title: Liver sample control (healthy) rep2

city: Brussels

first: Robim

last: Rodrigues

address: Laarbeeklaan 103

department: IVTD

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: 12.5 μg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, summarization (median polish) and normalization (quantile) were done with Robust Multi-array Analysis using RMAExpress v1.0.5

source_name: Liver sample control (healthy)

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip 3’ IVT Express Kit following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: hSKP-HPC: hSKP cells were cultivated using growth medium composed of DMEM+GLUTAMAX/F12 Nutrient Mixture (3:1; Life Technologies) supplemented with 7.33 IU/mL benzyl penicillin (Continental Pharma), 50 mg/mL streptomycin sulfate (Sigma-Aldrich), 2.5 mg/mL fungizone, 2 % (v/v) B27 Supplement (Life Technologies), 40 ng/mL basic fibroblast growth factor (FGF) 2 (Promega)  and 20 ng/mL epidermal growth factor (EGF) (Promega). Approximately two weeks after isolation, hSKP spheroids were dissociated to single cells using Liberase DH (Roche). The cells were subsequently cultivated as a moolayer. Hepatic differentiation of hSKP was carried out using a 24-day protocol in which cells were exposed in a time-dependent manner to the following growth factors and cytokines: Activin A (Life Technologies), FGF4 (Biosource), bone morphogenetic protein 4 (BMP4), hepatocyte growth factor (HGF) (Life Technologies), insulin-transferin-sodium selenite solution (ITS) (Sigma-Aldrich), dexamethasone (Sigma-Aldrich) and oncostatin M (Life Technologies). The obtained differentiated hepatocyte-like cells are referred to as hepatic progenitor cells (hSKP-HPC).   HepG2: HepG2 cells (ATCC; clone HB-8065) were recovered from liquid nitrogen and were cultured in 75 cm2 tissue culture flasks (Falcon) in a humidified incubator (37oC, 5% (v/v) CO2). The cell culture medium was composed of DMEM (Lonza) containing 10% (v/v) bovine calf serum (Gibco). The cells were passaged at sub confluence at least three times before use in exposure experiments. A seeding density of approximately 13,000 cells / cm2 was employed each time.  HepaRG: cryo-preserved differentiated HepaRG cells were obtained from Biopredic International and cultivated as per the supplier's instructions. The cells were cultivated using basal hepatic medium supplemented with HepaRG Maintenance and Metabolism Supplement (Biopredic International). During the exposure experiments the basal hepatic medium was supplemented with HepaRG Induction Supplement (Biopredic International).

extract_protocol: The isolation was conducted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich) following the manufacturer’s instructions.

treatment_protocol: Hepatic in vitro models, i.e. HepaRG, HepG2 and hSKP-HPC were exposed to acetaminophen for 24 hours at concentrations (IC10) of 13mM, 2mM and 18mM, respectively. Corresponding vehicle controls were incubated to the same medium without acetaminophen.

tag: subject status

value: healty control

value: liver


title: Liver sample APAP-induced ALF rep1

status: Public on Nov 04 2015

type: RNA

middle: M

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Liver sample APAP-induced ALF

value: patients suffering from acetaminophen-induced acute liver failure

tag: tissue


title: Liver sample control (healthy) rep1


title: CEM_BTZ7

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization on an Agilent SurePrint G3 Human CGH Microarray 4 x 180K array the design of which can be found in the Gene Expression Omnibus (GEO)[87] platform GPL8687 (http://www.ncbi. nlm.nih.gov/geo) was performed for 24h at 65 °C

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C (Agilent Technologies), and scans were quantified using the Agilent Feature Extraction software (version 10.5.1.1; Agilent Technologies, protocol CGH_105_Dec08) using default settings

data_processing: Genome data analysis was performed using R Version 2.6.2. The aCGH profiles were dewaved , and median was normalized. Segmentation was performed using the Bioconductor R-package DNAcopy version 1.22.1  and subsequently DNA copy number calls for loss, normal, gain or amplification were made using the using R-package CGHcall version 2.8.0

molecule: genomic DNA

source_name: CCRF-CEM resistant to 7 nM bortezomib, cultured in presence of 7nM bortezomib

label_protocol: labeling (Enzo Genomic DNA Labeling kit, Enzo Life Sciences, Raamsdonksveer, Netherlands) and purification were undertaken (QIAGEN MinElute PCR Purification Kit, Westburg, Leusden, Netherlands) with an elution volume of 2 × 10.5 μl, according to the manufacturer’s instructions. Cy3- and Cy5-labelled DNA samples were combined with Cot-1 DNA (Invitrogen, Breda, Netherlands)

growth_protocol: RPMI +10%fcs, in presence of indicated concentration of BTZ for several weeks

extract_protocol: DNA isolation was perfomed using column-based method (QIAamp DNA Mini Kit, Westburg, Leusden, Netherlands)

treatment_protocol: Cultured in presence of indicated concentration of BTZ for several weeks

tag: cell line

value: CCRF-CEM

tag: cell type

value: T Lymphoblast


title: CEM_BTZ200

source_name: CCRF-CEM resistant to 200 nM bortezomib,cultured in presence of 200nM bortezomib


title: Liver sample APAP-induced ALF rep2


title: CEM_BTZ100

source_name: CCRF-CEM resistant to 100 nM bortezomib,cultured in presence of 100nM bortezomib


title: Hu_REF_Cy3_2

source_name: Human Reference DNA (female)

value: homogeneous genomic human DNA pool from 100 female individuals


title: CEM_WT

source_name: CCRF-CEM-WT


title: HepG2 control, rep3

source_name: HepG not exposed

value: hepatic cell line

tag: exposed to

value: none (vehicle control)


title: Tamrabta_needles_3

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Gene expression in Tamrabta needles

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: The raw data preprocessing, quantile normalization and differential expressed gene analysis were done with the Limma package for R.

organism: Pinus pinaster

source_name: Tamrabta neeles replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were rooted cuttings of 17 months of age, planted in 2-l pots filled with a mixture of Sphagnum peat (PINSTRUD®) and vermiculite (VERLITE®) of grade 3, with a proportion 4:1 in volume. The entire experiment was performed at SERIDA’s greenhouse at Villaviciosa (Asturias, Spain). Potted plants were ferti-irrigated following the protocol by Majada et al. (2009, 5th Congreso Forestal Español. Ávila, 1–10.). Prior to the assessment, all branches were pruned to trigger the formation of new axillary shoots, mostly deriving from the activation of the proventitious meristems in the extant dwarf shoots. This was intended to be a ‘‘resetting’’ of the plants shoots, minimising the differences due to previous pruning done for cutting collection.

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

tag: organ

value: Adult needles

tag: provenance

value: Tamrabta

tag: culture

value: Rooted cuttings

tag: culture place


title: CEM_BTZ-200

source_name: CCRF-CEM resistant to 200 nM bortezomib, cultured in absence of bortezomib for several months


title: Liver sample APAP-induced ALF rep3


title: Tamrabta_needles_7

description: Gene expression in Tamrabta needles

source_name: Tamrabta neeles replicate 3

value: SERIDA’s greenhouse at Villaviciosa (Asturias, Spain)


title: HepG2 exposed to APAP, rep2

source_name: HepG2 exposed to APAP

value: acetaminophen


title: HepG2 control, rep2


title: Tamrabta_needles_8

description: Gene expression in Tamrabta needles

source_name: Tamrabta neeles replicate 4


title: HepG2 exposed to APAP, rep3


title: Leiria_needles_7

description: Gene expression in Leiria needles

source_name: Leiria neeles replicate 2

value: Leiria


title: Leiria_needles_8

description: Gene expression in Leiria needles

source_name: Leiria neeles replicate 3


title: Tamrabta_needles_6

description: Gene expression in Tamrabta needles

source_name: Tamrabta neeles replicate 2


title: Leiria_needles_6

description: Gene expression in Leiria needles

source_name: Leiria neeles replicate 1


title: HepG2 exposed to APAP, rep1


title: U2AF2 RIP SYNCRIP siRNA 3 [gene-level]

city: La Jolla

first: Thomas

middle: C

last: Whisenant

state: CA

address: 10550 North Torrey Pines Rd

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

description: SAMPLE 12

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4 on GCS 3000 7G

data_processing:
Expression intenisties at the probe set (exon) and transcript (gene) level were made with Expression Console (Affymetrix).
Gene level expression intensities were used as input into the R Bioconductor package limma for identification of differentially expressed genes (U2AF2 RIP Ctrl siRNA vs. U2AF2 RIP Specific siRNA)
Exon level expression intensitied were used as input into Alt-Analyze (Emig, et al) to identify differentially spliced exons (U2AFA2 RIP Ctrl siRNA vs. U2AF2 RIP Specific siRNA)
Please note that the 'U2AF2RIP_HTA2_all_siRNA_100414.xlsx' file includes multiple worksheets containing: 1) Differentially expressed genes in ctrl siRNA vs. U2AF1 siRNA; 2)Differntially spliced genes in ctrl siRNA vs. U2AF1 siRNA; 3)Differentially spliced exons in ctrl siRNA vs. U2AF1 siRNA; 4)Differentially expressed genes in ctrl siRNA vs. SYNCRIP siRNA; 5)Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 6)Differentially spliced exons in ctrl siRNA vs. SYNCRIP siRNA
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: U2AF2 RIP from SYNCRIP siRNA treatment of activated CD4 T cells

label_protocol: Biotinylated cDNA was prepared using the Ambion WT Expression Kit (Ambion) according to the manufacturer's instructions. cDNA was framented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Primary CD4 T cells cultured for two weeks in RPMI supplemented with 10% FBS, 30U/ml IL2, 100U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2

extract_protocol: Cell pellets were resuspended in TRIZOL reagent (Thermo) and the RNA was extracted according to manufacturer's protocol. RNA resuspended in nanopure water was purified over an Rneasy column (QIAGEN) and the polyA RNA was selected using oligo dT beads.

