title: Mature leaf 8WAT, no water deficit, PD inoculated, biological rep 1 [4I1L]


title: Blood, Subject 10017187, 369.8 hours since injury

status: Public on Feb 12 2013

type: RNA

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

country: USA

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: Affymetrix Power Tools version 1.8.6 RMA model

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix)

extract_protocol: Total RNA was purified using the Rneasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA)

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.

tag: tissue

value: White blood cells

tag: Sex

value: M

tag: age


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 2 [4I2E]

city: Davis

first: Douglas

middle: R

last: Cook

state: California

address: One Shields Aave

institute: University of California-Davis

hyb_protocol: Conducted at UC-Davis Genome Center according to Affymetrix protocol

data_processing: Probe signal intensities in *.DAT files were processed with the Affymetrix GCOS version 1.2 software package. Resulting *.CEL files were imported into the Bioconductor software suite (http://www.bioconductor.org, Gentleman et al., 2004) in R (Ihaka and Gentleman, 1996) for data quality control. Files were then analyzed using the AffylmGUI package procedure for time course experiments as described by Smyth (2005). The GC Robust Multichip Analysis (RMA) (Wu et al., 2004) in AffylmGUI was used for background adjustment, cross-chip quantile normalization and median polish summarization of probe level expression data using probe affinity data. Differentially expressed genes were identified using a moderated t-test with Benjamini-Hochberg adjustment for false discovery rate (Smyth, 2004). A standard linear model of the expression data for Limma was created and all possible contrasts within an irrigation treatment were calculated to identify differentially expressed genes. Two different sets of cut-offs were set to identify two distinct sets of differentially expressed genes. Genes in the first group have a log2 ratio (M) greater than or equal to 1 and a p-adjusted by false discovery rate (P) smaller than or equal to 0.05. Genes passing the more stringent cut-offs of the second group have an M smaller than 1, a P value smaller or equal to 0.01. Genes in both groups must have an empirical Bayes log odds of differential expression (B) greater than or equal to 0. Finally, a core set of differentially expressed genes was created by pulling together genes that were identified as differentially expressed in at least one of the performed contrasts. This final core set was used for subsequent expression analysis and interpretation.

organism: Vitis vinifera

source_name: Mature leaf from 2 year old-vine 4WAT, no water deficit, PD inoculated

label_protocol: Four ug of total RNA was used to make biotin-labeled cRNA targets using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) followed by cDNA cleanup, biotin labeling and fragmentation according to Affymetrix’s instructions.

growth_protocol: Two-year-old vines (Vitis vinifera L. cv. Cabernet sauvignon clone 8 on Freedom rootstock) were grown for one year under greenhouse conditions in 10” pots containing 50% by volume of Turface fritted clay (Profile products LLC, Buffalo Grove, USA) and 50% Pro-Mix BX peat moss (Premier Tech Ltd, Quebec, Canada) amended with 0.2 Kg per vine of 18-6-12 Multicote fertilizer (N-P-K; Schultz Co., Bridgeton, USA). Prior to bud break, plants were moved to growth chambers with a 14/10 hr light/dark period at a PPFD intensity of approximately 1000 mmol photons m-2 s-1; a 25/20 oC daily air temperature regime; and a 50/80% relative humidity for the photo and nictoperiod, respectively. Plants were organized in a block design of three rows with all treatments randomized in each row. Subsequent to a 4-week acclimation period, grapevines were pruned to produce a uniform shoot architecture consisting of two shoots per plant and ten leaves per shoot. Approximately two weeks after full bloom, the shoot apical meristems were removed to prevent further growth. Laterals were removed throughout the season to contain growth and ensure a uniform light environment. Vines were watered on a daily basis with nutrient solution (0.11 g/L of GrowMore 4-18-38, boron removed) using pressure compensated drip emitters, with watering rates depending on imposed treatment. Daily water uptake was calculated using a mini-lysimeter on plants watered to field capacity (100% water usage).

extract_protocol: Four weeks after the initiation of treatment, the third and fourth leaves were harvested from three plants of each treatment type and used for pre-symptomatic transcriptional analysis. At eight weeks following the treatments, when symptoms were evident on infected individuals, the 5th and 6th leaves from the same grapevines were harvested for the post-symptomatic transcriptional analysis. Total RNA was isolated as described in Iandolino et al (2004).

treatment_protocol: The estimated 100% water usage was used to establish treatment watering rates: 100% (water sufficient), 50% (moderate stress) and 25% (severe stress). Two different growth chambers were used to house the two different irrigation level experiments: a moderate water deficit (MD, vines irrigated at 50% of estimated daily vine water use) and a severe water deficit (SD, vines irrigated at 25% of estimated daily vine water use). Five different treatments were imposed in each chamber: a non-inoculated control (N), a mock inoculated control (vines inoculated with deionized water, M) and a PD inoculated treatment (I), all of them irrigated at a 100% of estimated daily vine water use. In addition, a PD inoculated (ID) and a non-inoculated (D) treatment was irrigated at the pre-established fraction of full daily water use. Each treatment was replicated 4 times. X. fastidiosa strain Fetzer was grown at 28 C on PD3 agar medium for two weeks (Davis et al. 1981), at which point bacterial cells were harvested into 2 ml of sterile water and adjusted to OD600=0.25 (108 cells/ml). Five µl of bacterial suspension was placed in triplicate on the basal internode of each shoot and a 27 gauge hypodermic needle pushed through the inoculum droplet into the stem to facilitate uptake into the vascular system.

tag: organ

value: Mature leaf

tag: cultivar

value: Cabernet sauvignon clone 8

tag: plant age

value: 2-year old vine

value: 4 weeks after inoculation treatment (WAT)


title: Mature leaf 4WAT, moderate water deficit, PD inoculated, biological rep 1 [4ID1E]

scan_protocol: Conducted at UC-Davis Genome Center according to Affymetrix protocol

source_name: Mature leaf from 2 year old-vine 4WAT, moderate water deficit, PD inoculated


title: Blood, Subject 10078209, 320.8 hours since injury

value: F


title: Blood, Subject 9998998, 39.5 hours since injury


title: Blood, Subject 9885016, 262.2 hours since injury


title: Blood, Subject 9998998, 222.7 hours since injury


title: Blood, Subject 9699116, 36.5 hours since injury


title: HuRef lymphoblastoid cell line_Illumina

type: genomic

city: Toronto

first: Andy

last: Pang

state: ON

address: MaRS Centre - East Tower, 101 College Street, Room 14-701

country: Canada

institute: The Centre for Applied Genomics

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software.

hyb_protocol: DNA was amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The array was washed and scanned using Illumina BeadArray Reader.

data_processing:
The chip was analyzed using Illumina's Beadstudio software 3.3 with a gencall cutoff of 0.1 and call rate cutoff of 98%. QuantiSNP and iPattern were used to identify CNVs. The processed_intensity file includes the SNP calls and the GFF file includes the genomic coordinates and direction of calls (i.e., gain or loss).
Genome build: NCBI Build 36.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: HuRef lymphoblastoid cell line

label_protocol:
As per the manufacturer's (Illumina) protocol.
C and G nucleotides were biotin labeled; A and T nucleotides were dinitrophenyl labeled.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: cell line

value: HuRef

tag: cell type

value: lymphoblastoid

tag: gender

value: male


title: Mature leaf 8WAT, no water deficit, mock inoculated, biological rep 2 [4N2L]

description: Technical rep values for each probe were averaged to have a mean value for the biological rep in the Matrix Template

source_name: Mature leaf from 2 year old-vine 8WAT, no water deficit, mock inoculated

value: 8 weeks after inoculation treatment (WAT)


title: Mature leaf 8WAT, no water deficit, mock inoculated, biological rep 3 [4N3L]


title: Mature leaf 4WAT, moderate water deficit, mock inoculated, biological rep 2 [4D3E]

source_name: Mature leaf from 2 year old-vine 4WAT, moderate water deficit, mock inoculated


title: Mature leaf 4WAT, moderate water deficit, mock inoculated, biological rep 1 [4D2E]


title: Mature leaf 8WAT, moderate water deficit, mock inoculated, biological rep 2 [4D3L]

source_name: Mature leaf from 2 year old-vine 8WAT, moderate water deficit, mock inoculated


title: Mature leaf 8WAT, moderate water deficit, mock inoculated, biological rep 3 [4D4L]


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 1 [4I1E]


title: Blood, Subject 9577776, 485.6 hours since injury


title: Blood, Subject 9581615, 879.3 hours since injury


title: Mature leaf 4WAT, moderate water deficit, mock inoculated, biological rep 3 [4D4E]


title: Mature leaf 8WAT, no water deficit, mock inoculated, biological rep 1 [4N1L]


title: Blood, Subject 9699116, 516 hours since injury

source_name: Subject 9699116, 516 hours since injury


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 3 [4N3E]

source_name: Mature leaf from 2 year old-vine 4WAT, no water deficit, mock inoculated


