE.t


title: 102261-10_germ cell tumor_I.TE.t


title: 102261-02_germ cell tumor_I.TE.s.m


title: 102229-23_germ-cell tumor cell line_2102Ep

tag: cell line

value: germ cell tumor (GCT) cell line 2102Ep

value: modelling type II GCTs


title: 102229-15_germ cell tumor_SE

source_name: SE

value: SE


title: 102261-07_germ cell tumor_I.TE.t


title: 102229-24_germ-cell tumor cell line_NCCIT

source_name: NCCIT

value: germ cell tumor (GCT) cell line NCCIT


title: 102229-17_germ cell tumor_SE


title: 102261-08_germ cell tumor_I.TE.t


title: 102229-20_germ cell tumor_SE


title: 102261-01_germ cell tumor_I.TE.s.m


title: 102229-19_germ cell tumor_SE


title: 102229-14_germ cell tumor_SE


title: 102229-21_germ-cell tumor cell line_TCam2

value: germ cell tumor (GCT) cell line TCam2


title: 102229-18_germ cell tumor_SE

value: germ cell tumor (GCT)


title: 102229-22_germ-cell tumor cell line_NT2

value: germ cell tumor (GCT) cell line NT2


title: 102229-11_germ cell tumor_SE

value: type II GCT


title: 102229-13_germ cell tumor_SE


title: 102229-12_germ cell tumor_SE


title: 102229-07_germ cell tumor_SS

source_name: SS

value: SS

value: type III GCT


title: female liver_RAD21_genome tiling

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

country: USA

institute: University of Washington

hyb_protocol: Standard NimbleGen or Agilent protocol

scan_protocol: Standard NimbleGen or Agilent protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 or MM9 coordinates

organism: Mus musculus

source_name: RAD21 ChIP DNA from mouse female adult liver

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

extract_protocol: Several million cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

tag: genotype/variation

value: wild type

value: female

value: Liver

tag: chip antibody

tag: antibody vendor/catalog

value: Abcam (Cat#ab992)

source_name: ChIP input DNA

tag: antibody

tag: sample type

value: input


title: 102229-09_germ cell tumor_SE


title: 102229-08_germ cell tumor_SS


title: 102229-04_germ cell tumor_mNS

source_name: mNS

value: mNS


title: WD44ES_D15_CTCF_genome tiling

description: Derived from male BL6 blastcysts

source_name: CTCF ChIP DNA from mouse male WD44 ES cells differentiated at Day 15

growth_protocol: ES cells were differentiated using a standard embroid body (EB) protocol.

treatment_protocol: No treatment

value: male

tag: cell type

value: WD44 ES cells differentiated for 15 days

tag: strain

value: CTCF

value: Millipore (Cat#07-729)


title: PGK12.1ES_D0_CTCF_genome tiling

description: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

source_name: CTCF ChIP DNA from mouse female PGK12.1 ES cells differentiated at Day 0

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

value: PGK12.1 ES cells


title: NASH [0599_SEN_252185017026_S01_CGH_107_Sep09_1_2]

value: NASH

value: lymphocytes

value: Female


title: Fatbody_UV12h_sample2

type: RNA

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

country: Japan

institute: Research Organization of Information and Systems

description: Gene expression in 3day fifth instar larvae of UV treatment for 12 hours

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies). 1.65ug of Cy3-labelled cRNA was mixed, fragmented and hybridized to the silkworm 4 x 44 K oligo-microarray slide at 65 degrees Celsius for 17 hours with shaking at 10 rpm. The array was washed in Agilent Gene Expression Wash Buffer 1 for 1min at room temperature and Agilent Gene Expression Wash Buffer 2 for 1min at 37 degrees Celsius.

scan_protocol: Intensities of the hybridized probes were detected with an Agilent G2565B Microarray Scanner at 10-mm scan resolution.

data_processing: Signals were extracted with G2565AA Feature Extraction Software v.9.5 (Agilent Techonologies). The raw data in text files were normalized 'per spot' and 'per chip' using GeneSpring GX v.10.3 (Agilent Techonologies).

molecule: total RNA

organism: Bombyx mori

source_name: fatbody, 3 day of fifth instar larvae, domestic silkworm, Kinshu x Showa

label_protocol: Total RNA(300ng) was processed for Cy3-labelled cRNA synthesis using the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions (Agilent Technologies). The Cy3-labelled cRNA was purified using RNeasy Mini Kit (Qiagen) and quantified on an Agilent 2100 and Nano Drop 1000 Spectrophotometer.

extract_protocol: Total RNA from control or UV treated fatbody were isolated using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Total RNA was quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)

treatment_protocol: Silkworms were reared on fresh mulberry leaves and kept at 25 degrees Celsius on a 12-hour light/12-hour dark cycle.

value: fatbody

tag: developmental stage

value: 3day fifth instar larvae

tag: stress

value: UV

tag: time


title: PGK12.1ES_D15_CTCF_genome tiling

source_name: CTCF ChIP DNA from mouse female PGK12.1 ES cells differentiated at Day 15

value: wild type

value: PGK12.1 ES cells differentiated for 15 days

value: 129 female crossed to a (129 X PGK)F1 male.


title: Fatbody_control_sample2

description: Gene expression in 3day fifth instar larvae of control

value: ctrl

value: control


title: male liver_RAD21_genome tiling

source_name: RAD21 ChIP DNA from mouse male adult liver

value: Liver

value: Abcam (Cat#ab992)

value: input


title: 102229-05_germ cell tumor_SS

value: germ cell tumor (GCT)

tag: histology

value: SS

tag: subtype

value: type III GCT


title: 102229-01_germ cell tumor_mNS

tag: tissue

value: mNS

value: type II GCT


title: 102229-16_germ cell tumor_SE

value: SE


title: 102229-10_germ cell tumor_SE


title: WD44ES_D0_CTCF_genome tiling

description: Derived from male BL6 blastcysts

source_name: CTCF ChIP DNA from mouse male WD44 ES cells differentiated at Day 0

value: male

value: WD44 ES cells

value: CTCF

value: Millipore (Cat#07-729)


title: 102133-44_germ cell tumor_EC

source_name: EC

value: EC


title: 102133-42_germ cell tumor_EC


title: Fatbody_UV6h_sample1

description: Gene expression in 3day fifth instar larvae of UV treatment for 6 hours

value: fatbody

value: 3day fifth instar larvae

value: UV


title: 102133-45_germ cell tumor_EC


title: 102229-03_germ cell tumor_mNS


title: 102229-06_germ cell tumor_SS


title: 102133-43_germ cell tumor_EC


title: 102133-40_germ cell tumor_EC


title: Fatbody_control_sample1

value: ctrl

value: control


title: 102133-46_germ cell tumor_EC


title: 102133-37_germ cell tumor_EC


title: 102133-38_germ cell tumor_EC


title: 102133-41_germ cell tumor_mNS


title: 102133-34_germ cell tumor_EC


title: 102133-48_germ cell tumor_EC


title: 102133-36_germ cell tumor_EC


title: 102133-32_germ cell tumor_EC


title: 102133-33_germ cell tumor_mNS


title: 102133-47_germ cell tumor_EC


title: 102133-27_germ cell tumor_mNS


title: male liver_CTCF_genome tiling set37

source_name: CTCF ChIP DNA from mouse male adult liver

value: wild type

value: Liver

value: input


title: male embryo_CTCF_genome tiling set37

source_name: CTCF ChIP DNA from mouse male 12.5dpc embryo

value: 12.5dpc embryo


title: 102133-31_germ cell tumor_mNS

value: germ cell tumor (GCT)

value: mNS


title: female embryo_CTCF_genome tiling set37

source_name: CTCF ChIP DNA from mouse female 12.5dpc embryo

value: female


title: 102133-39_germ cell tumor_mNS

value: type II GCT


title: 102133-28_germ cell tumor_EC


title: female liver_CTCF_genome tiling set37

source_name: CTCF ChIP DNA from mouse female adult liver


title: 102133-35_germ cell tumor_EC


title: 102133-22_germ cell tumor_EC


title: 102133-23_germ cell tumor_EC


title: 102133-21_germ cell tumor_mNS


title: 102229-02_germ cell tumor_mNS


title: 102133-29_germ cell tumor_mNS


title: purified DNAM-1+ NK cells sample 6

city: Herston

first: Jason

middle: Sewoong

last: Lee

state: QLD

address: 300 Herston Road

department: Department of Cell and Molecular Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

hyb_protocol: Labelled cRNA was hybridized to mouse WG-6 v2.0 Expression Beadchip array, and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

label: biotin

source_name: purified DNAM-1+ NK cells

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: strain background

value: spleen

value: DNAM-1+ NK


title: 102133-30_germ cell tumor_EC


title: purified DNAM-1+ NK cells sample 5

scan_protocol: Labelled cRNA was hybridized to mouse WG-6 v2.0 Expression Beadchip array, and then washed and scanned according to standard Illumina protocols.


