title: BJ_H3K4me1_PreFOXA2

status: Public on Feb 03 2018

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

library_source: genomic

data_processing:
Sequencing read were aligned to human genome (hg19) using bowtie with default parameters
Peaks for TF ChIPs were called using MACS2 and IDR framework.
IDR called FOXA2 peaks from several tissues were further processed using in-house pipeline. Peaks from different cells were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for all TFs, histone marks as well as ATAC signal
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with coordinates and RPKM.

molecule: genomic DNA

source_name: BJ Fibroblasts

growth_protocol: Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001).  Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF.  Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

treatment_protocol: To induce FOXA2, doxycycline was added at .5ug/mL. Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night.

tag: cell line

value: BJ Fibroblast

tag: chip antibody

tag: chip antibody info.

value: Active Motif 39297, Lot 21008001


title: BJ_H3K4me1

type: SRA

city: Cambridge

country: USA

organism: Homo sapiens


title: d0_4 (scRNA-Seq)

status: Public on Feb 15 2018

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description:
Fluidigm C1
GEN00026740

library_source: transcriptomic

data_processing:
alignment TopHat v2.0.12
subRead featureCounts v1.4.6
For single cell RNA-seq data quality control, we removed those genes that had zero expression in all single cells.
Supplementary_files_format_and_content: gene expression RPKM as tab-delimited text file

molecule: total RNA

source_name: undifferentiated hESC

growth_protocol: hESCs are routinely maintained in E8 medium (Stem Cell Technologies). For differentiation, Advanced RPMI 1640 (Gibco) was supplemented with l-glutamine and antibiotics, with Activin A (R & D Systems) and CHIR99021 (Tocris) added to specified concentrations and time.

extract_protocol:
Single-cell whole transcriptome amplification (WTA) was performed using the Fluidigm C1 Single-Cell Auto Prep System (C1 System) as per the manufacturer’s recommendations (full details available at Fluidigm.com). Briefly, cells from each time point were single cell collected with Accutase and were resuspended at a concentration of 250 cell per μL of complete media, mixed 7:3 with C1 suspension reagent (Fluidigm), and loaded onto C1 Single-Cell Auto Prep chips (C1 chips; Fluidigm). After loading, each of the cell isolation chambers on the C1 chip was optically inspected for the presence of a cell. Subsequently, these cells were lysed and SMART-Seq (Ramskold et al., 2012) whole transcriptome amplified (WTA) products were prepared with the C1 System using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) and protocols provided by Fluidigm.
WTA products were harvested from the C1 chip, diluted to a concentration of 0.15 ng/μL, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per the manufacturer’s recommendations. Finally, samples were sequenced deeply using either a HiSeq 2500 sequencer (50 bp paired-end reads).

tag: cell type

value: hESC

tag: protocol

value: undifferentiated hESC

tag: time


title: d0_1 (scRNA-Seq)

description:
Fluidigm C1
GEN00026736


title: 1-6_8830.R1

status: Public on Jan 26 2018

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description: ChIP-seq ChIPmentation DNA

data_processing:
Library strategy: ChIPmentation
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 (ChIP) or TopHat2 (RNA)
count reads with htseq-count
call peaks with MACS2
normalize sample with deeptools
Genome_build: Mus Musculus (mm10)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
bedgraph file with normalized mapped signal (ChIP)
narrowpeak / bed files with the called peaks (macs2)

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was extracted from tissue and cells using either the illustra RNAspin Mini Kit (GE Healthcare Life Sciences) or the Maxwell 16 LEV Simply RNA purification kit (Promega) as per manufacturers instructions.  RIN > 9.0
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: spleen