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 2 [4N2E]


title: Blood, Subject 9581615, 15.3 hours since injury


title: Mature leaf 8WAT, moderate water deficit, mock inoculated, biological rep 1 [4D2L]


title: Blood, Subject 9577776, 6.5 hours since injury

source_name: Subject 9577776, 6.5 hours since injury


title: Blood, Subject 9998998, 390.4 hours since injury


title: Blood, Subject 9462260, 280.9 hours since injury


title: Blood, Subject 9581615, 111.3 hours since injury


title: Blood, Subject 9462260, 16.1 hours since injury


title: Blood, Subject 9432730, 360.2 hours since injury


title: Blood, Subject 9581615, 544.4 hours since injury


title: Blood, Subject 9432730, 30.6 hours since injury


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 1 [4N1E]


title: Blood, Subject 9432730, 937.3 hours since injury


title: Blood, Subject 9577776, 149.5 hours since injury


title: aza_rep2b

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

country: Germany

institute: EMBL

description: Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine; biological replicate 2, technical replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using the lumi R package. Background subtraction was performed using the 'forcePositive' option to ensure that only positive values were achieved. Data was normalised using Robust Spline Normalisation

label: Biotin

organism: Mus musculus

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

growth_protocol: MEFs were cultured under standard conditions

extract_protocol: Total RNA was extracted with Trizol reagent according to manufacturers instructions followed by DNase I treatment. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MEFs were treated for 72 hours with either DMSO control or 1uM 5-aza-2'-deoxycytidine (Sigma)

tag: background strain

value: unknown [Lande-Diner et al 2007 (PMID:17311920)]

value: Mouse embryonic fibroblasts

tag: genotype


title: Blood, Subject 9295534, 353 hours since injury

source_name: Subject 9295534, 353 hours since injury


title: Blood, Subject 9305027, 61.1 hours since injury


title: Blood, Subject 9224540, 155.8 hours since injury


title: aza_rep1a

description: Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine; biological replicate 1, technical replicate 1


title: Blood, Subject 9305027, 355.8 hours since injury


title: Blood, Subject 9224540, 36.4 hours since injury


title: aza_rep2a

description: Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine; biological replicate 2, technical replicate 1


title: con_rep2a

description: Dnmt1+/+ mouse embryonic fibroblasts treated with DMSO control; biological replicate 2, technical replicate 1


title: con_rep2b

description: Dnmt1+/+ mouse embryonic fibroblasts treated with DMSO control; biological replicate 2, technical replicate 2


title: con_rep1b

description: Dnmt1+/+ mouse embryonic fibroblasts treated with DMSO control; biological replicate 1, technical replicate 2


title: Blood, Subject 9092445, 133.7 hours since injury


title: Blood, Subject 9224540, 494.5 hours since injury


title: Blood, Subject 9171091, 14.2 hours since injury


title: Blood, Subject 9112289, 60.2 hours since injury


title: aza_rep1b

description: Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine; biological replicate 1, technical replicate 2


title: Blood, Subject 9092445, 830.3 hours since injury


title: Blood, Subject 9305027, 17.9 hours since injury


title: con_rep1a

description: Dnmt1+/+ mouse embryonic fibroblasts treated with DMSO control; biological replicate 1, technical replicate 1


title: Blood, Subject 9105776, 726.5 hours since injury


title: Blood, Subject 8846868, 640.2 hours since injury


title: Blood, Subject 9105776, 200.7 hours since injury


title: Blood, Subject 8840395, 1552.1 hours since injury


title: Blood, Subject 8808968, 469.4 hours since injury


title: Blood, Subject 8846868, 88.9 hours since injury


title: Blood, Subject 8826596, 9122 hours since injury


title: Blood, Subject 8905476, 42.4 hours since injury


title: Blood, Subject 8840395, 802.4 hours since injury


title: Blood, Subject 8840395, 34.2 hours since injury


title: Blood, Subject 8808968, 114.4 hours since injury


title: Blood, Subject 8656000, 37.8 hours since injury


title: Blood, Subject 8826596, 50 hours since injury

source_name: Subject 8826596, 50 hours since injury


title: Blood, Subject 8840395, 274.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML279T)

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturer’s recommendations. Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in .txt format. Call rates for the entire group of samples included in this report were between 94.02% and 99.35%, with a mean call rate of 98.06%; none of the tumor DNA samples gave out-of-bounds results.
Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip, adapted to run on a 64-bit computer environment. To generate functional and practical displays of LOH, a two-step, internally developed, Java-based software analysis system was employed.  The Pre-LOH Unification Tool (PLUT) served to align all individual patient SNP calls to their respective dbSNP rs ID numbers and genomic physical positions prior to incorporation into the LOH tool version 2, an updated version of the LOH tool able to accommodate Affy SNP 6.0 array data.
Primary data description: dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol:
Purification_protocol: AML blast DNA used for SNP 6.0 profiling was extracted from negatively column enriched AML cell samples as described30 that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter31. CD33 and CD13 were then used in order to further discriminate myeloid blasts versus contaminating erythroid lineage or other non-myeloid cells.  Cells forming a dense population cloud on the CD33 versus CD13 plots that were either single marker positive or double positive were sorted.  Aliquots of final cell preparations were made for the majority of sorted samples and manually analyzed for cell composition using cytospins and blast counts.
Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

tag: tumor-enrollment or tumor-relapse or tumor-persistent vs normal

value: tumor-enrollment

value: purified AML blasts


title: Blood, Subject 8656000, 349.2 hours since injury


title: Blood, Subject 8368103, 8459.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML279T_PERSIST)

value: tumor-persistent


title: Blood, Subject 8656000, 158.1 hours since injury


title: Blood, Subject 8368103, 1672.1 hours since injury


title: Blood, Subject 8533166, 111.4 hours since injury


title: Blood, Subject 8533166, 543.9 hours since injury


title: primary human: buccal (MIAML257N_BU)

source_name: primary human: buccal

value: normal

value: buccal cells


title: primary human: buccal (MIAML279N_BU)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML257T)


title: Blood, Subject 8368103, 514.5 hours since injury

value: White blood cells

value: M


title: Blood, Subject 8368103, 1066.5 hours since injury


title: Blood, Subject 8329814, 2147.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML229T)


title: Blood, Subject 8329814, 510.2 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML192T_PERSIST)


title: Blood, Subject 8329814, 1013.9 hours since injury


title: primary human: buccal (MIAML163N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML163T_PERSISTENT)


title: Blood, Subject 8329814, 347.3 hours since injury


title: Blood, Subject 8329814, 79.5 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML257T_PERSISTENT)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML229T_PERSISTENT)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML132T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML163T)


title: Blood, Subject 8329814, 7.1 hours since injury

source_name: Subject 8329814, 7.1 hours since injury


title: primary human: buccal (MIAML229N_BU)


title: primary human: buccal (MIAML132N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML096T_PERSISTENT)


title: primary human: buccal (MIAML122N)


title: Blood, Subject 8604592, 76.7 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML122T_PERSIST)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML132T_PERSISTENT)


title: Blood, Subject 7946694, 40.1 hours since injury


title: primary human: buccal (MIAML192N)


title: Blood, Subject 7880568, 685.5 hours since injury


title: Blood, Subject 7961946, 14.3 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML192T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML122T)


title: Blood, Subject 7880568, 853.7 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML096T)


title: Blood, Subject 7880568, 180.9 hours since injury


title: Blood, Subject 7880568, 348.3 hours since injury


title: Blood, Subject 7692351, 38.7 hours since injury


title: primary human: buccal (MIAML061N_BU)


title: primary human: buccal (MIAML096N_BU_070610)


title: Blood, Subject 7549204, 20.3 hours since injury


title: Blood, Subject 7358650, 447.1 hours since injury


title: Blood, Subject 7358650, 1166.6 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML054T_PERSIST)


title: Blood, Subject 7358650, 206.5 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML061T_PERSIST)


title: Blood, Subject 7358650, 20.3 hours since injury


title: Blood, Subject 7323512, 564.7 hours since injury


title: Blood, Subject 7323512, 1405 hours since injury


title: Blood, Subject 7323512, 396.5 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML061T)


title: Blood, Subject 6844374, 61 hours since injury

source_name: Subject 6844374, 61 hours since injury


title: Blood, Subject 7323512, 62 hours since injury

source_name: Subject 7323512, 62 hours since injury


title: Blood, Subject 6795272, 900.4 hours since injury


title: Blood, Subject 6828937, 18.3 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML054T_010908)