title: 15m_hp_VH [NFND_251486811714_S01_GE2-v4_91_1_3]

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 825 ng of Cyanine 3-labelled and 825 ng of Cyanine 5-labelled cRNA per hybridization. The hybridization reactions were performed at  65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit with the 4X44K whole mouse genome chip (G4122F). After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitrile for one minute at room temperature.

scan_protocol: Chips were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1) and the GE2-v4_91 extraction protocol.

data_processing: Raw data filtering was performed in Microsoft Excel using any of the following criteria to discard spots: spots with more than 5% of saturated pixel in any of the two channels, spots flagged as “not found” by the Feature Extraction in any of the two channels, spots with a Signal/Noise ratio smaller than 3 in any of the two channels, where Signal = (median of the spot - median spot background level) and Noise is the IQR (interQuantileRange) of the median spot background. Data analysis was performed with R-Bionductor, Agilent GeneSpring GX ver 7.3 and Microsoft Excel. Data analysis was performed on filtered data using Agilent GeneSpring GX 7.3 and Microsoft Excel. Each array was normalized by the Lowess algorithm within GeneSpring, using 20% of data as smoothing window.

source_name: Wild type C57BL×SJLF2  mouse

label_protocol: 500ng of Poly A+RNA were labelled, using Cyanine 3-CTP or Cyanine 5-CTP (Perkin Elmer) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns

growth_protocol: AD11 transgenic mice (Ruberti et al., 2000) express a recombinant version of the monoclonal antibody mAb alfaD11 that specifically recognizes and neutralizes NGF (Cattaneo et al., 1988; Covaceuszach et al., 2008). AD11 mice were obtained by crossing two lines: one expressing only the Heavy VH chain and another expressing only the light VK chain of the antibody. The mouse line expressing only the VH chain (valled VH mice)  were used as transgenic control mice, that are consistently negative with respect to all the neurodegeneration markers across lifespan.

extract_protocol:
Hippocampus (HP), cortex (CTX) and basal forebrain (BFB) of the right hemisphere were dissected from the brains of freshly sacrificed mice AD11 and control VH, using RNAlater (Qiagen). A total of 60 female AD11 mice and 59 female control VH (5 per group) mice were used for this study: 5 AD11 and 4-5 control VH mice for each time point (1,3,6,15 months of age) and brain area(HP, CTX, BFB).
Total RNA was isolated from these brain areas using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the Agilent protocol. Aliquots from the same RNA sample, prepared (and pooled) from 2 whole brains of wild type mice, were used in all hybridizations as a Reference sample on Channel 1 (Cy3 labelling) to reduce and control the experimental variability.

value: wildtype

tag: age

value: 3 months

value: pool of whole brain from 2 mice

source_name: VH transgenic mouse

value: VH transgenic mouse

value: 15 months

value: hippocampus


title: 15m_hp_VH [NFND_251486811714_S01_GE2-v4_91_1_4]


title: 102133-26_germ cell tumor_mNS


title: purified DNAM-1+ NK cells sample 3


title: 102133-25_germ cell tumor_EC

value: EC


title: purified DNAM-1+ NK cells sample 4

value: wild type


title: 102133-19_germ cell tumor_mNS


title: Patski_stable control_promoter

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6.

organism: Mus musculus x Mus spretus

source_name: H3K27me3 ChIP DNA from Patski cells treated by negative control si&sh RNAs

treatment_protocol: Negative control si&shRNA treatment

value: Fibroblasts

value: control

value: Millipore (Cat#07-449)


title: 102133-20_germ cell tumor_EC

value: germ cell tumor (GCT)


title: purified DNAM-1+ NK cells sample 2


title: Patski_stable Firre KD_promoter

source_name: H3K27me3 ChIP DNA from Patski cells treated by Firre si&sh RNAs

treatment_protocol: Firre si&shRNA treatment

value: Firre knockdown

value: BL6/spretus hybrid embryonic kidney and has the inactive X from BL6.

source_name: ChIP input DNA

value: input


title: 102133-17_germ cell tumor_mNS

source_name: mNS

value: mNS

value: type II GCT


title: 15m_hp_AD11 [NFND_251486811877_S01_GE2-v4_91_1_4]

value: wildtype

source_name: AD11 anti-NGF transgenic mouse

value: AD11 anti-NGF transgenic mouse


title: 15m_hp_VH [NFND_251486811714_S01_GE2-v4_91_1_2]

value: 3 months

value: pool of whole brain from 2 mice


title: 102133-18_germ cell tumor_mNS


title: 15m_hp_VH [NFND_251486811714_S01_GE2-v4_91_1_1]

value: VH transgenic mouse

value: 15 months


title: 15m_hp_AD11 [NFND_251486811877_S01_GE2-v4_91_1_3]

value: hippocampus


title: 15m_hp_VH [NFND_251486811713_S01_GE2-v4_91_1_3]


title: 102133-16_germ cell tumor_mNS


title: purified DNAM-1- NK cells sample 6

source_name: purified DNAM-1- NK cells

value: wild type

value: spleen

value: DNAM-1- NK


title: purified DNAM-1+ NK cells sample 1

value: DNAM-1+ NK


title: 102133-15_germ cell tumor_mNS

value: germ cell tumor (GCT)


title: 102133-14_germ cell tumor_EC

value: EC


title: purified DNAM-1- NK cells sample 5


title: purified DNAM-1- NK cells sample 4


title: 15m_hp_AD11 [NFND_251486811713_S01_GE2-v4_91_1_2]


title: 15m_ctx_VH [NFND_251269423535_S01_GE2-v4_91]

value: cortex


title: 15m_hp_AD11 [NFND_251486811713_S01_GE2-v4_91_1_1]


title: 15m_ctx_VH [NFND_251269423491_S01_GE2-v4_91]


title: 15m_ctx_VH [NFND_251269423493_S01_GE2-v4_91]


title: 15m_ctx_VH [NFND_251269423532_S01_GE2-v4_91]


title: 15m_ctx_VH [NFND_251269423495_S01_GE2-v4_91]


title: purified DNAM-1- NK cells sample 3


title: purified DNAM-1- NK cells sample 2


title: 102133-06_germ cell tumor_EC


title: purified DNAM-1- NK cells sample 1


title: 6m_hp_VH [NFND_251486811446_S01_GE2-v4_91_1_4]

value: 6 months


title: 15m_ctx_AD11 [NFND_251269423534_S01_GE2-v4_91]


title: 6m_hp_VH [NFND_251486811446_S01_GE2-v4_91_1_3]


title: 102133-10_germ cell tumor_EC


title: 15m_ctx_AD11 [NFND_251269423494_S01_GE2-v4_91]


title: 15m_hp_AD11 [NFND_251486811877_S01_GE2-v4_91_1_2]


title: 15m_ctx_AD11 [NFND_251269423496_S01_GE2-v4_91]


title: 102133-09_germ cell tumor_EC


title: 15m_ctx_AD11 [NFND_251269423492_S01_GE2-v4_91]


title: 102133-11_germ cell tumor_EC


title: 102133-13_germ cell tumor_mNS

value: mNS


title: 102133-05_germ cell tumor_EC

value: type II GCT


title: 102133-08_germ cell tumor_mNS


title: 15m_ctx_AD11 [NFND_251269423490_S01_GE2-v4_91]

value: wildtype


title: M.tb_IL4IL13_28h_rep1

city: Yokohama

first: Harukazu

last: Suzuki

address: 1-7-22 Suehiro-Cho, Tsurumi-Ku,

department: Division of genomic technology

institute: Riken yokohama, Riken center for life science technology

description:
M.tb_IL4/IL13_28h_rep1
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi R (bioconductor)

label: BIOTIN

source_name: Bmdm cells

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

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

tag: background strain

value: BALB/c

tag: Sex

value: male

value: 8-12 weeks

value: bone marrow derive macrophage (Bmdm)


title: 102133-01_germ cell tumor_EC


title: 102133-02_germ cell tumor_mNS


title: 15m_bfb_VH [NFND_251269422743_S01_GE2-v4_91]

tag: genotype/variation

value: 3 months

value: pool of whole brain from 2 mice

value: VH transgenic mouse

value: 15 months

value: basal forebrain


title: 15m_bfb_VH [NFND_251269423499_S01_GE2-v4_91]


title: 15m_bfb_VH [NFND_251269423498_S01_GE2-v4_91]


title: 6m_hp_VH [NFND_251486811446_S01_GE2-v4_91_1_1]

value: hippocampus


title: 6m_hp_VH [NFND_251486811446_S01_GE2-v4_91_1_2]


title: 6m_hp_VH [NFND_251486811445_S01_GE2-v4_91_1_4]