treatment_protocol: Primary CD4 T cells cultured were treated with siRNA 24 hours prior to treatment with anti-CD3/CD26 activator beads (Thermo) for an additional 24 hours.

value: Primary CD4 T cells

tag: pretreated with

value: SYNCRIP siRNA for 24hrs

tag: activated with

value: anti-CD3/CD26 activator beads for 24 h

tag: passages

tag: rip antibody

value: U2AF2 antibody

tag: rip antibody vendor

value: Sigma

tag: rip antibody cat. #

tag: rip antibody lot #

tag: molecule subtype

value: U2AF2 RIP RNA


title: Leiria_needles_9

description: Gene expression in Leiria needles

source_name: Leiria neeles replicate 4


title: HepG2 control, rep1


title: U2AF2 RIP Control siRNA 6 [gene-level]

description: SAMPLE 9

source_name: U2AF2 RIP from Control siRNA treatment of activated CD4 T cells

value: Control siRNA for 24hrs


title: U2AF2 RIP SYNCRIP siRNA 1 [gene-level]

description: SAMPLE 10


title: U2AF2 RIP Control siRNA 5 [gene-level]

description: SAMPLE 8


title: U2AF2 RIP Control siRNA 4 [gene-level]

description: SAMPLE 7


title: U2AF2 RIP SYNCRIP siRNA 2 [gene-level]

description: SAMPLE 11


title: HepaRG exposed to APAP, rep2

source_name: HepaRG exposed to APAP

value: HepaRG


title: U2AF2 RIP U2AF1 siRNA 3 [gene-level]

description: SAMPLE 6

source_name: U2AF2 RIP from U2AF1 siRNA treatment of activated CD4 T cells

value: U2AF1 siRNA for 24hrs


title: HepaRG exposed to APAP, rep1

value: hepatic cell line


title: U2AF2 RIP U2AF1 siRNA 2 [gene-level]

description: SAMPLE 5


title: HepaRG exposed to APAP, rep3


title: Hu_REF_Cy3_3

source_name: Human Reference DNA (female)

value: homogeneous genomic human DNA pool from 100 female individuals


title: U2AF2 RIP U2AF1 siRNA 1 [gene-level]

description: SAMPLE 4


title: hSKP-HPC control, rep1

source_name: hSKP-HPC not exposed

value: hSKP-HPC

value: human skin-precursors-derived hepatocyte-like cells (hSKP-HPC)

value: none (vehicle control)


title: U2AF2 RIP Control siRNA 3 [gene-level]

description: SAMPLE 3


title: U2AF2 RIP SYNCRIP siRNA 2 [exon-level]

description: SAMPLE 11


title: U2AF2 RIP Control siRNA 2 [gene-level]

description: SAMPLE 2


title: U2AF2 RIP SYNCRIP siRNA 3 [exon-level]

description: SAMPLE 12


title: U2AF2 RIP Control siRNA 1 [gene-level]

description: SAMPLE 1


title: hSKP-HPC exposed to APAP, rep3

source_name: hSKP-HPC exposed to APAP


title: hSKP-HPC control, rep3


title: hSKP-HPC exposed to APAP, rep1


title: hSKP-HPC exposed to APAP, rep2


title: SRRM2 siRNA 3 [gene-level]

description: SAMPLE 21

data_processing:
Expression intenisties at the probe set (exon) and transcript (gene) level were made with Expression Console (Affymetrix).
Gene level expression intensities were used as input into the R Bioconductor package limma for identification of differentially expressed genes (Ctrl siRNA vs. Specific siRNA)
Exon level expression intensitied were used as input into Alt-Analyze (Emig, et al) to identify differentially spliced exons (Ctrl siRNA vs. Specific siRNA)
The Series supplementary 'TotalRNA_HTA2_all_siRNA_100414.xslx' file has multiple worksheets containing: 1) Differentially expressed genes in ctrl siRNA vs. U2AF1 siRNA; 2)Differntially spliced genes in ctrl siRNA vs. U2AF1 siRNA; 3)Differentially spliced exons in ctrl siRNA vs. U2AF1 siRNA; 4)Differentially expressed genes in ctrl siRNA vs. SRRM2 siRNA; 5)Differntially spliced genes in ctrl siRNA vs. SRRM2 siRNA; 6)Differentially spliced exons in ctrl siRNA vs. SRRM2 siRNA; 7)Differentially expressed genes in ctrl siRNA vs. SYNCRIP siRNA; 8)Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 9)Differentially spliced exons in ctrl siRNA vs. SYNCRIP siRNA; 10)Differentially expressed genes in ctrl siRNA vs. ILF2 siRNA; 11)Differntially spliced genes in ctrl siRNA vs. ILF2 siRNA; 12)Differentially spliced exons in ctrl siRNA vs. ILF2 siRNA
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: SRRM2 siRNA treatment of activated CD4 T cells

value: SRRM2 siRNA for 24hrs


title: SRRM2 siRNA 2 [gene-level]

description: SAMPLE 20


title: hSKP-HPC control, rep2


title: U2AF2 RIP SYNCRIP siRNA 1 [exon-level]

description: SAMPLE 10


title: U2AF2 RIP Control siRNA 6 [exon-level]

description: SAMPLE 9


title: ILF2 siRNA 3 [gene-level]

description: SAMPLE 18

source_name: ILF2 siRNA treatment of activated CD4 T cells

value: ILF2 siRNA for 24hrs


title: SRRM2 siRNA 1 [gene-level]

description: SAMPLE 19


title: P3_portal vein tumor thrombus

city: Shanghai

first: Huiyong

last: Yin

address: 320 Yueyang Road, Xuhui District

country: China

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

hyb_protocol: Samples were hybridized using GeneChip® 3' IVT Express Kit according to the manufacturer's instructions. Heat the hybridization cocktails at 99° for 5 minutes, then incubate the probe array filled with Pre-Hybridization Mix at 45℃ for 10 min with rotation. Transfer the cocktails to a 45℃ heat block for 5 min. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail. Place probe array into the hybridization oven, set to 45 °C. Hybridize for 16 hours.

scan_protocol: Affymetrix GeneChip® Scanner 3000 (GCS3000)

data_processing: Data were processed using Affymetrix Expression ConsoleTM Software Version 1.0 according to the User Guide. RMA analysis mainly includes 4 steps: background correction on the PM values; quantile normalization across all the chips in the experiment; log2 transformation; median polish summarization.

source_name: portal vein tumor thrombus

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip® 3' IVT Express Kit.

growth_protocol: Surgical fresh tissues from HCC patients' liver were stored at -80℃.

extract_protocol: Total RNA was isolated from about 30 mg tissues with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

value: portal vein tumor thrombus

tag: patient diagnosis

value: hepatocellular carcinoma


title: U2AF2 RIP Control siRNA 5 [exon-level]

description: SAMPLE 8

value: Primary CD4 T cells


title: P5_portal vein tumor thrombus

tag: tissue


title: ILF2 siRNA 2 [gene-level]

description: SAMPLE 17

value: anti-CD3/CD26 activator beads for 24 h


title: P4_portal vein tumor thrombus


title: SYNCRIP siRNA 6 [gene-level]

description: SAMPLE 15

source_name: SYNCRIP siRNA treatment of activated CD4 T cells

value: SYNCRIP siRNA for 24hrs


title: U2AF2 RIP Control siRNA 2 [exon-level]

description: SAMPLE 2

value: U2AF2 antibody

value: Sigma


title: ILF2 siRNA 1 [gene-level]

description: SAMPLE 16


title: U2AF2 RIP U2AF1 siRNA 3 [exon-level]

description: SAMPLE 6

value: U2AF2 RIP RNA


title: U2AF2 RIP Control siRNA 4 [exon-level]

description: SAMPLE 7

value: Control siRNA for 24hrs


title: SRRM2 siRNA 3 [exon-level]

description: SAMPLE 21


title: U2AF2 RIP U2AF1 siRNA 1 [exon-level]