title: Blood, Subject 6793503, 95.7 hours since injury


title: Blood, Subject 6795272, 36 hours since injury

source_name: Subject 6795272, 36 hours since injury


title: Blood, Subject 6793503, 311.5 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML274T_RELAPSE)

value: tumor-relapse


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML252T_RELAPSE_091411)


title: Blood, Subject 6358333, 39.4 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML274T)


title: primary human: buccal (MIAML252N_BU)


title: primary human: buccal (MIAML233N_BU)


title: Blood, Subject 6173557, 781.1 hours since injury


title: Blood, Subject 6358333, 375.6 hours since injury


title: Blood, Subject 6173557, 7547.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML193T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML159T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML233T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML159T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML252T)


title: Blood, Subject 6020657, 285.8 hours since injury


title: primary human: buccal (MIAML274N_BU_1)


title: primary human: buccal (MIAML054N)


title: Blood, Subject 6020657, 4.8 hours since injury

source_name: Subject 6020657, 4.8 hours since injury


title: primary human: buccal (MIAML193N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML130T_RELAPSE)


title: Blood, Subject 5970905, 1467.3 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML131T_RELAPSE)


title: Blood, Subject 5970905, 726 hours since injury

source_name: Subject 5970905, 726 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML137T)


title: primary human: buccal (MIAML137N)


title: Blood, Subject 6173557, 22.6 hours since injury


title: Blood, Subject 5970905, 411.2 hours since injury


title: primary human: buccal (MIAML131N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML137T_RELAPSE)


title: primary human: buccal (MIAML130N)


title: Blood, Subject 5970905, 243.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML131T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML193T)


title: primary human: buccal (MIAML159N)


title: Blood, Subject 5805341, 517.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML130T)


title: Blood, Subject 5805341, 252.6 hours since injury


title: Blood, Subject 5734455, 68.3 hours since injury


title: Blood, Subject 5805341, 38.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML233T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML129T_RELAPSE)


title: Blood, Subject 5414220, 8.6 hours since injury

source_name: Subject 5414220, 8.6 hours since injury


title: Blood, Subject 5601557, 61.8 hours since injury


title: Blood, Subject 5414220, 124 hours since injury

source_name: Subject 5414220, 124 hours since injury


title: Blood, Subject 5378535, 543.4 hours since injury


title: Blood, Subject 5970905, 51.6 hours since injury


title: Blood, Subject 5378535, 74.6 hours since injury


title: primary human: buccal (MIAML129N)


title: Blood, Subject 4902059, 1042 hours since injury


title: Blood, Subject 5069320, 11049.5 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML129T)


title: Blood, Subject 5069320, 58.2 hours since injury


title: Blood, Subject 4902059, 585.8 hours since injury


title: Blood, Subject 5069320, 245.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML126T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML109T_072208)


title: primary human: buccal (MIAML126N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML103T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML103T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML101T_RELAPSE)


title: primary human: buccal (MIAML103N)


title: Blood, Subject 4902059, 31.8 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML126T_RELAPSE)


title: primary human: buccal (MIAML101N)


title: Blood, Subject 4902059, 12.7 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML098T)


title: Blood, Subject 4870830, 363.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML098T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML101T)


title: primary human: buccal (MIAML095N)


title: primary human: buccal (MIAML109N_032009)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML095T)


title: Blood, Subject 4746192, 477.8 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML109T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML090T)


title: Blood, Subject 4766480, 60.2 hours since injury


title: Blood, Subject 4870830, 28.4 hours since injury


title: Blood, Subject 4746192, 263.8 hours since injury


title: Blood, Subject 4242914, 6632.9 hours since injury


title: Blood, Subject 4746192, 383.5 hours since injury


title: Blood, Subject 4242914, 8841.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML095T_RELAPSE)


title: Blood, Subject 4242914, 4832.7 hours since injury


title: Blood, Subject 4242914, 273.1 hours since injury


title: Blood, Subject 4242914, 58.5 hours since injury


title: Blood, Subject 3797846, 38.7 hours since injury


title: primary human: buccal (MIAML098N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML090T_RELAPSE_091411)


title: Blood, Subject 3764059, 125.6 hours since injury


title: primary human: buccal (MIAML081N)


title: Blood, Subject 3764059, 17.8 hours since injury


title: Blood, Subject 2990794, 6608.5 hours since injury


title: primary human: buccal (MIAML090N)


title: Blood, Subject 2990794, 680.5 hours since injury


title: Blood, Subject 2990794, 2078.8 hours since injury


title: Blood, Subject 2990794, 81.6 hours since injury


title: Blood, Subject 3298318, 120.6 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML078T_RELAPSE)


title: primary human: buccal (MIAML078N)


title: Blood, Subject 2861950, 337.3 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML081T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML081T_RELAPSE)


title: Blood, Subject 2490429, 4364.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML068T)


title: primary human: buccal (MIAML069N_BU)


title: Blood, Subject 2490429, 10051.4 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML078T)


title: Blood, Subject 2490429, 498 hours since injury

source_name: Subject 2490429, 498 hours since injury


title: Blood, Subject 2490429, 883 hours since injury

source_name: Subject 2490429, 883 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML069T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML069T_RELAPSE)


title: primary human: buccal (MIAML057N)


title: Blood, Subject 2490429, 19 hours since injury

source_name: Subject 2490429, 19 hours since injury


title: primary human: buccal (MIAML068N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML057T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML068T_RELAPSE)


title: Blood, Subject 4746192, 143.3 hours since injury


title: Blood, Subject 2415554, 337.2 hours since injury


title: Blood, Subject 2415554, 73.8 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML040T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML057T)


title: Blood, Subject 2058659, 411.3 hours since injury


title: Blood, Subject 2144435, 30 hours since injury

source_name: Subject 2144435, 30 hours since injury


title: primary human: buccal (MIAML040N)


title: primary human: buccal (MIAML044N)


title: Blood, Subject 2058659, 193.9 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML044T_RELAPSE)


title: Blood, Subject 2058659, 27.1 hours since injury


title: Blood, Subject 1593065, 957.6 hours since injury


title: Blood, Subject 1464254, 67.5 hours since injury


title: 2M_AlcoholvsControl

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

hyb_protocol: follow Agilent's two-color expression array hybridization protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Feature Extraction version 9.1was used to filter, normalize, and calculate the signal intensities and Cy5/Cy3 ratios.

source_name: pooled RNA from six alcohol-treated mice

label_protocol: Invitrogen SuperScript indirect cDNA labeling system

growth_protocol: Mice were 6-8 weeks old when the treatment started

extract_protocol: Total RNA extracted using Trizol followed by RNeasy Midi kit

treatment_protocol: Alcohol-treated mice were fed ad libitum a liquid diet containing 4% ethanol. Control animals were fed an isocaloric diet supplemented with maltose dextran

value: liver

tag: time-point

value: 2 month treatment

tag: strain

tag: treatment

value: alcohol-treated

source_name: pooled RNA from six control mice


title: 1M_AlcoholvsControl

value: 1 month treatment


title: Blood, Subject 1593065, 380.2 hours since injury


title: Blood, Subject 1180171, 924.9 hours since injury


title: Blood, Subject 1437553, 39.9 hours since injury

value: F


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML033T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML040T_RELAPSE)


title: 2M_ControlvsAlcohol

value: male


title: 4M_ControlvsAlcohol

value: 4 month treatment


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML033T)


title: primary human: buccal (MIAML036N)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML015T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML036T_RELAPSE)


title: 1M_ControlvsAlcohol


title: 4M_AlcoholvsControl


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML044T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML015T)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML036T)


title: Blood, Subject 1054825, 556.9 hours since injury


title: Blood, Subject 1054825, 103 hours since injury

source_name: Subject 1054825, 103 hours since injury


title: Blood, Subject 2415554, 507.1 hours since injury


title: primary human: buccal (MIAML033N)


title: Blood, Subject 872384, 1598.3 hours since injury


title: Blood, Subject 764107, 133.3 hours since injury


title: Blood, Subject 872384, 20.3 hours since injury

source_name: Subject 872384, 20.3 hours since injury


title: Blood, Subject 872384, 68.9 hours since injury

source_name: Subject 872384, 68.9 hours since injury


title: Blood, Subject 764107, 49.4 hours since injury

source_name: Subject 764107, 49.4 hours since injury


title: Blood, Subject 962714, 238.4 hours since injury


title: Blood, Subject 764107, 301 hours since injury

source_name: Subject 764107, 301 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML006T_RELAPSE)