title: 102133-04_germ cell tumor_mNS

value: germ cell tumor (GCT)


title: 15m_bfb_AD11 [NFND_251269422935_S01_GE2-v4_91]

value: AD11 anti-NGF transgenic mouse


title: M.tb_IFNg_72h_rep1

description:
M.tb_IFNg_72h_rep1
Replicate 1


title: 15m_bfb_AD11 [NFND_251269422937_S01_GE2-v4_91]


title: 15m_bfb_VH [NFND_251269422744_S01_GE2-v4_91]


title: 102133-03_germ cell tumor_EC

value: EC


title: 15m_bfb_VH [NFND_251269422746_S01_GE2-v4_91]


title: 6m_hp_AD11 [NFND_251486811445_S01_GE2-v4_91_1_3]

value: 6 months


title: M.tb_IFNg_28h_rep1

description:
M.tb_IFNg_28h_rep1
Replicate 1


title: M.tb_IL41L13_36h_rep1

description:
M.tb_IL4/IL13_36h_rep1
Replicate 1


title: 6m_hp_AD11 [NFND_251486811445_S01_GE2-v4_91_1_2]


title: 15m_bfb_AD11 [NFND_251269422748_S01_GE2-v4_91]


title: M.tb_IL4IL13_72h_rep1

description:
M.tb_IL4/IL13_72h_rep1
Replicate 1


title: M.tb_IFNg_36h_rep1

description:
M.tb_IFNg_36h_rep1
Replicate 1


title: 15m_bfb_AD11 [NFND_251269422936_S01_GE2-v4_91]


title: 15m_bfb_AD11 [NFND_251269422747_S01_GE2-v4_91]


title: 6m_hp_AD11 [NFND_251486811445_S01_GE2-v4_91_1_1]


title: 102133-07_germ cell tumor_EC


title: 3m_hp_VH [NFND_251269424595_S01_GE2-v4_91]


title: 3m_hp_VH [NFND_251269424599_S01_GE2-v4_91]


title: 6m_hp_AD11 [NFND_251486811444_S01_GE2-v4_91_1_4]


title: M.tb_36h_rep1

description:
M.tb_36h_rep1
Replicate 1


title: 3m_hp_VH [NFND_251269423831_S01_GE2-v4_91]


title: 3m_hp_AD11 [NFND_251269424596_S01_GE2-v4_91]


title: 3m_hp_AD11 [NFND_251269424598_S01_GE2-v4_91]


title: M.tb_28h_rep1

description:
M.tb_28h_rep1
Replicate 1


title: 3m_hp_VH [NFND_251269424597_S01_GE2-v4_91]


title: 6m_ctx_VH [NFND_251486811444_S01_GE2-v4_91_1_2]

value: cortex


title: 6m_ctx_VH [NFND_251486811444_S01_GE2-v4_91_1_1]


title: IL4IL13_36h_rep1

description:
IL4/IL13_36h_rep1
Replicate 1


title: M.tb_72h_rep1

description:
M.tb_72h_rep1
Replicate 1


title: 3m_hp_VH [NFND_251269423833_S01_GE2-v4_91]


title: 6m_ctx_VH [NFND_251486811420_S01_GE2-v4_91_1_3]


title: IL4IL13_28h_rep1

description:
IL4/IL13_28h_rep1
Replicate 1


title: 6m_hp_AD11 [NFND_251486811444_S01_GE2-v4_91_1_3]


title: 3m_hp_AD11 [NFND_251269423834_S01_GE2-v4_91]


title: 3m_ctx_VH [NFND_251269423545_S01_GE2-v4_91]


title: 6m_ctx_VH [NFND_251486811420_S01_GE2-v4_91_1_4]


title: 3m_ctx_VH [NFND_251269423542_S01_GE2-v4_91]


title: 3m_hp_AD11 [NFND_251269423832_S01_GE2-v4_91]


title: IFNg_72h_rep1

description:
IFNg_72h_rep1
Replicate 1


title: 3m_hp_AD11 [NFND_251269423830_S01_GE2-v4_91]


title: 3m_ctx_VH [NFND_251269423540_S01_GE2-v4_91]


title: 6m_ctx_VH [NFND_251486811420_S01_GE2-v4_91_1_2]


title: 6m_ctx_AD11 [NFND_251486811420_S01_GE2-v4_91_1_1]


title: 102133-12_germ cell tumor_EC

value: type II GCT


title: IL4IL13_72h_rep1

description:
IL4/IL 13_72h_rep1
Replicate 1


title: 3m_ctx_VH [NFND_251269423538_S01_GE2-v4_91]

value: wildtype


title: 6m_ctx_AD11 [NFND_251486811419_S02_GE2-v4_91_1_3]


title: 6m_ctx_AD11 [NFND_251486811419_S02_GE2-v4_91_1_4]


title: 3m_ctx_AD11 [NFND_251269423541_S01_GE2-v4_91]


title: Ust_36h_rep1

description:
Unstimulated 36h rep1
Replicate 1

value: BALB/c


title: 3m_ctx_VH [NFND_251269423536_S01_GE2-v4_91]


title: 3m_ctx_AD11 [NFND_251269423544_S01_GE2-v4_91]


title: 3m_ctx_AD11 [NFND_251269423531_S01_GE2-v4_91]


title: 3m_ctx_AD11 [NFND_251269423537_S01_GE2-v4_91]


title: IFNg_36h_rep1

description:
IFNg_36h_rep1
Replicate 1

value: male


title: 6m_ctx_AD11 [NFND_251486811419_S02_GE2-v4_91_1_2]


title: 3m_bfb_VH [NFND_251269423824_S01_GE2-v4_91]


title: IFNg_28h_rep1

description:
IFNg_28h_rep1
Replicate 1

value: 8-12 weeks


title: 3m_ctx_AD11 [NFND_251269423539_S01_GE2-v4_91]


title: 3m_bfb_VH [NFND_251269423822_S01_GE2-v4_91]


title: 3m_bfb_VH [NFND_251269423820_S01_GE2-v4_91]


title: Ust_72h_rep1

description:
Unstimulated 72h rep1
Replicate 1

value: bone marrow derive macrophage (Bmdm)


title: 3m_bfb_VH [NFND_251269423813_S01_GE2-v4_91]

value: 3 months


title: 6m_ctx_AD11 [NFND_251486811419_S02_GE2-v4_91_1_1]

value: pool of whole brain from 2 mice


title: 6m_bfb_VH [NFND_251486811716_S01_GE2-v4_91_1_2]

value: VH transgenic mouse


title: 3m_bfb_AD11 [NFND_251269423823_S01_GE2-v4_91]


title: 3m_bfb_AD11 [NFND_251269423821_S01_GE2-v4_91]


title: M.tb_IL4IL13_36h_rep2

description:
M.tb_IL4/IL13_36h_rep2
Replicate 2


title: 3m_bfb_VH [NFND_251269423811_S01_GE2-v4_91]


title: M.tb_IL4IL13_72h_rep2

description:
M.tb_IL4/IL13_72h_rep2
Replicate 2


title: 3m_bfb_AD11 [NFND_251269423814_S01_GE2-v4_91]


title: 3m_bfb_AD11 [NFND_251269423812_S01_GE2-v4_91]


title: 6m_bfb_VH [NFND_251486811448_S01_GE2-v4_91_1_3]


title: 6m_bfb_AD11 [NFND_251486811448_S01_GE2-v4_91_1_1]


title: 6m_bfb_VH [NFND_251486811448_S01_GE2-v4_91_1_4]


title: 6m_bfb_VH [NFND_251486811448_S01_GE2-v4_91_1_2]


title: 6m_bfb_AD11 [NFND_251486811447_S01_GE2-v4_91_1_4]


title: 6m_bfb_AD11 [NFND_251486811447_S01_GE2-v4_91_1_2]


title: M.tb_IFNg_36h_rep2

description:
M.tb_IFNg_36h_rep2
Replicate 2


title: M.tb_IFNg_72h_rep2

description:
M.tb_IFNg_72h_rep2
Replicate 2


title: 6m_bfb_AD11 [NFND_251486811447_S01_GE2-v4_91_1_3]


title: 3m_bfb_AD11 [NFND_251269423810_S01_GE2-v4_91]


title: M.tb_72h_rep2

description:
M.tb_72h_rep2
Replicate 2


title: M.tb_IL4IL13_28h_rep2

description:
M.tb_IL4/IL13_28h_rep2
Replicate 2


title: Ust_28h_rep1

description:
Unstimulated 28h rep1
Replicate 1


title: M.tb_IFNg_28h_rep2

description:
M.tb_IFNg_28h_rep2
Replicate 2


title: M.tb_36h_rep2

description:
M.tb_36h_rep2
Replicate 2


title: 6m_bfb_AD11 [NFND_251486811447_S01_GE2-v4_91_1_1]


title: CD4_CNS_MOG_3

city: Mainz

first: Volker

last: Siffrin

address: Langenbeckstrasse 1

department: Department of Neurology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz, Germany

description: C57BL/6 mice were immunized with MOG35-55 peptide. CD4+ T cells were isolated from the CNS of diseased mice at the peak of EAE.