description: SAMPLE 4

value: U2AF1 siRNA for 24hrs


title: P2_portal vein tumor thrombus


title: U2AF2 RIP U2AF1 siRNA 2 [exon-level]

description: SAMPLE 5


title: U2AF2 RIP Control siRNA 3 [exon-level]

description: SAMPLE 3


title: U2AF2 RIP Control siRNA 1 [exon-level]

description: SAMPLE 1


title: ILF2 siRNA 3 [exon-level]

description: SAMPLE 18


title: T5_liver tumor tissue

source_name: liver tumor tissue

value: liver tumor tissue


title: SRRM2 siRNA 2 [exon-level]

description: SAMPLE 20


title: SYNCRIP siRNA 5 [gene-level]

description: SAMPLE 14


title: Control siRNA 6 [gene-level]

description: SAMPLE 12

source_name: Control siRNA treatment of activated CD4 T cells


title: SRRM2 siRNA 1 [exon-level]

description: SAMPLE 19


title: SYNCRIP siRNA 4 [gene-level]

description: SAMPLE 13


title: SYNCRIP siRNA 3 [gene-level]

description: SAMPLE 9


title: T4_liver tumor tissue


title: ILF2 siRNA 2 [exon-level]

description: SAMPLE 17


title: Control siRNA 5 [gene-level]

description: SAMPLE 11


title: Control siRNA 4 [gene-level]

description: SAMPLE 10


title: T2_liver tumor tissue


title: SYNCRIP siRNA 2 [gene-level]

description: SAMPLE 8


title: T1_liver tumor tissue


title: SYNCRIP siRNA 1 [gene-level]

description: SAMPLE 7


title: N4_para-carcinoma liver

source_name: para-carcinoma liver

value: para-carcinoma liver


title: U2AF1 siRNA 3 [gene-level]

description: SAMPLE 6

source_name: U2AF1 siRNA treatment of activated CD4 T cells


title: P1_portal vein tumor thrombus


title: Control siRNA 6 [exon-level]

description: SAMPLE 12


title: N5_para-carcinoma liver


title: N1_para-carcinoma liver


title: N3_para-carcinoma liver


title: Control siRNA 3 [gene-level]

description: SAMPLE 3


title: Control siRNA 5 [exon-level]

description: SAMPLE 11


title: U2AF1 siRNA 2 [gene-level]

description: SAMPLE 5


title: N2_para-carcinoma liver


title: SYNCRIP siRNA 6 [exon-level]

description: SAMPLE 15


title: SYNCRIP siRNA 5 [exon-level]

description: SAMPLE 14


title: SYNCRIP siRNA 4 [exon-level]

description: SAMPLE 13


title: mock3

city: Bentley

first: James

last: Hane

state: WA

address: Kent Street

department: Environment and Agriculture

country: Australia

institute: Curtin University

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Genespring GX and IWGSC MIPS v2.2 InterpPro, Pfam and GO functional annotations via mapping probes to the wheat transcriptome (IWGSC MIPS v2.2) [32,33] by Blat (-fastMap).

organism: Triticum aestivum

source_name: wheat seedlings mock-infection control

label_protocol: Standard Agilent protocol

growth_protocol: growth at 22oC, 16h light photoperiod (100 µM.m-1.sec-1)

extract_protocol: Qiagen RNA easy kit on root tissues

treatment_protocol: infection as per PMID 14714870 with modified temperature 16oC

tag: developmental stage

value: seedling

tag: infection

value: control

value: root


title: ILF2 siRNA 1 [exon-level]

description: SAMPLE 16

tag: cell type


title: U2AF1 siRNA 1 [gene-level]

description: SAMPLE 4


title: stimulated subject 287_case

status: Public on Nov 03 2015

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
subject 287
Sample 594

hyb_protocol: Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 and v4 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).

scan_protocol: Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio.

data_processing:
Microarray expression analysis was performed in R (http://www.r-project.org/). All 29,075 probes present on both microarrays (excluding X and Y chromosomes as well as cross-hybridizing probes) were first filtered by an Illumina detection P value of 0.05 in at least 50% of the samples, leaving 11,994 expressed probes for further analysis. Subsequently, each transcript was transformed and normalized through variance stabilization and normalization (VSN). Filtered data was controlled for confounding by batch effects or unknown factors using Surrogate Variable Analysis with the sva package in Bioconductor.
Raw and processed data are available on the series record. Processed data contains the VSN normalized and transformed signal.

source_name: whole blood

label_protocol: Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).

value: whole blood

tag: gender

value: male

tag: stimulus

value: stimulated

tag: sample type

value: case


title: Control siRNA 1  [gene-level]

description: SAMPLE 1

value: Primary CD4 T cells


title: baseline subject 287_case

description:
subject 287
Sample 593

value: baseline


title: stimulated subject 284_case

description:
subject 284
Sample 592

value: female


title: stimulated subject 280_case

description:
subject 280
Sample 590


title: baseline subject 284_case

description:
subject 284
Sample 591


title: SYNCRIP siRNA 2 [exon-level]

description: SAMPLE 8

value: SYNCRIP siRNA for 24hrs

value: anti-CD3/CD26 activator beads for 24 h


title: baseline subject 280_case

description:
subject 280
Sample 589


title: Control siRNA 4 [exon-level]

description: SAMPLE 10


title: baseline subject 270_case

description:
subject 270
Sample 587


title: Nalm6-WT1

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

description: The aRNA from the amplification of  total RNA sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit (AM1753).

hyb_protocol: Reagents (Ambion AM8740) according the manufacturer’s instructions.  Following fragmentation, dry samples down completely in a speed-vac.  Resuspend each pair of samples in the appropriate Tracking Control and add Hybridization Solution Master Mix according to manufacturer’s instructions. (Roche NimbleGen).Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions. Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.

scan_protocol: Dry the array slide completely. Place slide in a fresh tube and add 2.5 ml of Dye Saver. (Genisphere Inc). Coat   the slide with DyeSaver by rotating the tube manually for 45 seconds. Spin at 700 RPM for 3 seconds down to remove excess DyeSaver.Remove from tube and allow to air dry briefly in a hood. Scan using Axon GenePix 4000B.

data_processing: The data from “pair” files were loaded into ArrayStar. RMA (Robust Multi-array Average) method with “quantile” type was used to normalize the data. Base 2 log signal values were transferred from the linear values. The three replicates of each probe were then averaged to be used as the gene expression values. The gene expression values of the probes in the same gene were averaged further.

source_name: ALL leukemia cells

label_protocol: The 1ug of total RNA sample was amplied using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit (AM1753). Follow the manufacturer’s protocol for one cycle amplification.  4) Dye couple 15 ug of aRNA with Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions. A 10x dilution should have approximately 60 ng/ul of material with a range of 50-100 ng/ul

growth_protocol: 10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in  2x10^5 to 1x10^6

extract_protocol: Total RNA from 5x10^6 Nalm6 cells were isoalted by  using the RNeasy mini isolation kit (Qiagen) (n=3).

value: pre-B ALL leukemia cells


title: Nalm6-WT3


title: stimulated subject 270_case

description:
subject 270
Sample 588


title: ag82

source_name: wheat seedlings infected with Rhizoctonia solani AG8

value: Rhizoctonia solani AG8


title: ag81


title: ag83


title: mock1


title: baseline subject 269_case

description:
subject 269
Sample 585


title: stimulated subject 269_case

description:
subject 269
Sample 586


title: Nalm6-WT2


title: T3_liver tumor tissue

value: hepatocellular carcinoma


title: stimulated subject 257_case

description:
subject 257
Sample 582


title: U2AF1 siRNA 3 [exon-level]

description: SAMPLE 6

value: U2AF1 siRNA for 24hrs


title: baseline subject 266_case

description:
subject 266
Sample 583


title: SYNCRIP siRNA 3 [exon-level]

description: SAMPLE 9


title: baseline subject 251_case

description:
subject 251
Sample 579


title: baseline subject 246_case

description:
subject 246
Sample 578


title: stimulated subject 251_case

description:
subject 251
Sample 580


title: stimulated subject 247_case

description:
subject 247
Sample 576


title: U2AF1 siRNA 2 [exon-level]

description: SAMPLE 5


title: stimulated subject 239_case

description:
subject 239
Sample 570


title: stimulated subject 244_case

description:
subject 244
Sample 574


title: baseline subject 239_case

description:
subject 239
Sample 569


title: baseline subject 245_case

description:
subject 245
Sample 571


title: baseline subject 244_case

description:
subject 244
Sample 573


title: stimulated subject 245_case

description:
subject 245
Sample 572


title: baseline subject 238_case

description:
subject 238
Sample 567


title: stimulated subject 238_case

description:
subject 238
Sample 568


title: U2AF1 siRNA 1 [exon-level]

description: SAMPLE 4


title: baseline subject 237_case

description:
subject 237
Sample 565


title: baseline subject 247_case

description:
subject 247
Sample 575


title: stimulated subject 237_case

description:
subject 237
Sample 566


title: Control siRNA 2 [gene-level]