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML006T)


title: Blood, Subject 962714, 22.6 hours since injury

source_name: Subject 962714, 22.6 hours since injury


title: Blood, Subject 648231, 8.4 hours since injury

source_name: Subject 648231, 8.4 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML002T_RELAPSE)


title: Blood, Subject 564731, 237.3 hours since injury


title: primary human: buccal (MIAML002N_BU)

source_name: primary human: buccal


title: primary human: buccal (MIAML006N)


title: Blood, Subject 628704, 541.4 hours since injury


title: CC26 HP1 RNAi

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: cells treated with HP1 dsRNA for 3 days, transfected with 20 μg Dam-only expression plasmid/2*10e6 cells, harvested the next day

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area.

data_processing: Scans were processed with NimbleScan 2.3 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios, normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate') and then median centered. All four scan intensities were processed in that way, and the highest intensity not suffering from overt saturation in either replicate was retained and used for further analyses.

label: cy3, cy5

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CC26-Dam, HP1 knockdown

label_protocol: 1 µg purified methyl-PCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWMycDam-ACT5C was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: For DamID samples, sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003).

treatment_protocol: cells treated with HP1 dsRNA for 3 days, transfected with 20 μg CC26-Dam expression plasmid/2*10e6 cells, harvested the next day

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CC4 HP1 RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CC4-Dam, HP1 knockdown

treatment_protocol: cells treated with HP1 dsRNA for 3 days, transfected with 20 μg CC4-Dam expression plasmid/2*10e6 cells, harvested the next day


title: CC26 control RNAi

description: cells treated with white dsRNA for 3 days, transfected with 20 μg Dam-only expression plasmid/2*10e6 cells, harvested the next day

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CC26-Dam, white knockdown

treatment_protocol: cells treated with white dsRNA for 3 days, transfected with 20 μg CC26-Dam expression plasmid/2*10e6 cells, harvested the next day


title: CC4 control RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CC4-Dam, white knockdown

treatment_protocol: cells treated with white dsRNA for 3 days, transfected with 20 μg CC4-Dam expression plasmid/2*10e6 cells, harvested the next day


title: SSL1 replicate 1

description: SSL1 DamID untreated Kc167 cells

data_processing:
Scans were processed with NimbleScan 2.3 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios, normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate') and then median centered. All four scan intensities were processed in that way, and the highest intensity not suffering from overt saturation in either replicate was retained and used for further analyses.
norm_aggregated_tiling_arrays.txt: Aggregation of the tiling array data to fragments between to DpnI cut sites ('GATC fragments').  This dataset includes the 52 newly obtained DamID datasets and 52 previously published DamID datasets (from GSE22069).  Each column represents one protein, corresponding to the sample name in the metadata excel sheet. Values are average normalized log2(channel1/channel2).
disc_aggregated_tiling_arrays.txt: Each dataset included in the file 'norm_aggregated_tiling_arrays.txt' has been individually binarized by applying a 3-state Hidden Markov Model. Calls are bound (1) and unbound (0) for each GATC fragment. Details are described in the accompanying manuscript.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SSL1-Dam

treatment_protocol: Cells transfected with 20 μg SSL1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 526747, 27.1 hours since injury

source_name: Subject 526747, 27.1 hours since injury


title: primary human: blood or bone marrow, FACS sort-purified AML blasts (MIAML002T)


title: SSL1 replicate 2

description: SSL1 DamID untreated Kc167 cells


title: Blood, Subject 628704, 37.5 hours since injury

source_name: Subject 628704, 37.5 hours since injury


title: Blood, Subject 521404, 375.5 hours since injury


title: Blood, Subject 521404, 1017.7 hours since injury


title: MES4 replicate 1

description: MES4 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MES4-Dam

treatment_protocol: Cells transfected with 20 μg MES4-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 521404, 9.7 hours since injury

source_name: Subject 521404, 9.7 hours since injury


title: MES4 replicate 2

description: MES4 DamID untreated Kc167 cells


title: CG2540 replicate 2

description: CG2540 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG2540-Dam

treatment_protocol: Cells transfected with 20 μg CG2540-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG15436 replicate 1

description: CG15436 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG15436-Dam

treatment_protocol: Cells transfected with 20 μg CG15436-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 465597, 365.9 hours since injury


title: CG5274 replicate 2

description: CG5274 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG5274-Dam

treatment_protocol: Cells transfected with 20 μg CG5274-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG5274 replicate 1

description: CG5274 DamID untreated Kc167 cells


title: MAF-S replicate 1

description: MAF-S DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MAF-S-Dam

treatment_protocol: Cells transfected with 20 μg MAF-S-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG15436 replicate 2

description: CG15436 DamID untreated Kc167 cells


title: Blood, Subject 465597, 30.6 hours since injury

source_name: Subject 465597, 30.6 hours since injury


title: CG33213 replicate 2

description: CG33213 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG33213-Dam

treatment_protocol: Cells transfected with 20 μg CG33213-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: MAF-S replicate 2

description: MAF-S DamID untreated Kc167 cells


title: JIGR1 replicate 1

description: JIGR1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing JIGR1-Dam

treatment_protocol: Cells transfected with 20 μg JIGR1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 412828, 49.8 hours since injury

source_name: Subject 412828, 49.8 hours since injury

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.


title: UBC-E2H replicate 1

description: UBC-E2H DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing UBC-E2H-Dam

treatment_protocol: Cells transfected with 20 μg UBC-E2H-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: JIGR1 replicate 2

description: JIGR1 DamID untreated Kc167 cells


title: CG2540 replicate 1

description: CG2540 DamID untreated Kc167 cells


title: UBC-E2H replicate 2

description: UBC-E2H DamID untreated Kc167 cells


title: Blood, Subject 465597, 197.6 hours since injury


title: ERR replicate 1

description: ERR DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing ERR-Dam

treatment_protocol: Cells transfected with 20 μg ERR-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: ERR replicate 2

description: ERR DamID untreated Kc167 cells


title: SBP2 replicate 2

description: SBP2 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SBP2-Dam

treatment_protocol: Cells transfected with 20 μg SBP2-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG33213 replicate 1

description: CG33213 DamID untreated Kc167 cells


title: Blood, Subject 255010, 117.3 hours since injury


title: Blood, Subject 412828, 141.9 hours since injury


title: Blood, Subject 400477, 49.1 hours since injury

source_name: Subject 400477, 49.1 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_50

description: Competitively hybridized to NimbleGen 42M CGH array.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned per the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Data were normalized by custom programs, and variants were called by the program GADA. The GFF file (linked to the Series record) includes the genomic coordinates and direction of calls (i.e., gain or loss).

source_name: HuRef lymphoblastoid cell line

label_protocol: As per the manufacturer's (NimbleGen) instructions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer.

value: HuRef

value: lymphoblastoid

source_name: NA15510 lymphoblastoid cell line

value: female

tag: sample type

value: reference


title: HuRef lymphoblastoid cell line, NimbleGen42M_51


title: CG8289 replicate 2

description: CG8289 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG8289-Dam

treatment_protocol: Cells transfected with 20 μg CG8289-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HuRef lymphoblastoid cell line_Affymetrix

description: Hybridized to Affy SNP 6.0.

hyb_protocol: Labeled DNA was hybridized to the array according to manufacturer's instructions. The array was washed using Affymetrix fluidics stations.

scan_protocol: The array was scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and CHP files (generated by Affymetrix Genotyping Console using the Birdseed algorithm) were used to call copy number variation by Partek GS, Genotyping Console v.3.0.2, BirdSuite v.1.5.2 and iPattern. The GFF file includes the genomic coordinates and direction of calls (i.e., gain or loss).
Genome build: NCBI Build 36.

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer.

treatment_protocol: None.


title: CG8924 replicate 2

description: CG8924 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG8924-Dam

treatment_protocol: Cells transfected with 20 μg CG8924-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG8924 replicate 1

description: CG8924 DamID untreated Kc167 cells


title: SBP2 replicate 1

description: SBP2 DamID untreated Kc167 cells


title: Blood, Subject 255010, 26.4 hours since injury

source_name: Subject 255010, 26.4 hours since injury


title: CG8289 replicate 1

description: CG8289 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_49


title: HuRef lymphoblastoid cell line, NimbleGen42M_48


title: CG7357 replicate 2

description: CG7357 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7357-Dam

treatment_protocol: Cells transfected with 20 μg CG7357-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 172837, 18.9 hours since injury

source_name: Subject 172837, 18.9 hours since injury


title: Blood, Subject 158464, 60.2 hours since injury

source_name: Subject 158464, 60.2 hours since injury


title: CG7357 replicate 1

description: CG7357 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_33


title: CG12744 replicate 2

description: CG12744 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG12744-Dam

treatment_protocol: Cells transfected with 20 μg CG12744-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG17153 replicate 1

description: CG17153 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG17153-Dam

treatment_protocol: Cells transfected with 20 μg CG17153-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, Subject 138472, 61.8 hours since injury

source_name: Subject 138472, 61.8 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_32


title: Blood, Subject 138472, 327.7 hours since injury


title: CG12744 replicate 1

description: CG12744 DamID untreated Kc167 cells


title: CG17153 replicate 2

description: CG17153 DamID untreated Kc167 cells


title: Blood, Subject 58049, 323.3 hours since injury

source_name: Subject 58049, 323.3 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_31


title: CG11802 replicate 2

description: CG11802 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG11802-Dam

treatment_protocol: Cells transfected with 20 μg CG11802-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HuRef lymphoblastoid cell line, NimbleGen42M_18


title: Lymphoblastoid NA18980 Cy5_Agilent244K

description:
NA18980-CY5
Competitively hybridized to custom Agilent 244k CGH array.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. The GFF file (linked to the Series record) includes the genomic coordinates and direction of calls (i.e., gain or loss).