value: HOXA9 Sigma Atlas Antibodies Cat#HPA061982 Lot#86503

tag: sample type

value: T-ALL - JAK3+HOXA9 - HOXA9 ChIP


title: 1-4_8828.R1

description: ChIP-seq ChIPmentation DNA

value: Cat#39297 Active Motif Lot#01714002

value: T-ALL - JAK3+HOXA9 -H3K4me1 ChIP


title: 1-2_8826.R1

description: ChIP-seq ChIPmentation DNA

value: H3K27me3 Cat#39155 Active Motif Lot#06517018

value: T-ALL - JAK3+HOXA9 - H3K27me3 ChIP


title: M049-input.R1

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3 - input ChIP


title: M049-H3K27me3.R1

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3 - H3K27me3 ChIP


title: M254_STAT5_CST

description: ChIP-seq ChIPmentation DNA

value: Cell Signaling Cat#8363 Lot9

value: T-ALL - JAK3+HOXA9 - STAT5 ChIP


title: M049-H3K27ac.R1

description: ChIP-seq ChIPmentation DNA

value: H3K27Ac Cat#39134 Active Motif Lot#20017009

value: T-ALL - JAK3 - H3K27ac ChIP


title: 1-3_8827.R1

description: ChIP-seq ChIPmentation DNA

value: H3K4me3 Cat#39159 Active Motif Lot#15617005

value: T-ALL - JAK3+HOXA9 - H3K4me3 ChIP


title: 1-1_8825.R1

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3+HOXA9 - H3K27ac ChIP


title: M049-H3K4me3.R1

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3 - H3K4me3 ChIP


title: M049-H3K4me1.R1

description: ChIP-seq ChIPmentation DNA

value: spleen

value: T-ALL - JAK3 - H3K4me1 ChIP


title: MLR_PB

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 (ChIP) or TopHat2 (RNA)
count reads with htseq-count
call peaks with MACS2
normalize sample with deeptools
Genome_build: Mus Musculus (mm10)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
bedgraph file with normalized mapped signal (ChIP)
narrowpeak / bed files with the called peaks (macs2)

source_name: Peripheral blood

value: Peripheral blood

value: AML - JAK3(M511I)+HOXA9


title: M006_STAT5_CST

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3 - STAT5 ChIP


title: MLR_S


title: M437_sorted_AML


title: M436_sorted_AML


title: M177S

value: AML - HOXA9


title: M180S


title: M176S


title: M254

value: CD8+ T-ALL - JAK3(M511I)+HOXA9


title: M436_sorted_T-ALL


title: M006

value: CD8+ T-ALL - JAK3(M511I)


title: 1-input_8831.R1

description: ChIP-seq ChIPmentation DNA

value: T-ALL - JAK3+HOXA9 - input ChIP


title: WT1_M3

source_name: thymus

value: thymus

value: CD8+ T-cell wild type


title: M437_sorted_T-ALL

source_name: Spleen

value: Spleen


title: M420_sorted_T-ALL


title: WT1_M1


title: M223


title: M420_sorted_AML


title: M179S


title: WT1_M2


title: HeLa_PPIH77_gene_rep2

status: Public on Dec 31 2017

type: RNA

city: Philadelphia

first: Tara

last: Davis

state: PA

department: Biochemistry and Molecular Biology

institute: Drexel University College of Medicine

hyb_protocol: Hybridization was conducted by the Molecular Profiling Facility at the University of Pennsylvania. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was conducted by the Molecular Profiling Facility at the University of Pennsylvania. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probeset and gene normalized data was calculated from cel files in Affymetrix Expression Console software using RMA with default parameters.

label: biotin

source_name: HeLa, PPIH77, rep2

label_protocol: Labeling was conducted by the Molecular Profiling Facility at the University of Pennsylvania. All protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: HeLa cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.

extract_protocol: total RNA was extracted and purified using the Bioline ISOLATE II kit according to manufacturer's instructions.

treatment_protocol: Cells were washed with 1X PBS before freezing in preparation for RNA extraction.

value: HeLa

tag: genotype/variation

value: PPIH knockdown


title: HeLa_SCR_gene_rep3

source_name: HeLa, SCR, rep3

value: SCR control


title: N2_rep 2

status: Public on Nov 20 2017

city: Amsterdam

first: Arwen

last: Gao

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center of Amsterdam

hyb_protocol: hybridized using the Agilent Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: An ArrayXS-200108 with WormBase WS241 genome build (OakLabs) was used and fluorescence signals were detected by the SureScan microarray Scanner (Agilent Technologies)

data_processing: Data of all samples were quantile normalized using the ranked median quantiles as described previously in Bolstad 2003 A comparison of normalization methods for high desity oligonucleotide array data based on variance and bias. Bioinformatics. 19, 185-193

organism: Caenorhabditis elegans

source_name: N2_HT115_replicate 2

label_protocol: RNA was amplified and labeled using a Low Input QuickAmp Labeling Kit (Agilent Technologies)