description: SAMPLE 2

value: Control siRNA for 24hrs


title: baseline subject 235_case

description:
subject 235
Sample 563


title: baseline subject 232_case

description:
subject 232
Sample 561


title: stimulated subject 235_case

description:
subject 235
Sample 564


title: baseline subject 231_case

description:
subject 231
Sample 559


title: stimulated subject 231_case

description:
subject 231
Sample 560


title: baseline subject 229_case

description:
subject 229
Sample 555


title: SYNCRIP siRNA 1 [exon-level]

description: SAMPLE 7


title: stimulated subject 229_case

description:
subject 229
Sample 556


title: stimulated subject 228_case

description:
subject 228
Sample 552


title: stimulated subject 230_case

description:
subject 230
Sample 558


title: baseline subject 228_case

description:
subject 228
Sample 551


title: stimulated subject 232_case

description:
subject 232
Sample 562


title: baseline subject 226_case

description:
subject 226
Sample 549


title: baseline subject 230_case

description:
subject 230
Sample 557


title: Control siRNA 2 [exon-level]

description: SAMPLE 2


title: baseline subject 224_case

description:
subject 224
Sample 545


title: baseline subject 227_case

description:
subject 227
Sample 553


title: stimulated subject 226_case

description:
subject 226
Sample 550


title: stimulated subject 227_case

description:
subject 227
Sample 554


title: stimulated subject 223_case

description:
subject 223
Sample 544


title: Control siRNA 1  [exon-level]

description: SAMPLE 1


title: stimulated subject 225_case

description:
subject 225
Sample 548


title: baseline subject 225_case

description:
subject 225
Sample 547


title: stimulated subject 222_case

description:
subject 222
Sample 542


title: stimulated subject 224_case

description:
subject 224
Sample 546


title: baseline subject 223_case

description:
subject 223
Sample 543


title: baseline subject 220_case

description:
subject 220
Sample 539


title: Control siRNA 3 [exon-level]