source_name: NA18980 lymphoblastoid cell line

label_protocol: As per the manufacturer's (Agilent) instructions.

source_name: NA10851 lymphoblastoid cell line


title: CG10267 replicate 2

description: CG10267 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG10267-Dam

treatment_protocol: Cells transfected with 20 μg CG10267-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: Blood, Subject 58049, 17.8 hours since injury

source_name: Subject 58049, 17.8 hours since injury


title: Lymphoblastoid NA12144 Cy5_Agilent244K

description:
NA12144-CY5
Competitively hybridized to custom Agilent 244k CGH array.

source_name: NA12144 lymphoblastoid cell line


title: Blood, Subject 35524, 28.8 hours since injury

source_name: Subject 35524, 28.8 hours since injury


title: CG5245 replicate 1

description: CG5245 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG5245-Dam

treatment_protocol: Cells transfected with 20 μg CG5245-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Lymphoblastoid NA18980 Cy3_Agilent244K

description:
NA18980-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: HuRef lymphoblastoid cell line, NimbleGen42M_16

source_name: HuRef lymphoblastoid cell line

source_name: NA15510 lymphoblastoid cell line


title: HuRef lymphoblastoid cell line, NimbleGen42M_17


title: CG5245 replicate 2

description: CG5245 DamID untreated Kc167 cells


title: CG10267 replicate 1

description: CG10267 DamID untreated Kc167 cells


title: Blood, control 1829766

source_name: Control

value: White Blood Cells


title: CG10949 replicate 1

description: CG10949 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG10949-Dam

treatment_protocol: Cells transfected with 20 μg CG10949-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG4936 replicate 1

description: CG4936 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG4936-Dam

treatment_protocol: Cells transfected with 20 μg CG4936-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG3838 replicate 2

description: CG3838 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG3838-Dam

treatment_protocol: Cells transfected with 20 μg CG3838-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG10949 replicate 2

description: CG10949 DamID untreated Kc167 cells


title: Lymphoblastoid NA12144 Cy3_Agilent244K

description:
NA12144-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: CG4936 replicate 2

description: CG4936 DamID untreated Kc167 cells


title: CG11802 replicate 1

description: CG11802 DamID untreated Kc167 cells


title: Blood, control 17587105

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.


title: Blood, control 8915966


title: Lymphoblastoid NA18576 Cy5_Agilent244K

description:
NA18576-CY5
Competitively hybridized to custom Agilent 244k CGH array.

source_name: NA18576 lymphoblastoid cell line


title: Lymphoblastoid NA19099 Cy5_Agilent244K

description:
NA19099-CY5
Competitively hybridized to custom Agilent 244k CGH array.

source_name: NA19099 lymphoblastoid cell line


title: CG3838 replicate 1

description: CG3838 DamID untreated Kc167 cells


title: Lymphoblastoid NA18576 Cy3_Agilent244K

description:
NA18576-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: HuRef lymphoblastoid cell line, NimbleGen42M_01


title: CG7946 replicate 2

description: CG7946 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7946-Dam

treatment_protocol: Cells transfected with 20 μg CG7946-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, control 4609399


title: Lymphoblastoid NA19099 Cy3_Agilent244K

description:
NA19099-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: Blood, control 17268143


title: Blood, control 10689045


title: DMAP1 replicate 2

description: DMAP1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing DMAP1-Dam

treatment_protocol: Cells transfected with 20 μg DMAP1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, control 26878554


title: CG7946 replicate 1

description: CG7946 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing -Dam

treatment_protocol: Cells transfected with 20 μg -Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: DMAP1 replicate 1

description: DMAP1 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_15


title: Blood, control 11014402


title: Lymphoblastoid JCVI Cy5_Agilent244K

description:
JCVI-CY5
Competitively hybridized to custom Agilent 244k CGH array.

source_name: NA10851 lymphoblastoid cell line


title: Lymphoblastoid NA15510 Cy5_Agilent244K

description:
NA15510-CY5
Competitively hybridized to custom Agilent 244k CGH array.


title: HuRef lymphoblastoid cell line, NimbleGen42M_34


title: Lymphoblastoid JCVI Cy3_Agilent244K

description:
JCVI-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: HuRef lymphoblastoid cell line, NimbleGen42M_53


title: CG9797 replicate 2

description: CG9797 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG9797-Dam

treatment_protocol: Cells transfected with 20 μg CG9797-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: Blood, control 16912123-2


title: CG9797 replicate 1

description: CG9797 DamID untreated Kc167 cells


title: Blood, control 8491576


title: Lymphoblastoid NA18500 Cy5_Agilent244K

description:
NA18500-CY5
Competitively hybridized to custom Agilent 244k CGH array.

source_name: NA18500 lymphoblastoid cell line


title: HuRef lymphoblastoid cell line, NimbleGen42M_55


title: CG14962 replicate 1

description: CG14962 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG14962-Dam

treatment_protocol: Cells transfected with 20 μg CG14962-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Lymphoblastoid NA15510 Cy3_Agilent244K

description:
NA15510-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: control [SAMPLES 1-4]

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

description:
SAMPLE 1: epilepsy biopsies
SAMPLE 2: epilepsy biopsies
SAMPLE 3: epilepsy biopsies replicates
SAMPLE 4: epilepsy biopsies replicates
Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
The Arrays contained specific primers for 352 known human microRNA, 4 housekeeping genes (HKGs; hsa-SNORD48, hsa-SNORD47, hsa-SNORD44, and hsa-U6), 2 RNA-quality, and 2 polymerase chain reaction (PCR)–positive controls.
The ΔΔ Ct method was used to calculate the relative expression of microRNA in the control and astrocytic tumors. MicroRNAs with fold changes of 2 and with significant p value (p≤ 0.05) between the two groups were considered to be differentially expressed.

label: SYBR Green

source_name: Glia cells

label_protocol: For Real-Time PCR, the appropriated RT2 SYBR Green qPCR Master Mixes (SABiosciences) was added to the mix containing the first strand diluted and RNAse-free water.

extract_protocol: Total RNA isolation (30mg) was performed using the TRIzol® protocol (Invitrogen, USA) according to the manufacturer′s instructions

tag: disease state

value: control (patients with epilepsy)

value: Glia cells


title: CG14962 replicate 2

description: CG14962 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_46

source_name: HuRef lymphoblastoid cell line


title: HuRef lymphoblastoid cell line, NimbleGen42M_44

source_name: NA15510 lymphoblastoid cell line


title: Lymphoblastoid NA18500 Cy3_Agilent244K

description:
NA18500-CY3
Competitively hybridized to custom Agilent 244k CGH array.


title: astrocytic tumors [SAMPLES 5-12]

description:
SAMPLE 5: Pilocytic Astrocytoma
SAMPLE 6: GBM.  High grade tumor sample
SAMPLE 7: GBM.  High grade tumor sample
SAMPLE 8: Pilocytic Astrocytoma.  Low grade tumor sample
SAMPLE 9: GBM.  High grade tumor sample
SAMPLE 10: Diffuse Astrocytoma.  Low grade tumor sample
SAMPLE 11: GBM.  High grade tumor sample
SAMPLE 12: Pilocytic Astrocytoma.  Low grade tumor sample
Test

value: astrocytoma


title: Blood, control 7547283

source_name: Control

tag: tissue

value: M


title: CG7818 replicate 2

description: CG7818 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7818-Dam

treatment_protocol: Cells transfected with 20 μg CG7818-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, control 27020842

tag: Sex


title: CG7818 replicate 1

description: CG7818 DamID untreated Kc167 cells

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: 14 day DEX treated MuRF1 knockout rep3

first: J.

middle: David

last: Furlow

state: CA

address: One Shields Avenue

institute: UC Davis

description: replicate 3

data_processing: The data were normalised using quantile normalization with Illumina BeadStudio v3.2.3 software and background was subtracted

source_name: 14 day DEX treated MuRF1 knockout rep3

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

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

treatment_protocol: Animals were provided with  3 mg/kg water soluble dexamethasone in their drinking water for 3 or 14 days; control animals were housed in parallel without dexamethasone provided.