hyb_protocol: Cy3-labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent-026655 Whole Mouse Genome Oligo Microarrays (4x44K, v2) using Agilent's recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: CD4+ T cells, EAE induced by MOG35-55-peptide

label_protocol: 100ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the LIQA Kit (Agilent Technologies) following the manufacturer's protocol.

extract_protocol: RNA was extracted using NucleoSpin® RNA II (MACHEREY-NAGEL) following manufacturer's instructions.

tag: strain/background

value: central nervous system

value: CD4+ T cells


title: IL4IL13_72h_rep2

description:
IL4/IL 13_72h_rep2
Replicate 2


title: CD4_CNS_MOG_1


title: M.tb_28h_rep2

description:
M.tb_28h_rep2
Replicate 2


title: CD4_CNS_MOG_2


title: IL4IL13_36h_rep2

description:
IL4/IL13_36h_rep2
Replicate 2


title: 1m_hp_VH [NFND_251486812129_S01_GE2-v4_91_1_2]

value: 1 month

value: hippocampus


title: CD4_CNS_1

description: In vitro differentiated B6.2d2 Th17 cells were adoptively transferred into lymphopenic Rag1-/- mice and re-isolated from the CNS at the peak of EAE symptoms.

source_name: CD4+ T cells, EAE induced by adoptively transferred Th17 cells


title: 1m_hp_VH [NFND_251486812129_S01_GE2-v4_91_1_1]


title: CD4_CNS_3


title: Th17_culture_3

description: Naive B6.2d2 CD4+ T cells were differentiated in vitro using differentiated Th17 cell.

source_name: in vitro differentiated Th17 cells

value: T cell culture

value: Th17 cells


title: CD4_CNS_2


title: Th17_culture_1


title: Th17_culture_2


title: Twist1-induced day 12, rep 3

city: Aurora

first: David

last: Drasin

state: CO

department: Pharmacology

institute: University of Colorado AMC

description:
T d12-3
Biological replicate 3 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 12 days with 4-OHT.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer-defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system-related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meet at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between control and test sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: HMLE, inducible TWIST1 vector, day 12

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: Cells were maintained in MEGM media.

extract_protocol: Total RNA was extracted using miRNeasy Micro (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells were treated with fresh media containing 20nM 4-OHT every 2 days.

tag: cell line

value: HMLE

tag: stably expressing

value: inducible TWIST1 vector

tag: treatment

tag: time point

value: day 12


title: Twist1-induced day 12, rep 2

description:
T d12-2
Biological replicate 2 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 12 days with 4-OHT.


title: Naive_3

description: Naive CD4+ T cells were isolated from the spleen of B6.2d2 transgenic mice with MOG-specific T cell receptors.

source_name: naive CD4+ T cells

value: spleen

tag: cell type


title: 1m_hp_VH [NFND_251486812128_S01_GE2-v4_91_1_4]

value: wildtype


title: IL4IL13_28h_rep2

description:
IL4/IL13_28h_rep2
Replicate 2

value: BALB/c

value: male


title: Twist1-induced day 4, rep 1

description:
T d4-1
Biological replicate 1 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 4 days with 4-OHT.

source_name: HMLE, inducible TWIST1 vector, day 4

value: day 4


title: Twist1-induced day 4, rep 2

description:
T d4-2
Biological replicate 2 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 4 days with 4-OHT.


title: Twist1-induced day 4, rep 3

description:
T d4-3
Biological replicate 3 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 4 days with 4-OHT.


title: Twist1-induced day 12, rep 1

description:
T d12-1
Biological replicate 1 of 3. HMLE cells stably expressing an inducible TWIST1 vector, treated 12 days with 4-OHT.


title: 1m_hp_VH [NFND_251486812128_S01_GE2-v4_91_1_2]

value: 3 months


title: 1m_hp_AD11 [NFND_251486812127_S01_GE2-v4_91_1_4]

value: pool of whole brain from 2 mice

value: AD11 anti-NGF transgenic mouse


title: Naive_1


title: 1m_hp_VH [NFND_251486812128_S01_GE2-v4_91_1_3]

value: VH transgenic mouse


title: IFNg_36h_rep2

description:
IFNg_36h_rep2
Replicate 2

value: 8-12 weeks

value: bone marrow derive macrophage (Bmdm)


title: IFNg_28h_rep2

description:
IFNg_28h_rep2
Replicate 2


title: Control day 12, rep 3

description:
V d12-3
Biological replicate 3 of 3. HMLE cells stably expressing a control empty vector, treated 12 days with 4-OHT.

source_name: HMLE, empty control vector, day 12

value: empty vector


title: Control day 12, rep 2

description:
V d12-2
Biological replicate 2 of 3. HMLE cells stably expressing a control empty vector, treated 12 days with 4-OHT.


title: IFNg_72h_rep2

description:
IFNg_72h_rep2
Replicate 2


title: Naive_2

value: CD4+ T cells


title: 1m_hp_AD11 [NFND_251486812127_S01_GE2-v4_91_1_2]

value: 1 month

value: hippocampus


title: Ust_72h_rep2

description:
Unstimulated 72h rep2
Replicate 2


title: Ust_36h_rep2

description:
Unstimulated 36h rep2
Replicate 2


title: 1m_hp_AD11 [NFND_251486812127_S01_GE2-v4_91_1_3]


title: Control day 4, rep 3

description:
V d4-3
Biological replicate 3 of 3. HMLE cells stably expressing a control empty vector, treated 4 days with 4-OHT.

source_name: HMLE, empty control vector, day 4

value: HMLE


title: 1m_ctx_VH [NFND_251486812126_S01_GE2-v4_91_1_3]

source_name: Wild type C57BL×SJLF2  mouse

value: cortex


title: 1m_hp_AD11 [NFND_251486812127_S01_GE2-v4_91_1_1]


title: 1m_hp_AD11 [NFND_251486812126_S01_GE2-v4_91_1_4]


title: 1m_ctx_VH [NFND_251486812126_S01_GE2-v4_91_1_2]

source_name: VH transgenic mouse


title: 1m_ctx_VH [NFND_251486812126_S01_GE2-v4_91_1_1]


title: 1m_ctx_VH [NFND_251486811718_S01_GE2-v4_91_1_4]


title: Ust_28h_rep2

description:
Unstimulated 28h rep2
Replicate 2


title: Control day 4, rep 1

description:
V d4-1
Biological replicate 1 of 3. HMLE cells stably expressing a control empty vector, treated 4 days with 4-OHT.


title: Control day 4, rep 2

description:
V d4-2
Biological replicate 2 of 3. HMLE cells stably expressing a control empty vector, treated 4 days with 4-OHT.


title: Control day 12, rep 1

description:
V d12-1
Biological replicate 1 of 3. HMLE cells stably expressing a control empty vector, treated 12 days with 4-OHT.

value: day 12


title: Patski_transitory CTCF KD_promoter

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6.

source_name: H3K27me3 ChIP DNA from Patski cells treated by CTCF siRNAs (Invitrogen)

treatment_protocol: CTCF siRNA treatment

value: Fibroblasts

value: CTCF knockdown

tag: strain

tag: chip antibody

tag: antibody vendor/catalog

value: Millipore (Cat#07-449)

tag: antibody

tag: sample type

value: input


title: 1m_ctx_AD11 [NFND_251486811716_S01_GE2-v4_91_1_4]

value: wildtype

value: 3 months

tag: tissue


title: 1m_ctx_AD11 [NFND_251486811716_S01_GE2-v4_91_1_3]

value: pool of whole brain from 2 mice

value: AD11 anti-NGF transgenic mouse


title: 1m_ctx_AD11 [NFND_251486811718_S01_GE2-v4_91_1_1]


title: 1m_ctx_VH [NFND_251486811718_S01_GE2-v4_91_1_3]

value: VH transgenic mouse


title: PB73

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description: GRC225-EC73; The GRC# is the study#  and the EC# is the animal number

hyb_protocol: Samples were hybridized on to (Mouse Ref-8 V2.0 Expression BeadChip) which a multi sample format allowing 8 samples per chip

scan_protocol: Arrays were scanned on the iScan module and raw data (.idat files) were obtained using the illumina iScan control software Operating Software (version v3.3.28) and analyzed by GenomeStudio® (Illumina Inc.)

data_processing: For analysis of microarray data, raw intensities were quantile normalized from the Illumina Genome Studio® (Illumina Inc.).