description: SAMPLE 3


title: baseline subject 222_case

description:
subject 222
Sample 541


title: stimulated subject 218_case

description:
subject 218
Sample 536


title: stimulated subject 215_case

description:
subject 215
Sample 534


title: stimulated subject 197_case

description:
subject 197
Sample 532


title: stimulated subject 220_case

description:
subject 220
Sample 540


title: stimulated subject 179_case

description:
subject 179
Sample 524


title: stimulated subject 177_case

description:
subject 177
Sample 522


title: stimulated subject 266_case

description:
subject 266
Sample 584


title: stimulated subject 173_case

description:
subject 173
Sample 512


title: stimulated subject 175_case

description:
subject 175
Sample 516


title: stimulated subject 172_case

description:
subject 172
Sample 510


title: baseline subject 173_case

description:
subject 173
Sample 511


title: baseline subject 218_case

description:
subject 218
Sample 535


title: stimulated subject 185_case

description:
subject 185
Sample 530


title: baseline subject 171_case

description:
subject 171
Sample 507


title: baseline subject 179_case

description:
subject 179
Sample 523


title: stimulated subject 169_case

description:
subject 169
Sample 504


title: baseline subject 177_case

description:
subject 177
Sample 521


title: stimulated subject 171_case

description:
subject 171
Sample 508


title: baseline subject 168_case

description:
subject 168
Sample 501


title: stimulated subject 170_case

description:
subject 170
Sample 506


title: baseline subject 185_case

description:
subject 185
Sample 529


title: baseline subject 170_case

description:
subject 170
Sample 505


title: stimulated subject 167_case

description:
subject 167
Sample 498


title: baseline subject 215_case

description:
subject 215
Sample 533


title: baseline subject 172_case

description:
subject 172
Sample 509


title: baseline subject 169_case

description:
subject 169
Sample 503


title: baseline subject 166_case

description:
subject 166
Sample 499


title: stimulated subject 168_case

description:
subject 168
Sample 502


title: stimulated subject 163_case

description:
subject 163
Sample 492


title: baseline subject 175_case

description:
subject 175
Sample 515


title: stimulated subject 162_case

description:
subject 162
Sample 490


title: baseline subject 197_case

description:
subject 197
Sample 531


title: mock2

value: seedling


title: stimulated subject 161_case

description:
subject 161
Sample 488


title: baseline subject 164_case

description:
subject 164
Sample 493


title: baseline subject 161_case

description:
subject 161
Sample 487


title: stimulated subject 165_case

description:
subject 165
Sample 496


title: stimulated subject 166_case

description:
subject 166
Sample 500


title: baseline subject 160_case

description:
subject 160
Sample 485


title: stimulated subject 160_case

description:
subject 160
Sample 486


title: stimulated subject 158_case

description:
subject 158
Sample 482


title: baseline subject 163_case

description:
subject 163
Sample 491


title: baseline subject 165_case

description:
subject 165
Sample 495


title: baseline subject 167_case

description:
subject 167
Sample 497


title: stimulated subject 157_case

description:
subject 157
Sample 480


title: stimulated subject 154_case

description:
subject 154
Sample 476


title: stimulated subject 156_case

description:
subject 156
Sample 478


title: stimulated subject 246_case

description:
subject 246
Sample 577


title: baseline subject 162_case

description:
subject 162
Sample 489


title: baseline subject 155_case

description:
subject 155
Sample 473


title: baseline subject 157_case

description:
subject 157
Sample 479


title: stimulated subject 164_case

description:
subject 164
Sample 494


title: baseline subject 152_case

description:
subject 152
Sample 469


title: stimulated subject 153_case

description:
subject 153
Sample 472


title: baseline subject 156_case

description:
subject 156
Sample 477


title: baseline subject 153_case

description:
subject 153
Sample 471


title: stimulated subject 152_case

description:
subject 152
Sample 470


title: baseline subject 158_case

description:
subject 158
Sample 481


title: stimulated subject 150_case

description:
subject 150
Sample 466


title: baseline subject 257_case

description:
subject 257
Sample 581


title: baseline subject 147_case

description:
subject 147
Sample 461


title: stimulated subject 151_case

description:
subject 151
Sample 468


title: baseline subject 143_case

description:
subject 143
Sample 451


title: baseline subject 137_case

description:
subject 137
Sample 449


title: baseline subject 150_case

description:
subject 150
Sample 465


title: stimulated subject 121_case

description:
subject 121
Sample 448


title: stimulated subject 143_case

description:
subject 143
Sample 452


title: baseline subject 151_case

description:
subject 151
Sample 467


title: baseline subject 148_case

description:
subject 148
Sample 459


title: stimulated subject 147_case

description:
subject 147
Sample 462


title: stimulated subject 111_case

description:
subject 111
Sample 436


title: stimulated subject 148_case

description:
subject 148
Sample 460


title: baseline subject 111_case

description:
subject 111
Sample 435


title: stimulated subject 155_case

description:
subject 155
Sample 474


title: baseline subject 154_case

description:
subject 154
Sample 475


title: baseline subject 144_case

description:
subject 144
Sample 453


title: stimulated subject 144_case

description:
subject 144
Sample 454


title: baseline subject 96_case

description:
subject 96
Sample 431


title: baseline subject 149_case

description:
subject 149
Sample 463


title: baseline subject 97_case

description:
subject 97
Sample 429


title: baseline subject 113_case

description:
subject 113
Sample 441


title: stimulated subject 90_case

description:
subject 90
Sample 426


title: stimulated subject 149_case

description:
subject 149
Sample 464


title: baseline subject 91_case

description:
subject 91
Sample 427


title: stimulated subject 97_case

description:
subject 97
Sample 430


title: stimulated subject 55_case

description:
subject 55
Sample 412


title: baseline subject 89_case

description:
subject 89
Sample 423


title: stimulated subject 137_case

description:
subject 137
Sample 450


title: stimulated subject 42_case

description:
subject 42
Sample 383


title: stimulated subject 96_case

description:
subject 96
Sample 432


title: baseline subject 88_case

description:
subject 88
Sample 421


title: stimulated subject 41_case

description:
subject 41
Sample 385


title: stimulated subject 113_case

description:
subject 113
Sample 442


title: baseline subject 90_case

description:
subject 90
Sample 425


title: stimulated subject 91_case

description:
subject 91
Sample 428


title: stimulated subject 16_case

description:
subject 16
Sample 354


title: baseline subject 55_case

description:
subject 55
Sample 411


title: baseline subject 121_case

description:
subject 121
Sample 447


title: baseline subject 297_case

description:
subject 297
Sample 337


title: stimulated subject 88_case

description:
subject 88
Sample 422


title: stimulated subject 297_case

description:
subject 297
Sample 338


title: baseline subject 296_control

description:
subject 296
Sample 335

value: control


title: baseline subject 42_case

description:
subject 42
Sample 384


title: baseline subject 295_control

description:
subject 295
Sample 333


title: baseline subject 294_control

description:
subject 294
Sample 331


title: stimulated subject 296_control

description:
subject 296
Sample 336


title: stimulated subject 294_control

description:
subject 294
Sample 332


title: baseline subject 16_case

description:
subject 16
Sample 353


title: stimulated subject 293_control

description:
subject 293
Sample 330


title: stimulated subject 291_control

description:
subject 291
Sample 326


title: stimulated subject 290_control

description:
subject 290
Sample 324


title: stimulated subject 89_case

description:
subject 89
Sample 424


title: baseline subject 290_control

description:
subject 290
Sample 323


title: stimulated subject 295_control

description:
subject 295
Sample 334


title: stimulated subject 292_control

description:
subject 292
Sample 328


title: baseline subject 293_control

description:
subject 293
Sample 329


title: baseline subject 41_case

description:
subject 41
Sample 386


title: stimulated subject 289_control

description:
subject 289
Sample 320


title: baseline subject 292_control

description:
subject 292
Sample 327


title: baseline subject 291_control

description:
subject 291
Sample 325


title: baseline subject 286_control

description:
subject 286
Sample 317


title: baseline subject 282_control

description:
subject 282
Sample 309


title: stimulated subject 281_control

description:
subject 281
Sample 314


title: baseline subject 288_control

description:
subject 288
Sample 321


title: baseline subject 289_control

description:
subject 289
Sample 319


title: stimulated subject 286_control

description:
subject 286
Sample 318


title: baseline subject 285_control

description:
subject 285
Sample 315


title: stimulated subject 276_control

description:
subject 276
Sample 304


title: stimulated subject 288_control

description:
subject 288
Sample 322


title: baseline subject 279_control

description:
subject 279
Sample 307


title: baseline subject 281_control

description:
subject 281
Sample 313


title: stimulated subject 279_control

description:
subject 279
Sample 308


title: baseline subject 278_control

description:
subject 278
Sample 311


title: stimulated subject 275_control

description:
subject 275
Sample 302


title: baseline subject 276_control

description:
subject 276
Sample 303


title: stimulated subject 278_control

description:
subject 278
Sample 312


title: baseline subject 273_control

description:
subject 273
Sample 295


title: baseline subject 277_control

description:
subject 277
Sample 297


title: stimulated subject 282_control

description:
subject 282
Sample 310


title: baseline subject 274_control

description:
subject 274
Sample 299


title: baseline subject 283_control

description:
subject 283
Sample 305


title: stimulated subject 283_control

description:
subject 283
Sample 306


title: stimulated subject 272_control

description:
subject 272
Sample 294


title: stimulated subject 268_control

description:
subject 268
Sample 290


title: stimulated subject 274_control

description:
subject 274
Sample 300


title: baseline subject 272_control

description:
subject 272
Sample 293


title: stimulated subject 265_control

description:
subject 265
Sample 286


title: baseline subject 275_control

description:
subject 275
Sample 301


title: stimulated subject 273_control

description:
subject 273
Sample 296


title: baseline subject 268_control

description:
subject 268
Sample 289


title: stimulated subject 277_control

description:
subject 277
Sample 298


title: baseline subject 267_control

description:
subject 267
Sample 291


title: stimulated subject 285_control

description:
subject 285
Sample 316


title: stimulated subject 267_control

description:
subject 267
Sample 292


title: stimulated subject 264_control

description:
subject 264
Sample 284


title: stimulated subject 263_control

description:
subject 263
Sample 288


title: baseline subject 264_control

description:
subject 264
Sample 283


title: baseline subject 262_control

description:
subject 262
Sample 281


title: baseline subject 265_control

description:
subject 265
Sample 285


title: baseline subject 263_control

description:
subject 263
Sample 287


title: stimulated subject 261_control

description:
subject 261
Sample 280


title: stimulated subject 259_control

description:
subject 259
Sample 278


title: baseline subject 258_control

description:
subject 258
Sample 271


title: baseline subject 261_control

description:
subject 261
Sample 279


title: baseline subject 255_control

description:
subject 255
Sample 269


title: stimulated subject 252_control

description:
subject 252
Sample 268


title: baseline subject 259_control

description:
subject 259
Sample 277


title: baseline subject 271_control

description:
subject 271
Sample 275


title: stimulated subject 255_control

description:
subject 255
Sample 270


title: baseline subject 260_control

description:
subject 260
Sample 273


title: stimulated subject 249_control

description:
subject 249
Sample 264


title: stimulated subject 253_control

description:
subject 253
Sample 265


title: stimulated subject 258_control

description:
subject 258
Sample 272


title: stimulated subject 262_control

description:
subject 262
Sample 282


title: stimulated subject 250_control

description:
subject 250
Sample 260


title: baseline subject 250_control

description:
subject 250
Sample 259


title: stimulated subject 248_control

description:
subject 248
Sample 256


title: baseline subject 248_control

description:
subject 248
Sample 255


title: baseline subject 243_control

description:
subject 243
Sample 257


title: baseline subject 252_control

description:
subject 252
Sample 267


title: stimulated subject 260_control

description:
subject 260
Sample 274


title: baseline subject 253_control

description:
subject 253
Sample 266


title: baseline subject 249_control

description:
subject 249
Sample 263


title: stimulated subject 254_control

description:
subject 254
Sample 262


title: stimulated subject 241_control

description:
subject 241
Sample 251


title: stimulated subject 240_control

description:
subject 240
Sample 250


title: baseline subject 240_control

description:
subject 240
Sample 249


title: baseline subject 254_control

description:
subject 254
Sample 261


title: stimulated subject 271_control

description:
subject 271
Sample 276


title: stimulated subject 256_control

description:
subject 256
Sample 254


title: stimulated subject 193_control

description:
subject 193
Sample 216


title: baseline subject 241_control

description:
subject 241
Sample 252


title: baseline subject 193_control

description:
subject 193
Sample 215


title: stimulated subject 92_control

description:
subject 92
Sample 184


title: baseline subject 92_control

description:
subject 92
Sample 183


title: stimulated subject 101_control

description:
subject 101
Sample 138


title: baseline subject 134_control

description:
subject 134
Sample 133


title: stimulated subject 93_control

description:
subject 93
Sample 158


title: baseline subject 124_control

description:
subject 124
Sample 131


title: baseline subject 256_control

description:
subject 256
Sample 253


title: baseline subject 101_control

description:
subject 101
Sample 137


title: stimulated subject 134_control

description:
subject 134
Sample 134


title: stimulated subject 124_control

description:
subject 124
Sample 132


title: stimulated subject 243_control

description:
subject 243
Sample 258


title: baseline subject 93_control

description:
subject 93
Sample 157


title: baseline subject 131_control

description:
subject 131
Sample 115


title: stimulated subject 119_control

description:
subject 119
Sample 130


title: stimulated subject 109_control

description:
subject 109
Sample 128


title: stimulated subject 234_control

description:
subject 234
Sample 248


title: baseline subject 108_control

description:
subject 108
Sample 101


title: stimulated subject 98_control

description:
subject 98
Sample 112


title: stimulated subject 131_control

description:
subject 131
Sample 116


title: baseline subject 109_control

description:
subject 109
Sample 127


title: baseline subject 136_control

description:
subject 136
Sample 83


title: stimulated subject 107_control

description:
subject 107
Sample 88


title: stimulated subject 117_control

description:
subject 117
Sample 82


title: stimulated subject 136_control

description:
subject 136
Sample 84


title: baseline subject 107_control

description:
subject 107
Sample 87


title: stimulated subject 108_control

description:
subject 108
Sample 102


title: baseline subject 234_control

description:
subject 234
Sample 247


title: stimulated subject 115_control

description:
subject 115
Sample 74


title: baseline subject 115_control

description:
subject 115
Sample 73


title: baseline subject 117_control

description:
subject 117
Sample 81


title: stimulated subject 123_control

description:
subject 123
Sample 58


title: stimulated subject 87_control

description:
subject 87
Sample 60


title: baseline subject 119_control

description:
subject 119
Sample 129


title: baseline subject 87_control

description:
subject 87
Sample 59


title: baseline subject 242_control

description:
subject 242
Sample 9


title: stimulated subject 242_control

description:
subject 242
Sample 10


title: baseline subject 181_case

description:
subject 181
Sample 1


title: baseline subject 98_control

description:
subject 98
Sample 111


title: stimulated subject 236_case

description:
subject 236
Sample 4


title: baseline subject 236_case

description:
subject 236
Sample 3


title: stimulated subject 181_case

description:
subject 181
Sample 2


title: baseline subject 123_control

description:
subject 123
Sample 57


title: Baseline subject 16

description:
Sample name: Sample 31
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

hyb_protocol: Standard Illumina protocol, HumanMethylation450.

scan_protocol: Standard Illumina protocol, BeadStudio.