tag: age

value: 4 months

value: triceps surae muscle


title: HuRef lymphoblastoid cell line, NimbleGen42M_39

description: Competitively hybridized to NimbleGen 42M CGH array.


title: Blood, control 1136230


title: 14 day DEX treated MuRF1 knockout rep1

description: replicate 1

source_name: 14 day DEX treated MuRF1 knockout rep1


title: 14 day DEX treated MuRF1 knockout rep2

description: replicate 2

source_name: 14 day DEX treated MuRF1 knockout rep2


title: HuRef lymphoblastoid cell line, NimbleGen42M_30


title: HuRef lymphoblastoid cell line, NimbleGen42M_37


title: Blood, control 18506903


title: CG16817 replicate 2

description: CG16817 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG16817-Dam

treatment_protocol: Cells transfected with 20 μg CG16817-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: 14 day untreated MuRF1 knockout rep3

description: replicate 3

source_name: 14 day untreated MuRF1 knockout rep3


title: 14 day untreated MuRF1 knockout rep1

description: replicate 1

source_name: 14 day untreated MuRF1 knockout rep1


title: CG7006 replicate 2

description: CG7006 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7006-Dam

treatment_protocol: Cells transfected with 20 μg CG7006-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HuRef lymphoblastoid cell line, NimbleGen42M_35


title: HuRef lymphoblastoid cell line, NimbleGen42M_28


title: Blood, control 8478360


title: Blood, control 17043147


title: 14 day DEX treated wild type rep3

description: replicate 3

source_name: 14 day DEX treated wild type rep3


title: Blood, control 18000027


title: Blood, control 21473827


title: 14 day untreated MuRF1 knockout rep2

description: replicate 2

source_name: 14 day untreated MuRF1 knockout rep2


title: CG7006 replicate 1

description: CG7006 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: CG16817 replicate 1

description: CG16817 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_21


title: CG3909 replicate 2

description: CG3909 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG3909-Dam

treatment_protocol: Cells transfected with 20 μg CG3909-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: 14 day DEX treated wild type rep2

description: replicate 2

source_name: 14 day DEX treated wild type rep2


title: CG5181 replicate 2

description: CG5181 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG5181-Dam

treatment_protocol: Cells transfected with 20 μg CG5181-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: 14 day untreated wild type rep2

description: replicate 2

source_name: 14 day untreated wild type rep2


title: Blood, control 19297865-2


title: CG3909 replicate 1

description: CG3909 DamID untreated Kc167 cells


title: 14 day untreated wild type rep3

description: replicate 3

source_name: 14 day untreated wild type rep3


title: Blood, control 16912123-1

source_name: Control


title: CG5181 replicate 1

description: CG5181 DamID untreated Kc167 cells


title: ISWI replicate 2

description: ISWI DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing ISWI-Dam

treatment_protocol: Cells transfected with 20 μg ISWI-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HuRef lymphoblastoid cell line, NimbleGen42M_14

source_name: HuRef lymphoblastoid cell line

source_name: NA15510 lymphoblastoid cell line


title: HuRef lymphoblastoid cell line, NimbleGen42M_12


title: Blood, control 11908009


title: Blood, control 19802493


title: Blood, control 7474474


title: HuRef lymphoblastoid cell line, NimbleGen42M_05


title: CG11723 replicate 2

description: CG11723 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG11723-Dam

treatment_protocol: Cells transfected with 20 μg CG11723-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HuRef lymphoblastoid cell line, NimbleGen42M_19


title: 3 day DEX treated MuRF1 knockout rep2

description: replicate 2

source_name: 3 day DEX treated MuRF1 knockout rep2


title: ko_rep3

description: Dnmt1-/- mouse embryonic fibroblasts; replicate 3

source_name: Dnmt1-/- mouse embryonic fibroblasts

treatment_protocol: Not applicable

value: unknown [Lande-Diner et al 2007 (PMID:17311920)]

value: Mouse embryonic fibroblasts


title: Blood, control 17930391


title: 14 day untreated wild type rep1

description: replicate 1

source_name: 14 day untreated wild type rep1


title: HuRef lymphoblastoid cell line, NimbleGen42M_03


title: 3 day DEX treated MuRF1 knockout rep3

description: replicate 3

source_name: 3 day DEX treated MuRF1 knockout rep3


title: ISWI replicate 1

description: ISWI DamID untreated Kc167 cells


title: CG11723 replicate 1

description: CG11723 DamID untreated Kc167 cells


title: ko_rep2

description: Dnmt1-/- mouse embryonic fibroblasts; replicate 2


title: Blood, control 29091703


title: 14 day DEX treated wild type rep1

description: replicate 1

source_name: 14 day DEX treated wild type rep1


title: 3 day DEX treated MuRF1 knockout rep1

description: replicate 1

source_name: 3 day DEX treated MuRF1 knockout rep1


title: Blood, control 3511111


title: Blood, control 22062194


title: CG15514 replicate 2

description: CG15514 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG15514-Dam

treatment_protocol: Cells transfected with 20 μg CG15514-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: 3 day untreated MuRF1 knockout rep3

description: replicate 3

source_name: 3 day untreated MuRF1 knockout rep3


title: Blood, control 22680057

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.


title: 3 day untreated MuRF1 knockout rep2

description: replicate 2

source_name: 3 day untreated MuRF1 knockout rep2


title: 3 day untreated MuRF1 knockout rep1

description: replicate 1

source_name: 3 day untreated MuRF1 knockout rep1


title: CG17385 replicate 1

description: CG17385 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG17385-Dam

treatment_protocol: Cells transfected with 20 μg CG17385-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: ko_rep1

description: Dnmt1-/- mouse embryonic fibroblasts; replicate 1


title: wt_rep3

description: Dnmt1+/+ mouse embryonic fibroblasts; replicate 3

source_name: Dnmt1+/+ mouse embryonic fibroblasts


title: Blood, control 32378500

source_name: Control


title: CG15514 replicate 1

description: CG15514 DamID untreated Kc167 cells


title: 3 day DEX treated wild type rep3

description: replicate 3

source_name: 3 day DEX treated wild type rep3


title: 3 day DEX treated wild type rep2

description: replicate 2

source_name: 3 day DEX treated wild type rep2


title: CG17385 replicate 2

description: CG17385 DamID untreated Kc167 cells


title: Blood, control 10378715


title: 6 DAH endosperm 2

city: Itakura

first: Naoki

last: Hirotsu

state: Gunma

address: 1-1-1 Izumino

department: Life Sciences

country: Japan

institute: Toyo University

description: US22502590_251524111185_S01_GE2-v5_95_Feb07_1_4

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

organism: Oryza sativa

source_name: 6 DAH endosperm NIL(TGW6)

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: Rice plants were grown in a paddy field in Tsukuba, Japan during a normal rice growing season in 2008. Developing endosperm were collected.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: sample

value: endosperm

tag: developmental stage

value: 6 days after flowering

source_name: 6 DAH endosperm Nipponbare

value: Nipponbare


title: Blood, control 13057592


title: Blood, control 32292315


title: 6 DAH endosperm 1

description: US22502590_251524111185_S01_GE2-v5_95_Feb07_1_3

tag: cultivar


title: HuRef lymphoblastoid cell line, NimbleGen42M_10

source_name: HuRef lymphoblastoid cell line

tag: cell line

value: male

source_name: NA15510 lymphoblastoid cell line


title: 3 day DEX treated wild type rep1

description: replicate 1

source_name: 3 day DEX treated wild type rep1


title: wt_rep2

description: Dnmt1+/+ mouse embryonic fibroblasts; replicate 2


title: RPS9 replicate 2

description: RPS9 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RPS9-Dam

treatment_protocol: Cells transfected with 20 μg RPS9-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

tag: cell type


title: CG7745 replicate 2

description: CG7745 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7745-Dam

treatment_protocol: Cells transfected with 20 μg CG7745-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG7745 replicate 1

description: CG7745 DamID untreated Kc167 cells


title: 3 DAH endosperm 2

description: US22502590_251524111185_S01_GE2-v5_95_Feb07_1_2

source_name: 3 DAH endosperm NIL(TGW6)

value: 3 days after flowering

source_name: 3 DAH endosperm Nipponbare


title: wt_rep1

description: Dnmt1+/+ mouse embryonic fibroblasts; replicate 1


title: Blood, control 19107727

value: F


title: 3 day untreated wild type rep2

description: replicate 2

source_name: 3 day untreated wild type rep2


title: RPS9 replicate 1

description: RPS9 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: 3 day untreated wild type rep3

description: replicate 3

source_name: 3 day untreated wild type rep3


title: CG4617 replicate 2

description: CG4617 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG4617-Dam

treatment_protocol: Cells transfected with 20 μg CG4617-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Blood, control 16952213


title: 3 day untreated wild type rep1

description: replicate 1

source_name: 3 day untreated wild type rep1


title: IT4 Total

city: Nantes

first: Cyrille

last: Féray

address: 1 rue Gaston Veil

country: France

institute: Faculté de médecine de Nantes

description:
US82400123_251485032977_S01_GE2-v5_95_Feb07_1_3.txt
total cytosolic RNA from infected-treated cells - replicate 4

hyb_protocol: 500 nanograms each of Cy3- and Cy5-labeled cRNA were mixed and hybridized on an Agilent 4x44 k microarray slide.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: In order to compare multiple conditions (infected, non-infected, and infected-treated cells, and each sample cytosolic, non-polysomal and polysomal RNA), the samples have been allocated in pairs of Cy3 and Cy5 labelled RNA, taking care of equally reparting each condition in Cy3 and Cy5 labelling, and of mixing different conditions in each pair of samples. The Cy3 and Cy5 rawdata have been then independently normalized with lowess algorithm to the median profile of all the samples.