source_name: phenobarbital

label_protocol: Biotin-labeled cRNA was produced from 200ng total RNA using the Illumina TotalPrep RNA Amplification kit (cat# AMIL1791).

extract_protocol: Approximately 20 mg of archived frozen liver tissue was homogenized in RNAzol®RT ( Molecular Research Center, Cincinnati, Ohio) using ceramic beads in the Precellys® 24 homogenizer (Bertin Technologies, Villeurbanne, France).

treatment_protocol: Dichloroacetic acid (CAS 79-43-6, Aldrich, Milwaukee, WI) and phenobarbital (PB) (CAS 50-06-6, Sima Chemical Co., St.Louis, MO) were administered in the drinking water.

tag: strain background

tag: gender

value: male

value: 7 days

tag: treated with

value: dH2O with 0.06% PB for 10 wks followed by dH2O for 90wks

value: liver


title: 1m_ctx_AD11 [NFND_251486811713_S01_GE2-v4_91_1_4]

tag: age

value: 1 month


title: Cerebellum_Depression

city: Wakayama city

first: Yuta

last: Yamamoto

address: 811-1 Kimiidera

institute: Wakayama Medical  University

description: Gene expression in the prefrontal cortex of depressive rats

hyb_protocol: Hybridization was performed at 65ºC for 17 h.

scan_protocol: After washing, fluorescence intensity was assayed using a scanner (G2565BA; Agilent).

data_processing: The signal intensities were quantified and analyzed by subtracting background fluorescence using Feature Extraction software (Agilent) and then normalized by GeneSpring 12.0 software (Agilent).

organism: Rattus norvegicus

source_name: cerebellum, depressive group

label_protocol: An equal amount of RNA from four rats in each group was pooled and used for microarray analysis. The quality of purified RNA was assessed using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA). Total RNA (400 ng) was first reverse transcribed using a T7 sequence-conjugated oligo dT primer. At the same time, we used a One Color RNA Spike-In Kit (Agilent) to adjust microarray data. Synthesis, amplification, and labeling of complementary RNA (cRNA) with Cy3 dye were performed according to the manufacturer’s protocols.

extract_protocol: Total RNA was isolated immediately from these samples using an RNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: To prepare RNA samples, 50 rats subjected to the FST one week before were sacrificed at 14:00 under general anesthesia with isoflurane. The whole rat brain was removed after systemic perfusion with cold phosphate-buffered saline through the heart using a syringe attached to a 21-G needle. Coronal brain sections (1 mm thick) were prepared on ice, using a brain slicer (Muromachi Kikai, Tokyo, Japan). The prefrontal cortex was sliced between 3.2 and 4.2 mm anterior to the bregma, and the cerebellum between 9.8 and 10.8 mm posterior to the bregma according to a stereotaxic atlas.

value: cerebellum

tag: state

value: depressive

tag: Sex


title: 1m_ctx_AD11 [NFND_251486811718_S01_GE2-v4_91_1_2]

tag: genotype/variation

value: cortex


title: Patski_transitory Firre KD_promoter

source_name: H3K27me3 ChIP DNA from Patski cells treated by Firre siRNAs (Invitrogen)

treatment_protocol: Firre siRNA treatment

value: Fibroblasts

value: Firre knockdown

value: BL6/spretus hybrid embryonic kidney and has the inactive X from BL6.

source_name: ChIP input DNA


title: PrefrontalCortex_Control

description: Gene expression in the prefrontal cortex of control rats

source_name: prefrontal cortex, control

value: prefrontal cortex

value: control


title: Patski_transitory control_promoter

source_name: H3K27me3 ChIP DNA from Patski cells treated by negative control siRNAs (Invitrogen)

treatment_protocol: Negative control siRNA treatment

value: Millipore (Cat#07-449)

value: input


title: PrefrontalCortex_Depression

description: Gene expression in the cerebellum of depressive rats

source_name: prefrontal cortex, depressive group


title: PB64

description: GRC225-EC64; The GRC# is the study#  and the EC# is the animal number


title: PB45

description: GRC225-EC45; The GRC# is the study#  and the EC# is the animal number


title: 1m_bfb_VH [NFND_251486812130_S01_GE2-v4_91_1_4]

value: wildtype

value: 3 months

value: pool of whole brain from 2 mice

value: basal forebrain


title: 1m_bfb_VH [NFND_251486811823_S01_GE2-v4_91_1_4]

value: VH transgenic mouse


title: 1m_bfb_VH [NFND_251486811823_S01_GE2-v4_91_1_3]


title: PB24

description: GRC225-EC24; The GRC# is the study#  and the EC# is the animal number

value: male

value: 7 days

value: dH2O with 0.06% PB for 10 wks followed by dH2O for 90wks

value: liver


title: male embryo_CTCF_genome tiling set38

source_name: CTCF ChIP DNA from mouse male 12.5dpc embryo

value: wild type

value: 12.5dpc embryo

value: CTCF

value: Millipore (Cat#07-729)


title: female embryo_CTCF_genome tiling set38

source_name: CTCF ChIP DNA from mouse female 12.5dpc embryo

value: female


title: male liver_CTCF_genome tiling set38

source_name: CTCF ChIP DNA from mouse male adult liver

value: Liver


title: female liver_CTCF_genome tiling set38

source_name: CTCF ChIP DNA from mouse female adult liver


title: Cerebellum_Control

description: Gene expression in the cerebellum of control rats

source_name: cerebellum, control

value: cerebellum

value: control


title: PB82

description: GRC225-EC82; The GRC# is the study#  and the EC# is the animal number


title: DCA361

description: GRC225-EC361; The GRC# is the study#  and the EC# is the animal number

source_name: DCA

value: DCA (3.5 g/L) for 10 wks followed for 90 wks dH20


title: DCA366

description: GRC225-EC366; The GRC# is the study#  and the EC# is the animal number


title: Murine liver with 8 weeks of CCL4 treatments replicate  1

status: Public on Feb 25 2015

city: Baltimore

first: Tyler

middle: J

last: Creamer

state: Maryland

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

description: 8 weeks Ct1

scan_protocol: The array was run on the 7900HT from Applied Biosystems.

data_processing:
Geometric mean was used for global normalization of the plate.
DataAssist Software v0.50
Study: Mouse Array A GN
Maximum allowable CT value: 38.0
Allow undetermined CT value: No
Exclude outliers among replicates: Yes
Normalization method: Geometric Mean
Selected Controls: All (Global Normalization)
Reference: not treated

source_name: 8 weeks of CCL4 treatments

growth_protocol: All mice were females that were 4 weeks of age at the begining of treatment.

extract_protocol: Total RNA was isolated using miRvana miRNA Isolation Kit as per manufacturers protocol.

treatment_protocol: Carbon tetrachloride was diluted with corn oil and injected intraperitenially biweekly (1mg/kg)

value: 4wks at the begining of the treatment

value: carbon tetrachloride (CCl4) for 8 wk


title: DCA357

description: GRC225-EC357; The GRC# is the study#  and the EC# is the animal number


title: Murine liver with 4 weeks of CCL4 treatments replicate  2

description: 4 weeks Ct2

source_name: 4 weeks of CCL4 treaments

value: carbon tetrachloride (CCl4) for 4 wk


title: 1m_bfb_AD11 [NFND_251486812130_S01_GE2-v4_91_1_2]

source_name: Wild type C57BL×SJLF2  mouse

value: wildtype

value: 3 months

value: pool of whole brain from 2 mice

source_name: AD11 anti-NGF transgenic mouse

value: AD11 anti-NGF transgenic mouse

value: 1 month

value: basal forebrain


title: DCA335

description: GRC225-EC335; The GRC# is the study#  and the EC# is the animal number

value: male

value: 7 days

value: liver


title: 1m_bfb_AD11 [NFND_251486812130_S01_GE2-v4_91_1_3]


title: 1m_bfb_AD11 [NFND_251486812130_S01_GE2-v4_91_1_1]


title: Murine liver with 4 weeks of CCL4 treatments replicate  1

description: 4 weeks Ct1

value: female


title: Murine liver with 1 week of CCl4 treatments replicate  2

description: 1 week Ct2

source_name: 1 week of CCl4 treatments

value: carbon tetrachloride (CCl4) for 1 wk


title: 1m_bfb_AD11 [NFND_251486812129_S01_GE2-v4_91_1_3]


title: cont104

description: GRC225-EC104; The GRC# is the study#  and the EC# is the animal number

source_name: control

value: deionized water alone (dH2O, control)


title: cont115

description: GRC225-EC115; The GRC# is the study#  and the EC# is the animal number


title: cont101

description: GRC225-EC101; The GRC# is the study#  and the EC# is the animal number


title: Murine liver with 8 weeks of CCL4 treatments replicate  2

description: 8 weeks Ct2


title: Normal murine liver replicate 2

description: not treated Ct2

source_name: Normal

value: none (control)


title: Murine liver with 1 week of CCl4 treatments replicate  1

description: 1 week Ct1


title: Normal murine liver replicate 1

description: not treated Ct1


title: 1m_bfb_AD11 [NFND_251486812129_S01_GE2-v4_91_1_4]


title: cont117

description: GRC225-EC117; The GRC# is the study#  and the EC# is the animal number


title: SL1344_mouse_IgG_ChIP_chip

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: biological replicate 1

hyb_protocol: Cy3 labeled ChIP DNA and Cy5 labeled Input genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using a GenePix 4000B scanner (Axon Instruments). Cy3 and Cy5 images were acquired at 10 micron resolution. Quantification of fluorescent spot intensities and local background data was performed using the GenePix Pro 6.1 software supplied.