data_processing: Microarray methylation analysis was performed in R (http://www.r-project.org/). Quality control of methylation data, including intensity read outs, filtering (detection p-value > 0.01 in at least 75% of the samples), cellular composition estimation, as well as beta and M-value calculation were done using the minfi Bioconductor R package version 1.10.2. Filtered beta values were reduced by eliminating any CpG sites on sex chromosomes, as well as probes found to have SNPs at the CpG site itself or in the single-base extension site with a MAF ≥ 1% in the 1,000 Genomes Project European population and/or non-specific binding probes according to 4. Additionally, we performed a re-alignment of the array probe sequences using Bismark. This yielded a total of 425,883 CpG sites for further analysis. The data were then normalized with functional normalization. Technical batch effects were identified by inspecting the association of the first principal components of the methylation levels with processing (experiment) date as technical batch. The data were then adjusted using ComBat.

source_name: whole blood, control, baseline

extract_protocol: Invitrogen Puregene Genomic DNA kit.

tag: subject

tag: disease state

tag: age

tag: dna methylation-predicted age

tag: treatment

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes


title: Stimulated subject 30

description:
Sample name: Sample 58
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, control, stimulated

label_protocol: Standard Illumina protocol, HumanMethylation450.

tag: tissue

value: dexamethasone stimulated


title: Stimulated subject 21

description:
Sample name: Sample 41
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: whole blood


title: Baseline subject 21

description:
Sample name: Sample 40
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: male


title: Baseline subject 30

description:
Sample name: Sample 59
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 59

description:
Sample name: Sample 115
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, case, stimulated

value: major depressive disorder


title: RAD21 mutant Q592 CB539

city: Stanford

first: Ravi

last: Majeti

state: California

address: 235 Campus Drive

institute: Stanford University

description: Claire Mazumdar_CB539-RAD21 Q592^_(HG-U133_Plus_2)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GenePattern (ExpressionFileCreator)

source_name: CD34+ enriched cord blood

label_protocol: standard Affymetrix protocol

growth_protocol: CD34+ cells were cultured in HPGM + cytokines for 72hrs

extract_protocol: Qiagen RNAeasy Mini Kit

treatment_protocol: Cells were lentivirally transduced and GFP+ sorted after 72 hrs and subjected to RNA extraction

value: cord blood


title: RAD21 mutant E212 CB539

description: Claire Mazumdar_CB539-RAD21 E212^_(HG-U133_Plus_2)


title: Empty Vector Control CB539

description: Claire Mazumdar_CB539-Empty_(HG-U133_Plus_2)


title: Baseline subject 59

description:
Sample name: Sample 114
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, case, baseline


title: RAD21 WT CB535

description: Claire Mazumdar_CB535-RAD21 WT_(HG-U133_Plus_2)


title: Stimulated subject 62

description:
Sample name: Sample 121
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: RAD21 mutant Q592 CB535

description: Claire Mazumdar_CB535-RAD21 Q592^_(HG-U133_Plus_2)


title: Empty Vector Control CB534

description: Claire Mazumdar_CB534-Empty_(HG-U133_Plus_2)


title: Empty Vector Control CB535

description: Claire Mazumdar_CB535-Empty_(HG-U133_Plus_2)


title: RAD21 WT CB534

description: Claire Mazumdar_CB534-RAD21 WT_(HG-U133_Plus_2)


title: Baseline subject 40

description:
Sample name: Sample 79
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 62

description:
Sample name: Sample 120
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Great Dane 19

city: Hannover

first: Julia

last: Metzger

address: Buenteweg 17 p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine

hyb_protocol: Illumina commercial service

scan_protocol: Illumina commercial service

data_processing: Genomic DNA was genotyped on the Illumina high density BeadChip

label: Cy3 and Cy5

organism: Canis lupus familiaris

source_name: Ichthyosis

label_protocol: Illumina commercial service

extract_protocol: Extraction of DNA was performed using a standard ethanol fraction

tag: breed

value: Great Dane

tag: diagnosis

value: Ichthyosis


title: Great Dane 17


title: Great Dane 20


title: RAD21 mutant E212 CB534

description: Claire Mazumdar_CB534-RAD21 E212^_(HG-U133_Plus_2)


title: SMC1A WT CB531

description: Claire Mazumdar_CB531-SMC1A WT_(HG-U133_Plus_2)


title: Great Dane 2


title: Great Dane 3


title: Great Dane 18


title: Great Dane 11


title: Great Dane 5


title: Great Dane 15


title: Baseline subject 64

description:
Sample name: Sample 124
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: gender

value: baseline


title: Great Dane 7


title: SMC1A Mutant R711G CB531

description: Claire Mazumdar_CB531-SMC1A R711G_(HG-U133_Plus_2)


title: SMC1A WT CB530

description: Claire Mazumdar_CB530-SMC1A WT_(HG-U133_Plus_2)


title: Empty Vector Control CB531

description: Claire Mazumdar_CB531-Empty_(HG-U133_Plus_2)


title: Great Dane 8


title: Empty Vector Control CB530

description: Claire Mazumdar_CB530-Empty_(HG-U133_Plus_2)


title: Great Dane 12


title: SMC1A Mutant R711G CB530

description: Claire Mazumdar_CB530-SMC1A R711G_(HG-U133_Plus_2)


title: Great Dane 22


title: Stimulated subject 40

description:
Sample name: Sample 78
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: female


title: Great Dane 14


title: Great Dane 13


title: sensitive skin with lactic acid challenge (set 2)

city: Seoul

first: Eun Ju

last: Kim

address: 101 Daehakro Jongnogu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

description:
Gene expression data from skin with seborrheic keratosis
sensitive LA set2

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were normalized and analyzed with dChip software (Li and Wong, PNAS 2001;98:31-36).

label_protocol: Affymetrix protocol

extract_protocol: Two-mm punch biopsy was performed from skin with sensitive skin and non-sensitive skin following lactic acid or normal saline application. RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

treatment_protocol: 10% lactic acid challenge or 0.9% normal saline application

value: skin

tag: tissue type

value: sensitive skin (seborrheic keratosis)

tag: agent

value: lactic acid


title: Great Dane 10


title: Great Dane 4


title: Great Dane 16


title: Great Dane 9


title: Great Dane 6


title: sensitive skin with lactic acid challenge (set 3)

description:
Gene expression data from skin with seborrheic keratosis
sensitive LA set3


title: Great Dane 1


title: Baseline subject 39

description:
Sample name: Sample 76
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: subject


title: Stimulated subject 64

description:
Sample name: Sample 125
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: disease state


title: Stimulated subject 39

description:
Sample name: Sample 77
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: age


title: Great Dane 21


title: Baseline subject 51

description:
Sample name: Sample 99
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: dna methylation-predicted age


title: Baseline subject 75

description:
Sample name: Sample 146
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: treatment


title: Stimulated subject 75

description:
Sample name: Sample 147
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: cd8 t cells


title: Baseline subject 27

description:
Sample name: Sample 53
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: cd4 t cells


title: stimulated subject 219_case

description:
subject 219
Sample 538

tag: stimulus

value: stimulated

tag: sample type

value: case


title: Stimulated subject 27

description:
Sample name: Sample 52
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: natural killer cells

tag: b cells

tag: monocytes


title: baseline subject 219_case

description:
subject 219
Sample 537

tag: tissue


title: baseline subject 183_case

description:
subject 183
Sample 527


title: stimulated subject 183_case

description:
subject 183
Sample 528


title: stimulated subject 180_case

description:
subject 180
Sample 526


title: sensitive skin with normal saline application (set 1)

description:
Gene expression data from skin with seborrheic keratosis
sensitive NS set1

value: normal saline


title: sensitive skin with normal saline application (set 3)

description:
Gene expression data from skin with seborrheic keratosis
sensitive NS set3


title: non-sensitive skin with normal saline application (set 2)

description:
Gene expression data from control skin
non-sensitive NS set2

value: non-sensitive skin (control)


title: non-sensitive skin with lactic acid challenge (set 3)

description:
Gene expression data from control skin
non-sensitive LA set3


title: sensitive skin with normal saline application (set 2)

description:
Gene expression data from skin with seborrheic keratosis
sensitive NS set2


title: non-sensitive skin with lactic acid challenge (set 1)

description:
Gene expression data from control skin
non-sensitive LA set1


title: baseline subject 176_case

description:
subject 176
Sample 517


title: non-sensitive skin with normal saline application (set 1)

description:
Gene expression data from control skin
non-sensitive NS set1


title: stimulated subject 178_case

description:
subject 178
Sample 520


title: Stimulated subject 31

description:
Sample name: Sample 60
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: control

tag: granulocytes


title: Baseline subject 70

description:
Sample name: Sample 136
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: gender


title: Baseline subject 31

description:
Sample name: Sample 61
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: non-sensitive skin with normal saline application (set 3)

description:
Gene expression data from control skin
non-sensitive NS set3

tag: tissue type


title: sensitive skin with lactic acid challenge (set 1)

description:
Gene expression data from skin with seborrheic keratosis
sensitive LA set1