source_name: Huh7 cells infected with HCV JFH1 and treated with antiprotease - replicate 4

label_protocol: cDNA synthesis and cRNA amplification were performed with the Agilent kit (Low RNA Input Linear Amplification Kit, two-colors).

extract_protocol: RNA from the polysomal or non-polysomal fractions pools and from an aliquot of non-fractionated supernatant (total cytosolic RNA) were then extracted with Trizol, and precipitated with isopropanol (Sigma). The quality of total and fractioned RNA was checked on an Agilent 2100 Bioanalyser.

tag: infection

tag: fraction

value: cytosolic RNA


title: IT4 Polysomal

description:
US82400123_251485032977_S01_GE2-v5_95_Feb07_1_1.txt
polysomal RNA from infected-treated cells - replicate 4

value: infected with HCV JFH1 and treated with antiprotease

value: polysomal RNA


title: Mef2a knockout tibialis anterior muscle at regeneration day 7

first: Frank

last: Naya

address: 24 Cummington Mall

institute: Boston University

description: Gene expression data from Mef2a KO mouse skeletal muscle at Regeneration Day 7

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Gene expression levels were generated using the Robust Multiarray Average (RMA) in Affymetrix Gene Expression Console.  Positive and negative control probesets were removed prior to differential expression analysis.

source_name: Total RNA from Mef2a knockout mouse tibialis anterior muscle, harvested seven days post-injury with 10uM cardiotoxin

label_protocol: standard Affymetrix protocol

growth_protocol: Mef2a KO and WT mice were aged normally to adulthood, and were used for this analysis between 2 and 4 months of age

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was extracted from injured WT (N=5) and KO (N=5) tibialis anterior muscles. Total RNA samples, at equimolar concentrations, were pooled from 5 animals to constitute final, pooled WT and KO RNA samples used for microarray analysis.

treatment_protocol: Adult KO and WT mice were treated by injection of 50ul, 10uM cardiotoxin into the right tibialis anterior muscle of the mouse hindlimb. Seven days post-injection, mice were sacrificed and injured tibialis anterior muscle was harvested for total RNA extraction.

value: tibialis anterior muscle

tag: genotype

value: Mef2a -/- (Mef2a KO)

value: 2-4 months


title: IT4 Non- Polysomal

description:
US82400123_251485032977_S01_GE2-v5_95_Feb07_1_4.txt
non-polysomal RNA from infected-treated cells - replicate 4

value: non-polysomal RNA


title: Wild type tibialis anterior muscle at regeneration day 7

description: Gene expression data from wild type mouse skeletal muscle at Regeneration Day 7

source_name: Total RNA from wild type mouse tibialis anterior muscle, harvested seven days post-injury with 10uM cardiotoxin

value: Mef2a +/+ (wild type)


title: Blood, control 20591195

source_name: Control

value: White Blood Cells

value: M


title: Blood, control 19297865-1


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 8

description: Competitively hybridized to Agilent 24M CGH array set.

scan_protocol: Scanned on an Agilent 3um-resolution scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.51.1) was used for background subtraction and Lowess normalization. The GFF file (linked to the Series record) includes the genomic coordinates and direction of calls (i.e., gain or loss).

value: HuRef

value: lymphoblastoid

tag: gender

value: female

value: reference


title: Blood, control 35028656

data_processing: Affymetrix Power Tools version 1.8.6 RMA model


title: 14 day denervated MuRF1 knockout rep3

description: replicate 3

source_name: 14 day denervated MuRF1 knockout rep3

treatment_protocol: Animals were subjected to unilateral sciatic nerve resection and RNA isolated from the denervated muscles after 3 or 14 days; control animals were housed in parallel without denervation.

value: 6 months

value: triceps surae muscle


title: 14 day denervated MuRF1 knockout rep2

description: replicate 2

source_name: 14 day denervated MuRF1 knockout rep2


title: 14 day denervated MuRF1 knockout rep1

description: replicate 1

source_name: 14 day denervated MuRF1 knockout rep1


title: CG7928 replicate 2

description: CG7928 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG7928-Dam

treatment_protocol: Cells transfected with 20 μg CG7928-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: IT3 Non- Polysomal

description:
US82400123_251485032977_S01_GE2-v5_95_Feb07_1_2.txt
non-polysomal RNA from infected-treated cells - replicate 3

source_name: Huh7 cells infected with HCV JFH1 and treated with antiprotease - replicate 3


title: CG7928 replicate 1

description: CG7928 DamID untreated Kc167 cells


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 23

source_name: HuRef lymphoblastoid cell line

value: male

source_name: NA15510 lymphoblastoid cell line


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 10


title: 14 day control MuRF1 knockout rep3

description: replicate 3

source_name: 14 day control MuRF1 knockout rep3


title: IT1 Total

description:
US82400123_251485032976_S01_GE2-v5_95_Feb07_1_2.txt
total cytosolic RNA from infected-treated cells - replicate 1

source_name: Huh7 cells infected with HCV JFH1 and treated with antiprotease - replicate 1

value: cytosolic RNA


title: 14 day control MuRF1 knockout rep2

description: replicate 2

source_name: 14 day control MuRF1 knockout rep2


title: IT3 Polysomal

description:
US82400123_251485032976_S01_GE2-v5_95_Feb07_1_3.txt
polysomal RNA from infected-treated cells - replicate 3

value: infected with HCV JFH1 and treated with antiprotease


title: IT1 Polysomal

description:
US82400123_251485032976_S01_GE2-v5_95_Feb07_1_1.txt
polysomal RNA from infected-treated cells - replicate 1

value: polysomal RNA


title: CG3313 replicate 1

description: CG3313 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG3313-Dam

treatment_protocol: Cells transfected with 20 μg CG3313-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: CG4617 replicate 1

description: CG4617 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG4617-Dam


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 15


title: CG2129 replicate 2

description: CG2129 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG2129-Dam

treatment_protocol: Cells transfected with 20 μg CG2129-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG2129 replicate 1

description: CG2129 DamID untreated Kc167 cells


title: CG3313 replicate 2

description: CG3313 DamID untreated Kc167 cells


title: 14 day denervated wild type rep3

description: replicate 3

source_name: 14 day denervated wild type rep3


title: 14 day control MuRF1 knockout rep1

description: replicate 1

source_name: 14 day control MuRF1 knockout rep1


title: IT1 Non- Polysomal

description:
US82400123_251485032976_S01_GE2-v5_95_Feb07_1_4.txt
non-polysomal RNA from infected-treated cells - replicate 1


title: CG5846 replicate 1

description: CG5846 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG5846-Dam

treatment_protocol: Cells transfected with 20 μg CG5846-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: 3 DAH endosperm 1

description: US22502590_251524111185_S01_GE2-v5_95_Feb07_1_1

source_name: 3 DAH endosperm Nipponbare

value: Nipponbare

value: endosperm

value: 3 days after flowering

source_name: 3 DAH endosperm NIL(TGW6)


title: CG5846 replicate 2

description: CG5846 DamID untreated Kc167 cells


title: NI14 Total

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_4.txt
total cytosolic RNA from non-infected cells - replicate 4

source_name: Huh7 cells (non-infected) - replicate 4

value: Non-infected


title: 14 day denervated wild type rep2

description: replicate 2

source_name: 14 day denervated wild type rep2


title: NI14 Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_2.txt
polysomal RNA from non-infected cells - replicate 4


title: 14 day control wild type rep3

description: replicate 3

source_name: 14 day control wild type rep3


title: 14 day denervated wild type rep1

description: replicate 1

source_name: 14 day denervated wild type rep1


title: NI14 Non- Polysomal

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_3.txt
non-polysomal RNA from non-infected cells - replicate 4

value: non-polysomal RNA


title: RAD21 replicate 2

description: RAD21 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RAD21-Dam

treatment_protocol: Cells transfected with 20 μg RAD21-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: NI13 Total