data_processing: The background subtracted median Cy3/Cy5 ratio were determined for each probe. Cy3/Cy5 values were then median normalised by dividing each microarray probe value by the median value.

label: Cy3 dCTP

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: IgG ChIP DNA

label_protocol: Fluorescent labeling of ChIP DNA  and  genomic Input DNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[80% of ChIP DNA sample and 200 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344  CspC 3xFLAG cells were inoculated 1:100 into 25 ml fresh Luria Broth (LB) and grown at 37degrees celsius in a shaking waterbath at 200 rpm until OD600 0.2

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS. DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. 1350 ul chromatin + 10 ug of FLAG monoclonal antibodies (Sigma-Aldrich, Cat. No. F3165) and 10 ug of normal mouse IgG (Millipore, catalogue number 12-371) were used for CspC ChIP and mock ChIP samples respectively. The samples were incubated at 4°C overnight on a rotating wheel. 50 μl of homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

value: SL1344 CspC 3xFLAG

label: Cy5 dCTP

source_name: Input genomic DNA


title: SL1344_CspC_ChIP_chip

description: biological replicate 1

source_name: CspC ChIP DNA


title: FFPE_breast_cancer_ER negative_4714730072_A

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The labeled PCR products were then captured on streptavidin paramagnetic beads, washed, and denatured to yield single-stranded fluorescent molecules which were hybridized to the Whole Genome gene expression BeadChips for 16 h at 58 °C.

scan_protocol: Illumina BeadArray Reader was used for scanning the arrays and Illumina BeadScan was used for image acquisition and recovery of primary data.

data_processing: Quality control on Illumina data and normalization, with the Robust Spline Normalization method, were performed using the lumi package.

source_name: breast cancer_ER negative

label_protocol: 200 ng total RNA were converted to cDNA using biotinylated oligo-dT18 and random nonamer primers, followed by immobilization to a streptavidin-coated solid support. The biotinylated cDNAs were then simultaneously annealed to a set of assay-specific oligonucleotides. Extension and ligation of the annealed oligonucleotides generated PCR templates that were amplified using fluorescence-labeled and biotinylated universal primers.

extract_protocol: Tissue was pulverized using a Mikrodismembrator (Braun Biotech International, Germany). Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions with an additional DNase digestion using the RNeasy kit (Qiagen, Valencia, CA).

tag: tissue type

value: FFPE primary breast cancer samples

tag: er status

value: negative


title: FFPE_breast_cancer_ER positive_4714730071_D

source_name: breast cancer_ER positive

value: positive


title: FFPE_breast_cancer_ER negative_4714730071_G


title: CordBlood_GDM_3

city: Nanjing

first: Shi

last: Zhonghua

address: Tianfei Lane, Mochou Road

country: China

institute: Nanjing Maternity and child health care hospital

description: Gene expression of umbilical cord vein blood plasma from GDM macrosomia_3

hyb_protocol: Step 5 Hybridization  Kit and Instruments:  Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):  10X Blocking Agent  25X Fragmentation Buffer  2x GEx Hybridization Buffer HI-RPM  Hybridization Chamber, stainless (Agilent p/n G2534A)  Hybridization Chamber gasket slides (Agilent p/n G2534-60003)  Hybridization oven (Agilent p/n G2545A)  Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)    Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    For 8*60K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul      4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60k  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60K  Volume Prepared 500ul 250ul 110ul 50ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.     Step 6 Microarray Wash  Kit and Instruments:  Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325)  Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326)  Magnetic stir bar (Corning p/n 401435)  Magnetic stir plate (Corning p/n 6795-410)  Slide-staining dish, with slide rack (Thermo Shandon p/n 121)    Procedure:  1. Prewarm enough volume of Gene Expression Wash Buffer 2 to 37°C.  2. Add the slide rack and stir bar to the staining dish.  3. Transfer the staining dish with the slide rack and stir bar to a magnetic stir plate.  4. Fill the staining dish with 100% acetonitrile.  5. Turn on the magnetic stir plate and adjust the speed to a setting of 4 (medium speed).  6. Wash for 5 minutes.  7. Discard the acetonitrile as is appropriate for your site.  8. Repeat step 2 to step 7.  9. Air dry the staining dish in the vented fume hood.  10. Wash all dishes, racks, and stir bars with Milli-Q water.   11. Completely fill slide-staining dish #1 with Gene Expression Wash Buffer 1 at room temperature.  12. Place a slide rack into slide-staining dish #2. Add a magnetic stir bar. Fill slide-staining dish #2 with enough Gene Expression Wash Buffer 1 at room temperature to cover the slide rack. Place this dish on a magnetic stir plate.  13. Place the empty dish #3 on the stir plate and add a magnetic stir bar. Do not add the prewarmed (37°C) Gene Expression Wash Buffer 2 until the first wash step has begun.  14. Remove one hybridization chamber from incubator and record time. Record whether bubbles formed during hybridization and if all bubbles are rotating freely.   15. Prepare the hybridization chamber disassembly.  a) Place the hybridization chamber assembly on a flat surface and loosen the thumbscrew, turning counterclockwise.  b) Slide off the clamp assembly and remove the chamber cover.  c) With gloved fingers, remove the array-gasket sandwich from the chamber base by grabbing the slides from their ends. Keep the microarray slide numeric barcode facing up as you quickly transfer the sandwich to slide-staining dish #1.  d) Without letting go of the slides, submerge the array-gasket sandwich into slide-staining dish #1 containing Gene Expression Wash Buffer 1.  16. With the sandwich completely submerged in Gene Expression Wash Buffer 1, pry the sandwich open from the barcode end only:  a) Slip one of the blunt ends of the forceps between the slides.  b) Gently turn the forceps upwards or downwards to separate the slides.  c) Let the gasket slide drop to the bottom of the staining dish.  d) Remove the microarray slide and place into slide rack in the slide-staining dish #2 containing Gene Expression Wash Buffer 1 at room temperature.   17. When all slides in the group are placed into the slide rack in slide-staining dish #2, stir using setting 4 for 1 minute.  18. During this wash step, remove Gene Expression Wash Buffer 2 from the 37°C water bath and pour into the slide-staining dish #3.  19. Transfer slide rack to slide-staining dish #3 containing Gene Expression Wash Buffer 2 at elevated temperature. Stir using setting 4 for 1 minute.   20. Slowly remove the slide rack minimizing droplets on the slides. It should take 5 to 10 seconds to remove the slide rack.  21. Scan slides immediately to minimize the impact of environmental oxidants on signal intensities.

scan_protocol: Step 7 Scanning  Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Step 8 Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: Mixed umbilical cord vein blood plasma of ten GDM macrosomia cases_3,replicate 1

label_protocol: Step 3 Prepare labeling reaction  Kit:  Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)    Procedure:  1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.     Step 4 Purify the labeled/amplified RNA and labeled cRNA QC  Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2. Add 350 μL of Buffer RLT and mix well by pipetting.  3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).   From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.   Blank the instrument with 1.5 μL of 1x labeling solution.   Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).   The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: Step 2 Total RNA Clean-up and RNA QC  Kits and Reagents:  RNasey Mini Kit(Qiagen p/n 74104):      Buffer RPE  Buffer RLT  RNeasy Mini spin column  NanoDrop ND-1000  Baseline-ZERO DNase(EPICENTRE, Cat. Nos. DB0711K)    Things to do before starting:  1. Buffer RPE is supplied as a concentrate. Before using for the first time, add 4 volumes of ethanol (96–100%) as indicated on the bottle to obtain a working solution.    Procedure:  1. Mix the following in a microcentrifuge tube:  Redissolved RNA ≤85ul  10×Reaction buffer 10ul  Baseline-ZERO DNase 5ul  RNase-free water X ul  Total volume 100ul  2. Incubate at 37°C for 30 minutes.  3. Add 350 μl Buffer RLT, and mix well.  4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5.  5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through.  6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through.  7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane.  8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min.  9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA.  10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