tag: agent


title: stimulated subject 159_case

description:
subject 159
Sample 484


title: baseline subject 180_case

description:
subject 180
Sample 525


title: baseline subject 178_case

description:
subject 178
Sample 519


title: stimulated subject 176_case

description:
subject 176
Sample 518


title: Baseline subject 77

description:
Sample name: Sample 151
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: subject


title: stimulated subject 146_case

description:
subject 146
Sample 457


title: Stimulated subject 77

description:
Sample name: Sample 150
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: disease state

value: dexamethasone stimulated


title: stimulated subject 174_case

description:
subject 174
Sample 514

value: whole blood


title: stimulated subject 145_case

description:
subject 145
Sample 456

value: male


title: baseline subject 174_case

description:
subject 174
Sample 513


title: Baseline subject 12

description:
Sample name: Sample 23
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: age


title: Stimulated subject 12

description:
Sample name: Sample 24
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: dna methylation-predicted age


title: baseline subject 159_case

description:
subject 159
Sample 483


title: non-sensitive skin with lactic acid challenge (set 2)

description:
Gene expression data from control skin
non-sensitive LA set2


title: baseline subject 145_case

description:
subject 145
Sample 455


title: stimulated subject 116_case

description:
subject 116
Sample 444


title: stimulated subject 118_case

description:
subject 118
Sample 446


title: stimulated subject 114_case

description:
subject 114
Sample 440


title: baseline subject 114_case

description:
subject 114
Sample 439


title: Stimulated subject 70

description:
Sample name: Sample 137
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: major depressive disorder

tag: treatment


title: baseline subject 146_case

description:
subject 146
Sample 458


title: stimulated subject 100_case

description:
subject 100
Sample 434


title: baseline subject 116_case

description:
subject 116
Sample 443


title: Baseline subject 48

description:
Sample name: Sample 94
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: cd8 t cells


title: baseline subject 118_case

description:
subject 118
Sample 445


title: stimulated subject 70_case

description:
subject 70
Sample 418


title: Baseline subject 54

description:
Sample name: Sample 105
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: cd4 t cells


title: baseline subject 61_case

description:
subject 61
Sample 419

tag: stimulus


title: baseline subject 70_case

description:
subject 70
Sample 417

tag: sample type


title: stimulated subject 112_case

description:
subject 112
Sample 437


title: baseline subject 112_case

description:
subject 112
Sample 438


title: stimulated subject 61_case

description:
subject 61
Sample 420


title: Stimulated subject 54

description:
Sample name: Sample 104
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: natural killer cells


title: Baseline subject 7

description:
Sample name: Sample 13
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: b cells


title: Stimulated subject 7

description:
Sample name: Sample 14
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: monocytes


title: stimulated subject 67_case

description:
subject 67
Sample 416

tag: tissue


title: Baseline subject 49

description:
Sample name: Sample 95
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: granulocytes


title: Stimulated subject 49

description:
Sample name: Sample 96
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: gender


title: baseline subject 100_case

description:
subject 100
Sample 433


title: baseline subject 67_case

description:
subject 67
Sample 415


title: Stimulated subject 8

description:
Sample name: Sample 15
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 54_case

description:
subject 54
Sample 409


title: Stimulated subject 69

description:
Sample name: Sample 135
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 62_case

description:
subject 62
Sample 413


title: stimulated subject 54_case

description:
subject 54
Sample 410


title: stimulated subject 52_case

description:
subject 52
Sample 406


title: baseline subject 52_case

description:
subject 52
Sample 405


title: stimulated subject 53_case

description:
subject 53
Sample 407


title: baseline subject 53_case

description:
subject 53
Sample 408


title: Baseline subject 69

description:
Sample name: Sample 134
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 51_case

description:
subject 51
Sample 404


title: baseline subject 50_case

description:
subject 50
Sample 401


title: baseline subject 51_case

description:
subject 51
Sample 403


title: baseline subject 49_case

description:
subject 49
Sample 399


title: stimulated subject 47_case

description:
subject 47
Sample 396


title: stimulated subject 50_case

description:
subject 50
Sample 402


title: stimulated subject 46_case

description:
subject 46
Sample 394


title: stimulated subject 49_case

description:
subject 49
Sample 400


title: Stimulated subject 66

description:
Sample name: Sample 128
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 8

description:
Sample name: Sample 16
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 71

description:
Sample name: Sample 139
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 47_case

description:
subject 47
Sample 395


title: Baseline subject 79

description:
Sample name: Sample 155
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 48_case

description:
subject 48
Sample 397


title: stimulated subject 45_case

description:
subject 45
Sample 392


title: Stimulated subject 79

description:
Sample name: Sample 154
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 48_case

description:
subject 48
Sample 398


title: Stimulated subject 71

description:
Sample name: Sample 138
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 45_case

description:
subject 45
Sample 391


title: stimulated subject 43_case

description:
subject 43
Sample 388


title: baseline subject 62_case

description:
subject 62
Sample 414


title: baseline subject 44_case

description:
subject 44
Sample 389


title: baseline subject 46_case

description:
subject 46
Sample 393


title: stimulated subject 40_case

description:
subject 40
Sample 382


title: baseline subject 40_case

description:
subject 40
Sample 381


title: Stimulated subject 68

description:
Sample name: Sample 133
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 44_case

description:
subject 44
Sample 390


title: Baseline subject 53

description:
Sample name: Sample 103
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 38_case

description:
subject 38
Sample 377


title: Stimulated subject 11

description:
Sample name: Sample 21
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 43_case

description:
subject 43
Sample 387


title: Stimulated subject 53

description:
Sample name: Sample 102
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 68

description:
Sample name: Sample 132
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 39_case

description:
subject 39
Sample 380


title: baseline subject 37_case

description:
subject 37
Sample 375


title: stimulated subject 36_case

description:
subject 36
Sample 372


title: baseline subject 36_case

description:
subject 36
Sample 371


title: Baseline subject 66

description:
Sample name: Sample 129
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 81

description:
Sample name: Sample 159
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 81

description:
Sample name: Sample 158
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 33_case

description:
subject 33
Sample 368


title: baseline subject 34_case

description:
subject 34
Sample 369


title: Baseline subject 42

description:
Sample name: Sample 82
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 35_case

description:
subject 35
Sample 374


title: stimulated subject 37_case

description:
subject 37
Sample 376


title: Baseline subject 11

description:
Sample name: Sample 22
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 42

description:
Sample name: Sample 83
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 33_case

description:
subject 33
Sample 367


title: baseline subject 35_case

description:
subject 35
Sample 373


title: stimulated subject 32_case

description:
subject 32
Sample 366


title: stimulated subject 34_case

description:
subject 34
Sample 370


title: baseline subject 32_case

description:
subject 32
Sample 365


title: Stimulated subject 10

description:
Sample name: Sample 19
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 33

description:
Sample name: Sample 65
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 38_case

description:
subject 38
Sample 378


title: stimulated subject 27_case

description:
subject 27
Sample 364


title: baseline subject 20_case

description:
subject 20
Sample 359


title: Baseline subject 10

description:
Sample name: Sample 20
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 17_case

description:
subject 17
Sample 356


title: Baseline subject 4

description:
Sample name: Sample 7
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 17_case

description:
subject 17
Sample 355


title: baseline subject 39_case

description:
subject 39
Sample 379


title: stimulated subject 22_case

description:
subject 22
Sample 362


title: baseline subject 27_case

description:
subject 27
Sample 363


title: Baseline subject 33

description:
Sample name: Sample 64
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 5_case

description:
subject 5
Sample 346


title: baseline subject 22_case

description:
subject 22
Sample 361


title: stimulated subject 18_case

description:
subject 18
Sample 358


title: baseline subject 18_case

description:
subject 18
Sample 357


title: Stimulated subject 4

description:
Sample name: Sample 8
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 20_case

description:
subject 20
Sample 360


title: Stimulated subject 58

description:
Sample name: Sample 112
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 36

description:
Sample name: Sample 70
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 14_case

description:
subject 14
Sample 351


title: stimulated subject 13_case

description:
subject 13
Sample 350


title: baseline subject 4_case

description:
subject 4
Sample 347


title: Baseline subject 58

description:
Sample name: Sample 113
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 2_case

description:
subject 2
Sample 342


title: Stimulated subject 26

description:
Sample name: Sample 51
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 2_case

description:
subject 2
Sample 341


title: Baseline subject 19

description:
Sample name: Sample 36
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 19

description:
Sample name: Sample 37
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 1_case

description:
subject 1
Sample 340


title: Stimulated subject 20

description:
Sample name: Sample 39
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 13_case

description:
subject 13
Sample 349


title: Baseline subject 36

description:
Sample name: Sample 71
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 3_case

description:
subject 3
Sample 344


title: stimulated subject 14_case

description:
subject 14
Sample 352


title: baseline subject 5_case

description:
subject 5
Sample 345


title: baseline subject 217_control

description:
subject 217
Sample 243


title: Baseline subject 37

description:
Sample name: Sample 72
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 217_control