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_2.txt
total cytosolic RNA from non-infected cells - replicate 3

source_name: Huh7 cells (non-infected) - replicate 3


title: NI13 Polysomal

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_1.txt
polysomal RNA from non-infected cells - replicate 3


title: RAD21 replicate 1

description: RAD21 DamID untreated Kc167 cells


title: 14 day control wild type rep1

description: replicate 1

source_name: 14 day control wild type rep1


title: ADA2B replicate 2

description: ADA2B DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing ADA2B-Dam

treatment_protocol: Cells transfected with 20 μg ADA2B-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 21

source_name: HuRef lymphoblastoid cell line

source_name: NA15510 lymphoblastoid cell line


title: ADA2B replicate 1

description: ADA2B DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: NI13 Non- Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_1.txt
non-polysomal RNA from non-infected cells - replicate 3


title: 3 day denervated MuRF1 knockout rep3

description: replicate 3

source_name: 3 day denervated MuRF1 knockout rep3


title: 14 day control wild type rep2

description: replicate 2

source_name: 14 day control wild type rep2


title: 3 day denervated MuRF1 knockout rep1

description: replicate 1

source_name: 3 day denervated MuRF1 knockout rep1


title: NI12 Total

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_3.txt
total cytosolic RNA from non-infected cells - replicate 2

source_name: Huh7 cells (non-infected) - replicate 2


title: 3 day control MuRF1 knockout rep3

description: replicate 3

source_name: 3 day control MuRF1 knockout rep3


title: NI12 Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_1.txt
polysomal RNA from non-infected cells - replicate 2


title: 3 day denervated MuRF1 knockout rep2

description: replicate 2

source_name: 3 day denervated MuRF1 knockout rep2


title: L(1)G0004 replicate 1

description: L(1)G0004 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing L(1)G0004-Dam

treatment_protocol: Cells transfected with 20 μg L(1)G0004-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: NI12 Non- Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_4.txt
non-polysomal RNA from non-infected cells - replicate 2


title: 3 day control MuRF1 knockout rep2

description: replicate 2

source_name: 3 day control MuRF1 knockout rep2


title: CG4886 replicate 2

description: CG4886 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG4886-Dam

treatment_protocol: Cells transfected with 20 μg CG4886-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: RYBP replicate 2

description: RYBP DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RYBP-Dam

treatment_protocol: Cells transfected with 20 μg RYBP-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: L(1)G0004 replicate 2

description: L(1)G0004 DamID untreated Kc167 cells


title: 3 day control MuRF1 knockout rep1

description: replicate 1

source_name: 3 day control MuRF1 knockout rep1


title: RYBP replicate 1

description: RYBP DamID untreated Kc167 cells


title: 3 day denervated wild type rep3

description: replicate 3

source_name: 3 day denervated wild type rep3


title: NI11 Polysomal

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_2.txt
polysomal RNA from non-infected cells - replicate 1

source_name: Huh7 cells (non-infected) - replicate 1


title: NI11 Total

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_3.txt
total cytosolic RNA from non-infected cells - replicate 1


title: HuRef lymphoblastoid cell line, NimbleGen42M_54

description: Competitively hybridized to NimbleGen 42M CGH array.


title: CG4886 replicate 1

description: CG4886 DamID untreated Kc167 cells


title: 3 day denervated wild type rep2

description: replicate 2

source_name: 3 day denervated wild type rep2


title: CG5168 replicate 1

description: CG5168 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG5168-Dam

treatment_protocol: Cells transfected with 20 μg CG5168-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: NI11 Non- Polysomal

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_1.txt
non-polysomal RNA from non-infected cells - replicate 1


title: HuRef lymphoblastoid cell line, NimbleGen42M_52

source_name: HuRef lymphoblastoid cell line

source_name: NA15510 lymphoblastoid cell line


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 9

description: Competitively hybridized to Agilent 24M CGH array set.


title: HuRef lymphoblastoid cell line, NimbleGen42M_29


title: HuRef lymphoblastoid cell line, NimbleGen42M_38


title: INF14 Total

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_4.txt
total cytosolic RNA from JFH1-infected cells - replicate 4

source_name: Huh7 cells infected with HCV JFJ1 - replicate 4

value: infected with HCV JFJ1


title: 3 day denervated wild type rep1

description: replicate 1

source_name: 3 day denervated wild type rep1


title: HuRef lymphoblastoid cell line, NimbleGen42M_47


title: HuRef lymphoblastoid cell line, NimbleGen42M_45


title: CG1847 replicate 2

description: CG1847 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG1847-Dam

treatment_protocol: Cells transfected with 20 μg CG1847-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: CG1847 replicate 1

description: CG1847 DamID untreated Kc167 cells


title: INF14 Polysomal

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_3.txt
polysomal RNA from JFH1-infected cells - replicate 4


title: CG5168 replicate 2

description: CG5168 DamID untreated Kc167 cells


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 7


title: HuRef lymphoblastoid cell line, NimbleGen42M_27


title: 3 day control wild type rep3

description: replicate 3

source_name: 3 day control wild type rep3


title: HuRef lymphoblastoid cell line, NimbleGen42M_36


title: INF14 Non- Polysomal

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_4.txt
non-polysomal RNA from JFH1-infected cells - replicate 4


title: INF13 Total

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_3.txt
total cytosolic RNA from JFH1-infected cells - replicate 3

source_name: Huh7 cells infected with HCV JFJ1 - replicate 3


title: CG3771 replicate 2

description: CG3771 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing CG3771-Dam

treatment_protocol: Cells transfected with 20 μg CG3771-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 16


title: 3 day control wild type rep2

description: replicate 2

source_name: 3 day control wild type rep2


title: INF13 Non- Polysomal

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_1.txt
non-polysomal RNA from JFH1-infected cells - replicate 3


title: INF13 Polysomal

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_2.txt
polysomal RNA from JFH1-infected cells - replicate 3


title: HuRef lymphoblastoid cell line, NimbleGen42M_22


title: HuRef lymphoblastoid cell line, NimbleGen42M_20


title: INF12 Total

description:
US82400123_251485056795_S01_GE2-v5_95_Feb07_1_1.txt
total cytosolic RNA from JFH1-infected cells - replicate 2

source_name: Huh7 cells infected with HCV JFJ1 - replicate 2


title: HuRef lymphoblastoid cell line, NimbleGen42M_13


title: CG3771 replicate 1

description: CG3771 DamID untreated Kc167 cells


title: INF12 Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_4.txt
polysomal RNA from JFH1-infected cells - replicate 2


title: 3 day control wild type rep1

description: replicate 1

source_name: 3 day control wild type rep1


title: HuRef lymphoblastoid cell line, NimbleGen42M_11


title: INF12 Non- Polysomal

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_4.txt
non-polysomal RNA from JFH1-infected cells - replicate 2


title: TRIP1 replicate 1

description: TRIP1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing TRIP1-Dam

treatment_protocol: Cells transfected with 20 μg TRIP1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: INF11 Total

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_2.txt
total cytosolic RNA from JFH1-infected cells - replicate 1

source_name: Huh7 cells infected with HCV JFJ1 - replicate 1


title: INF11 Polysomal

description:
US82400123_251485056797_S01_GE2-v5_95_Feb07_1_2.txt
polysomal RNA from JFH1-infected cells - replicate 1


title: HEL25E replicate 1

description: HEL25E DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HEL25E-Dam

treatment_protocol: Cells transfected with 20 μg HEL25E-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: TRIP1 replicate 2

description: TRIP1 DamID untreated Kc167 cells


title: HuRef lymphoblastoid cell line, NimbleGen42M_02


title: HEL25E replicate 2

description: HEL25E DamID untreated Kc167 cells


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 20


title: INF11 Non- Polysomal

description:
US82400123_251485056796_S01_GE2-v5_95_Feb07_1_3.txt
non-polysomal RNA from JFH1-infected cells - replicate 1


title: HuRef lymphoblastoid cell line, NimbleGen42M_04


title: FaDu-pcDNA3

status: Public on Feb 11 2013

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

description: miRNA expression in FaDu-pcDNA3 stable clone

hyb_protocol: hybrization protocol was performed according to Agilent miRNA microarray system, and chamber type was Agilent microarray.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting. Scan speed was 25, and pixel resolution was 5 microns.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent). Data analysis by GeneSpring 7.3.1 (Agilent Technologies).

source_name: FaDu, pcDNA3 vector control expressing cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: all cell lines were growth in RPMI1640 containg 10% FBS, and were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted with Trizol reagent

treatment_protocol: no treatment was performed

value: Human hand and neck cancer cell

value: FaDu