treatment_protocol: Step 1 Prepare the RNA Sample  Kits and Reagents:  TRIzol® Reagent (Invitrogen life technologies)  Biopulverizer(biospec)  Mini-Bead-Beater-16(biospec)    Procedure:  1. Homogenization  a. Tissues  a) Cryopulverization of tissue using the Biopulverizer  * Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen.  * Place prefrozen tissue in the well of the mortar.  * Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS).  * Empty the powdered contents for subsequent homogenization or extraction procedures.              b) Homogenization using the Mini-Bead-Beater-16  * Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.   * Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten.  * Set the timer depending on the type of sample. Start the machine.   b. Cells Grown in Monolayer  Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.   c. Cells Grown in Suspension  Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of animal, plant or yeast cells, or per 1 × 107 bacterial cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.  2. Phase Separation  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  3. RNA Precipitation  Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.   4. RNA Wash  Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  5. Redissolving the RNA  At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

tag: disease state

value: GDM macrosomia

value: umbilical cord vein blood

tag: bmi before pregnancy

tag: birth weight of offspring(kg)

tag: gender of offspring

value: male:8; female:2


title: FFPE_breast_cancer_ER negative_4714730072_B


title: CordBlood_GDM_1

description: Gene expression of umbilical cord vein blood plasma from GDM macrosomia_1

source_name: Mixed umbilical cord vein blood plasma of ten GDM macrosomia cases_1,replicate 1

value: male:7; female:3


title: FFPE_breast_cancer_ER negative_4714730072_C


title: FFPE_breast_cancer_ER positive_4714730071_B


title: gpa1 gcr1 rep2

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

hyb_protocol: hybridization was carried out using Agilent’s In situ Hybridzation kit as per manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, 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 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 037661_D_F_20111130) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: 3-4 weeks old seedling

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Low Input RNA amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: the mutants and the wild type were grown on 1 X B5 medium hydroponically in growth chamber at 22+1°C with light intensity of 150 μM sec-1 m-2 and photoperiod of 16:8 hours of light:dark cycle after subjecting the seeds to cold treatment at 4°C for 2-3 days

extract_protocol: total RNA was extracted by using hot-phenol LiCl method described by pathak and lochab, 2010

tag: developmental stage

value: seedling

value: gpa1 gcr1 knockout double mutant


title: CordBlood_GDM_2

description: Gene expression of umbilical cord vein blood plasma from GDM macrosomia_2

source_name: Mixed umbilical cord vein blood plasma of ten GDM macrosomia cases_2,replicate 1


title: FFPE_breast_cancer_ER positive_4714730071_A


title: gpa1 gcr1 rep1


title: gcr1 rep2

value: gcr1 knockout mutant


title: FFPE_breast_cancer_ER positive_4714730071_E


title: gcr1 rep1


title: FFPE_breast_cancer_ER positive_4714730071_F


title: CordBlood_Control_3

description: Gene expression of umbilical cord vein blood plasma from normal control_3

source_name: Mixed umbilical cord vein blood plasma of ten normal cases_3,replicate 1

value: control


title: FFPE_breast_cancer_ER negative_4714730071_H


title: FFPE_breast_cancer_ER negative_4714730072_D


title: CordBlood_Control_2

description: Gene expression of umbilical cord vein blood plasma from normal control_2

source_name: Mixed umbilical cord vein blood plasma of ten normal cases_2,replicate 1


title: FFPE_breast_cancer_ER positive_4714730071_C


title: ws2 rep2

description: Control

value: wild type


title: CordBlood_Control_1

description: Gene expression of umbilical cord vein blood plasma from normal control_1

source_name: Mixed umbilical cord vein blood plasma of ten normal cases_1,replicate 1


title: gpa1 rep2

value: gpa1 knockout mutant


title: gpa1 rep1


title: FFPE_breast_cancer_DNA9217-012.CEL

hyb_protocol: Hybridization was performed according with the manufacturer's intructions

scan_protocol: Scanning was performed according with the manufacturer's intructions

data_processing: CEL files were imported using the affy package of Bioconductor, MAS5 normalized and log2 transformed

label_protocol: 5 µg of aDNAss were labeled using the Encore Biotin Module essentially according to manufacturer's inststructions

extract_protocol: Total RNA was extracted using a non commercially available kit by Roche. 100 ng of total RNA were amplified using the WT Ovation FFPE amplification system V2


title: ws2 rep1

description: Control


title: FFPE_breast_cancer_DNA9217-009.CEL


title: FFPE_breast_cancer_DNA9217-006.CEL


title: FFPE_breast_cancer_DNA9217-010.CEL


title: HCC827_ERLOTINIB_6h 2

city: Charlestown

first: Stephen

middle: Michael

last: Rothenberg

state: MA

address: 13th Street, Bldg. 149, 7th Floor

department: Cancer Center

institute: Massachusetts General Hospital

description: Gene expression data from HCC827 cells treated with 1uM various agents

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

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

data_processing: The data were analyzed with Jmp Genomics Version 10. Quality control was performed using the Distribution Analysis, Correlation and Principle Variance Components Analysis functions in Jmp Genomics.  Individual genes with statistically significantly altered expression after treatment (compared to untreated cells) were identified using ANOVA after model adjustment  for multiple hypothesis testing across LSMeans differences using the False Discovery Method of Benjamini and Hochberg (FDR) with Alpha set to 0.05.

label: Biotin

source_name: HCC827 cells treated with 1uM erlotinib for 6 hours

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: HCC827 cells plated in 6-well dishes the night before treatment in RPMI containing 10% fetal calf serum were treated as indicated for the time period indicated

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

treatment_protocol: Each agent was added to a final concentration of 1uM for the time period indicated

tag: cell type

value: lung cancer

tag: cell line

tag: genotype

value: EGFR DEL15

tag: treatment

value: ERLOTINIB

tag: dose

value: 1 uM

tag: time of treatment


title: FFPE_breast_cancer_DNA9217-005.CEL

value: FFPE primary breast cancer samples


title: FFPE_breast_cancer_DNA9217-003.CEL


title: HCC827_ERLOTINIB_6h 1


title: FFPE_breast_cancer_DNA9217-007.CEL

value: negative


title: HCC827_AZD6244_6h 3

source_name: HCC827 cells treated with 1uM AZD6244 for 6 hours


title: FFPE_breast_cancer_DNA9217-002.CEL

value: positive


title: FFPE_breast_cancer_DNA9217-011.CEL


title: HCC827_ERLOTINIB_12h

source_name: HCC827 cells treated with 1uM erlotinib for 12 hours


title: HCC827_BEZ235_6h 1

source_name: HCC827 cells treated with 1uM BEZ235 for 6 hours


title: FFPE_breast_cancer_DNA9217-004.CEL


title: HCC827_ERLOTINIB_3h

source_name: HCC827 cells treated with 1uM erlotinib for 3 hours


title: HCC827_ERLOTINIB_6h 3


title: FFPE_breast_cancer_DNA9217-001.CEL


title: HCC827_AZD6244_6h 1


title: HCC827_DMSO _24h

source_name: HCC827 cells treated with DMSO for 24 hours

value: DMSO


title: 1m_bfb_VH [NFND_251486811823_S01_GE2-v4_91_1_2]

source_name: Wild type C57BL×SJLF2  mouse

value: wildtype

tag: age

value: 3 months

tag: tissue

value: pool of whole brain from 2 mice

source_name: VH transgenic mouse

value: VH transgenic mouse

value: 1 month

value: basal forebrain


title: HCC827_BEZ235_6h 2


title: HCC827_DMSO_6h 2

source_name: HCC827 cells treated with DMSO for 6 hours


title: HCC827_BEZ235_6h 3


title: HCC827_AZD6244_6h 2


title: HCC827_DMSO_6h 1


title: HCC827_DMSO_6h 3


title: WT_Day0_rep3

city: Amsterdam

first: Ronald

middle: E

last: van Kesteren

address: De Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research

institute: VU University Amsterdam

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_1.txt; channel 2

hyb_protocol: Samples were hybridized to Agilent 4x44K whole mouse genome microarrays using standard Agilent protocols

scan_protocol: Arrays were scanned using an Agilent scanner and data were extracted using Agilent Feature Extraction software

data_processing: Data was background-corrected (method = Edwards, offset = 1) and subsequently log2-transformed and normalized using quantile normalization.