description:
subject 217
Sample 244


title: stimulated subject 4_case

description:
subject 4
Sample 348


title: Baseline subject 26

description:
Sample name: Sample 50
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 3_case

description:
subject 3
Sample 343


title: Stimulated subject 37

description:
Sample name: Sample 73
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 221_control

description:
subject 221
Sample 246


title: baseline subject 221_control

description:
subject 221
Sample 245


title: Stimulated subject 14

description:
Sample name: Sample 27
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 20

description:
Sample name: Sample 38
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 212_control

description:
subject 212
Sample 237


title: Stimulated subject 72

description:
Sample name: Sample 141
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 216_control

description:
subject 216
Sample 242


title: stimulated subject 214_control

description:
subject 214
Sample 240


title: baseline subject 216_control

description:
subject 216
Sample 241


title: baseline subject 1_case

description:
subject 1
Sample 339


title: Baseline subject 14

description:
Sample name: Sample 28
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 214_control

description:
subject 214
Sample 239


title: Baseline subject 72

description:
Sample name: Sample 140
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 13

description:
Sample name: Sample 26
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 206_control

description:
subject 206
Sample 234


title: stimulated subject 207_control

description:
subject 207
Sample 236


title: Stimulated subject 60

description:
Sample name: Sample 117
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 203_control

description:
subject 203
Sample 231


title: Baseline subject 35

description:
Sample name: Sample 68
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 60

description:
Sample name: Sample 116
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 61

description:
Sample name: Sample 118
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 202_control

description:
subject 202
Sample 230


title: Stimulated subject 35

description:
Sample name: Sample 69
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 206_control

description:
subject 206
Sample 233


title: Stimulated subject 13

description:
Sample name: Sample 25
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 74

description:
Sample name: Sample 144
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 61

description:
Sample name: Sample 119
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 74

description:
Sample name: Sample 145
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 25

description:
Sample name: Sample 48
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 203_control

description:
subject 203
Sample 232


title: stimulated subject 201_control

description:
subject 201
Sample 228


title: baseline subject 201_control

description:
subject 201
Sample 227


title: baseline subject 199_control

description:
subject 199
Sample 225


title: stimulated subject 212_control

description:
subject 212
Sample 238


title: Stimulated subject 25

description:
Sample name: Sample 49
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 82

description:
Sample name: Sample 161
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 38

description:
Sample name: Sample 75
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 207_control

description:
subject 207
Sample 235


title: Baseline subject 28

description:
Sample name: Sample 55
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 199_control

description:
subject 199
Sample 226


title: Stimulated subject 65

description:
Sample name: Sample 126
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 65

description:
Sample name: Sample 127
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 202_control

description:
subject 202
Sample 229


title: Stimulated subject 38

description:
Sample name: Sample 74
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 28

description:
Sample name: Sample 54
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 198_control

description:
subject 198
Sample 223


title: stimulated subject 198_control

description:
subject 198
Sample 224


title: Stimulated subject 82

description:
Sample name: Sample 160
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 5

description:
Sample name: Sample 10
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 195_control

description:
subject 195
Sample 219


title: baseline subject 196_control

description:
subject 196
Sample 221


title: stimulated subject 196_control

description:
subject 196
Sample 222


title: Stimulated subject 78

description:
Sample name: Sample 153
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 5

description:
Sample name: Sample 9
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 194_control

description:
subject 194
Sample 218


title: stimulated subject 192_control

description:
subject 192
Sample 214


title: baseline subject 194_control

description:
subject 194
Sample 217


title: Baseline subject 78

description:
Sample name: Sample 152
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 1

description:
Sample name: Sample 2
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 192_control

description:
subject 192
Sample 213


title: Baseline subject 1

description:
Sample name: Sample 1
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 191_control

description:
subject 191
Sample 212


title: stimulated subject 195_control

description:
subject 195
Sample 220


title: stimulated subject 190_control

description:
subject 190
Sample 210


title: baseline subject 190_control

description:
subject 190
Sample 209


title: Baseline subject 67

description:
Sample name: Sample 131
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 191_control

description:
subject 191
Sample 211


title: Baseline subject 17

description:
Sample name: Sample 33
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 17

description:
Sample name: Sample 32
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 67

description:
Sample name: Sample 130
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 44

description:
Sample name: Sample 87
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 188_control

description:
subject 188
Sample 206


title: baseline subject 189_control

description:
subject 189
Sample 207


title: stimulated subject 189_control

description:
subject 189
Sample 208


title: Baseline subject 15

description:
Sample name: Sample 30
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 44

description:
Sample name: Sample 86
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 57

description:
Sample name: Sample 111
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 187_control

description:
subject 187
Sample 204


title: Stimulated subject 15

description:
Sample name: Sample 29
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 57

description:
Sample name: Sample 110
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 187_control

description:
subject 187
Sample 203


title: Stimulated subject 45

description:
Sample name: Sample 89
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 186_control

description:
subject 186
Sample 202


title: baseline subject 188_control

description:
subject 188
Sample 205


title: Baseline subject 9

description:
Sample name: Sample 18
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 45

description:
Sample name: Sample 88
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 184_control

description:
subject 184
Sample 200


title: baseline subject 186_control

description:
subject 186
Sample 201


title: Stimulated subject 9

description:
Sample name: Sample 17
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 182_control

description:
subject 182
Sample 198


title: baseline subject 182_control

description:
subject 182
Sample 197


title: stimulated subject 8_control

description:
subject 8
Sample 196


title: Stimulated subject 18

description:
Sample name: Sample 35
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 8_control

description:
subject 8
Sample 195


title: Stimulated subject 46

description:
Sample name: Sample 90
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 46

description:
Sample name: Sample 91
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 18

description:
Sample name: Sample 34
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 56

description:
Sample name: Sample 109
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 210_control

description:
subject 210
Sample 192


title: Baseline subject 73

description:
Sample name: Sample 143
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 184_control

description:
subject 184
Sample 199


title: Gemcitabine-resistant PANC-1_biological  p23_3

city: Muenster

first: Sameer

last: Dhayat

address: Albert-Schweitzer-Campus 1 ( W1)

institute: Comprehensive Cancer Center Muenster

hyb_protocol: The original manufacturer´s (Affymetrix/Genisphere) protocol (FlashTag  Biotin HSR RNA) was used.

scan_protocol: The Affymetrix GeneChip System Scanner 3000 7G and the recommended scanning procedure für the performed arrays were used.

data_processing:
Partek´s Genomics Suite, miRNA workflow
Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish

source_name: PANC-1 with 17 cycles gemcitabine treatment

growth_protocol: PANC-1 cells were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM; Lonza, Walkersville, USA) supplemented with 10% heat inactivated fetal calf serum (Gibco, Carlsbad, USA), 2mM L-glutamine (Gibco), and 1mM sodium pyruvate (Sigma, St. Louis, USA) in a humidified incubator containing 95% air and 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from parental and chemoresistant PDAC cell lines using Trizol reagent (Qiagen, Hilden, Germany) and miRNeasy Mini Kits (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Gemcitabine-resistant PANC-1 (PANC-1-GR) cell clones were produced by exposing the parental cells to repeated pulsatile gemcitabine treatment over 3 days with constant sublethal concentrations followed by recovery-periods with agent-free medium until the cells recovered exponentially. Parental PANC-1 cells were treated with 0.4µM gemcitabine cycles for approximately 9 months.

tag: cell line background

tag: cell type

value: mutant p53 human pancreatic adenocarcinoma cell line

tag: cell clone

tag: cell subtype

value: Gemcitabine-resistant variants of PANC-1

tag: treated with

value: 17 cycles gemcitabine treatment

tag: morphology

value: plump rounded morphology and enhanced formation of pseudopodia


title: baseline subject 139_control

description:
subject 139
Sample 193

value: baseline


title: stimulated subject 139_control

description:
subject 139
Sample 194


title: Gemcitabine-resistant PANC-1_biological  p23_4

label_protocol: The original manufacturer´s (Affymetrix/Genisphere) protocol (FlashTag  Biotin HSR RNA) was used.


title: Gemcitabine-resistant PANC-1_biological  p23_2


title: Stimulated subject 56

description:
Sample name: Sample 108
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: subject

tag: disease state

tag: age

tag: dna methylation-predicted age

tag: treatment


title: parental PANC-1_biological  p23_2

source_name: PANC-1 without gemcitabine treatment

value: spindle-shaped cells


title: parental PANC-1_biological  p23_4


title: Baseline subject 63

description:
Sample name: Sample 122
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

value: female

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells


title: baseline subject 120_control

description:
subject 120
Sample 190

tag: tissue

tag: stimulus

tag: sample type


title: Stimulated subject 34

description:
Sample name: Sample 67
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: gender

tag: b cells

tag: monocytes

tag: granulocytes


title: Gemcitabine-resistant PANC-1_biological  p23_1

tag: cell line background

tag: cell type

tag: cell clone

tag: cell subtype

tag: treated with