label_protocol: Samples were amplified and labeled using standard Agilent protocols

extract_protocol: Total RNA was isolated using TRI Reagent according to the manufacturers guidelines

treatment_protocol: Sciatic nerves were lesioned and nerve endings were coaptated

tag: gender

value: Male

tag: strain

value: Wildtype

tag: day

value: control

value: DRG neurons

value: adult


title: KO_Day0_rep2

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_1.txt; channel 1


title: HCC827_ERLOTINIB_24h

source_name: HCC827 cells treated with 1uM erlotinib for 24 hours

value: lung cancer

value: EGFR DEL15

value: ERLOTINIB


title: WT_Day2_rep3

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_1.txt; channel 2


title: WT_Day5_rep3

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_1.txt; channel 2


title: KO_Day0_rep3

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_4.txt; channel 2


title: KO_Day2_rep4

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_4.txt; channel 2


title: KO_Day5_rep3

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_3.txt; channel 2


title: KO_Day5_rep4

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_4.txt; channel 2


title: WT_Day0_rep4

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_3.txt; channel 2


title: WT_Day2_rep4

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_3.txt; channel 2


title: WT_Day2_rep2

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_4.txt; channel 1


title: WT_Day5_rep4

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_2.txt; channel 2


title: KO_Day0_rep4

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_2.txt; channel 2


title: KO_Day2_rep3

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_2.txt; channel 2


title: KO_Day2_rep2

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_4.txt; channel 1


title: WT_Day5_rep2

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_3.txt; channel 1


title: WT_Day2_rep1

description: file name and channel: US22502676_251486838612_S01_GE2_107_Sep09_1_2.txt; channel 1


title: WT_Day0_rep2

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_3.txt; channel 1


title: 1m_bfb_VH [NFND_251486811823_S01_GE2-v4_91_1_1]

tag: genotype/variation


title: KO_Day2_rep1

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_1.txt; channel 1


title: KO_Day5_rep2

description: file name and channel: US22502676_251486838611_S01_GE2_107_Sep09_1_2.txt; channel 1


title: Effector cells from invitro stimulated CD8+ T cells on day5  Sample1

city: Sydney

first: Wolfgang

last: Weninger

state: NSW

address: Locked Bag 6, Newtown

institute: Centenary Institute

description: Effector CD62Llo CD44hi CD8+ T cells

hyb_protocol: by Ramaciotti Centre for Gene Function Analysis (The University of New South Wales, Sydney, NSW) according to the Affymetrix protocol

data_processing: The CEL files were analyzed using Bioconductor of R project. The raw intensity data of all samples were first RMA normalized and the differential expression analysis was conducted with the lmfit and ebayes model.

source_name: mouse splenocytes

growth_protocol: Naïve CD44lo CD8+ T cells were isolated from uninfected C57BL/6 mice and Kb-OVA257-264-specific CD8+ T cells were sorted on day7 p.i. with PR8-OVA or sorted from in vitro culture on day7 after stimulation with SIINFEKL peptide.

extract_protocol: Total RNA was extracted and purified with miRNeasy Micro Kit from QIAGEN.

tag: cd8+ t cell subsets

value: Kb-OVA257-264-specific CD62Llo CD44hi CD8+ T cells

tag: time points

value: Day5 post stimulation

tag: infection/ in vitro stimulation

value: In vitro stimulation with SIINFEKL peptide


title: Effector cells from invitro stimulated CD8+ T cells on day5  Sample2

description: Effector CD62Llo CD44hi CD8+ T cells

scan_protocol: by Ramaciotti Centre for Gene Function Analysis (The University of New South Wales, Sydney, NSW) according to the Affymetrix protocol

treatment_protocol: Naïve CD44lo CD8+ T cells were isolated from uninfected C57BL/6 mice and Kb-OVA257-264-specific CD8+ T cells were sorted on day7 p.i. with PR8-OVA or sorted from in vitro culture on day7 after stimulation with SIINFEKL peptide.


title: Smaller cell sized invitro stimulated CD8+ T cells on day7  Sample2

description: Activated CD44hi CD8+ T cells (small cell-size)

label_protocol: by Ramaciotti Centre for Gene Function Analysis (The University of New South Wales, Sydney, NSW) according to the Affymetrix protocol

value: Kb-OVA257-264-specific CD44hi CD8+ T cells (small cell-size)

value: Day7 post stimulation


title: WT_Day0_rep1

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_4.txt; channel 1


title: Effector memory virus specific CD8+ T cells from day42 p.i.  Sample1

description: Effector Memory CD62Llo CD44hi CD8+ T cells

value: Day42 p.i.

value: PR8-OVA influenza virus infection


title: Central memory virus specific CD8+ T cells from day42 p.i.  Sample2

description: Central Memory CD62Lhi CD44hi CD8+ T cells

value: Kb-OVA257-264-specific CD62Lhi CD44hi CD8+ T cells


title: Smaller cell sized invitro stimulated CD8+ T cells on day7  Sample1


title: Naïve CD8+ T cells Sample1

description: Naïve CD62Lhi CD44lo CD8+ T cells

value: Kb-OVA257-264-specific CD62Lhi CD44lo CD8+ T cells

value: Day0 (uninfected)

value: uninfected


title: Larger cell sized CD62Llo invitro stimulated CD8+ T cells on day7  Sample1

description: Activated CD62Llo CD44hi CD8+ T cells (small cell-size)

value: Kb-OVA257-264-specific CD62Llo CD44hi CD8+ T cells (large cell-size)


title: KO_Day5_rep1

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_1.txt; channel 1

value: Male

value: DRG neurons


title: Central memory virus specific CD8+ T cells from day42 p.i.  Sample1


title: C1498

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: mouse strain

hyb_protocol: Hybridized to Agilent-027414 array.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: C1498 clone

label_protocol: Probe labeling used Agilent Technologies Genomic DNA Enzymatic Labeling Kit. Labeling was performed following manufacturer's instructions.

extract_protocol: Chromosomal DNA were extracted using Qiagen DNA extraction Kit following manufacturer's instructions.

tag: strain/background

value: acute myeloid leukemia (AML) cell line

source_name: T leukocytes

value: T lymphocytes


title: KO_Day0_rep1

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_2.txt; channel 1

value: control

tag: developmental stage

value: adult


title: Larger cell sized invitro stimulated CD8+ T cells on day7  Sample1

description: Activated CD44hi CD8+ T cells (large cell-size)

value: Kb-OVA257-264-specific CD44hi CD8+ T cells (large cell-size)


title: WT_Day5_rep1

description: file name and channel: US22502676_251486838610_S01_GE2_107_Sep09_1_3.txt; channel 1

value: Wildtype


title: Smaller cell sized virus specific CD8+ T cells from day7 p.i.  Sample1

value: Kb-OVA257-264-specific CD44hi CD8+ T cells (small cell-size)

value: Day7 p.i.


title: Smaller cell sized virus specific CD8+ T cells from day7 p.i.  Sample2


title: E2 clone

description: mouse clone from strain

hyb_protocol: Hybridized to Agilent-027411 arrays.

source_name: E2 clone

tag: cell type


title: Larger cell sized invitro stimulated CD8+ T cells on day7  Sample2

value: Day7 post stimulation

value: In vitro stimulation with SIINFEKL peptide


title: FFPE_breast_cancer_DNA9217-008.CEL

source_name: breast cancer_ER negative

tag: tissue type

value: FFPE primary breast cancer samples

tag: er status

value: negative


title: F1 clone

description: mouse clone from strain

source_name: F1 clone

tag: cell line


title: G10 clone

description: mouse clone from strain

source_name: G10 clone


title: E7 clone

description: mouse clone from strain

source_name: E7 clone


title: Larger cell sized virus specific CD8+ T cells from day7 p.i.  Sample1

value: PR8-OVA influenza virus infection


title: Flu memory P14 CD8 T cells_rep2

city: Atlanta

first: Shruti

last: Subramaniam

state: GA

address: Clifton Road

institute: Emory University

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called PR8-33-2

hyb_protocol: Standard Affymetrix hybridization protocols for eukaryotic total RNA were used for the samples.All samples were hybed at 45C,16 hours,60 RPM in 640 Affymetrix Hyb oven. Affymetrix fludics program EUKGEWS2v4_450 was used for washing

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring

label: Generation of cDNA, amplification, biotinylation and fragmentation was performed using the NuGen Ovation biotin system.

source_name: Memory P14 T cells from spleen

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from sorted cells using a QIAGEN RNeasy kit according to the manufacturer's instructions.

treatment_protocol: P14 cells from spleen were sorted by flow cytometry based on CD8a and CD90.1 expression.

tag: C57BL/6 mice, 90 days after influenza virus infection.

tag: Mice infected with a recombinant influenza virus expressing LCMV gp33-41 in Neuraminidase stalk (PR8-33), by intranasal route.


title: Flu memory P14 CD8 T cells_rep1

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called PR8-33-1


title: Naive P14 CD8 T cells_rep2

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called Naïve-2

source_name: Naïve P14 T cells from spleen

tag: 6 week old naïve transgenic P14 mice on a C57BL/6 background.


title: LCMV memory P14 CD8 T cells_rep2

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called LCMV-2

tag: C57BL/6 mice, 90 days after LCMV infection.

tag: Mice infected with LCMV Armstrong by intraperitoneal route.