growth_protocol: C. elegans were routinely grown and maintained on nematode growth media (NGM) at 20ºC. Worms of each strain were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults and placed onto plates seeded with E. coli HT115. At the young adult stage, each strain was collected by washing them off the culture plates with M9 buffer and the worm pellet was washed with dH2O for three times before collection in a 2 mL Eppendorf tube, snap-frozen in liquid N2 and lyophilized overnight. For RNA extraction, 500 worms/tube was collected in four replicates per worm strain

extract_protocol: Total RNA was extracted using the standard Trizol method, followed by phenol-chloroform purification and further processing by OakLabs Gmbh (Germany);In short, RNA quality and quantity was assessed after DNase clean-up using a 2100 Bioanalyzer (Agilent Technologies). All samples had a RNA integrity value of ≥7.2

value: N2 (Bristol) wild type

value: whole worm

tag: developmental stage

value: young adult


title: N2_rep 1

source_name: N2_HT115_replicate 1


title: N2_rep 4

source_name: N2_HT115_replicate 4


title: HeLa_SCR_gene_rep1

source_name: HeLa, SCR, rep1


title: HeLa_PPIH77_gene_rep3

source_name: HeLa, PPIH77, rep3


title: subject_61-Blood-blood_97

status: Public on Jul 07 2017

city: New York

first: Eric

last: Schadt

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Gene expression were carried out using Affymetrix GeneChip HTHGU133+ (Affymetrix, Santa Clara, CA, USA Cat# 901262) according to the manufacturer’s protocol with the exception that dimethyl sulphoxide replaced the Tetramethylammonium Chloride Solution in the hybridization buffer.

scan_protocol: Arrays were washed and stained on the Affymetrix GeneChip Array Station then scanned on an HTAPS scanner.

data_processing: Array Studio software version 6.0 (OmicSoft Corp., St. Morrisville, NC) was used for data analysis. The microarray data were pre-processed and normalized using RMA. Log2 transformed data was used for statistical analysis.

label: NuGEN Encore Biotin Module

source_name: Blood

label_protocol: RNA samples were amplified by NuGEN Ovation RNA Amplification System V2 Whole Blood Solution (NuGEN, San Carlos, CA) and purified using Agencourt RNAClean magnetic beads.  Labeling was done using the NuGEN Encore Biotin Module (NuGEN). (Agencourt, Beverly, MA) on a Caliper SciClone robot.

extract_protocol: Total RNA including micro ribonucleic acids (miRNA) was isolated with PAXgene Blood RNA MDx Kit plus customized reagent BM3 (Cat#762431, lot 136237127) according to the manufacturer’s instructions (Qiagen Inc., Valencia, CA). Briefly, PAXgene Blood RNA Tubes were incubated at room temperature around 2 hrs before extraction. After centrifugation for 10 min at 3000–5000 x g, the pellet was re-suspended in 290 μl Buffer BR1 with 35 μl proteinase K. The remaining procedures were performed on a BioRobot Universal System using a customized protocol, PAXgene Blood RNA UNIV rcV73_miRNA Centocor.pro (Qiagen).

treatment_protocol: All blood samples were stored at −80 °C until RNA isolation was performed. Blood samples were hybridized by microarray for genome-wide mRNA expression profiling. Ileal, rectal, and colonic biopsies were collected at the screening visits from a sub-group of subjects who consented to this procedure. Biopsies were obtained from selected colonic sections, including the ascending, transverse, and descending colonic regions, and from both inflamed and non-involved areas. The inflamed regions were defined as the colonic segments with the most severe disease activity. Additional biopsies were collected from the terminal ileum and from the rectum (i.e., the distal 10 cm of the colon).

tag: diagnosis

value: inflammatory bowel disease

value: Blood

tag: age (yr)

tag: Sex

value: M

tag: inflammation


title: subject_223-Blood-blood_90


title: subject_146-Blood-blood_98

value: F


title: subject_366-Blood-blood_93


title: subject_252-Blood-blood_91


title: N2_rep 3

source_name: N2_HT115_replicate 3


title: subject_12-Blood-blood_92


title: HeLa_PPIH77_gene_rep1

source_name: HeLa, PPIH77, rep1


title: subject_23-Blood-blood_9


title: subject_70-Blood-blood_94


title: subject_28-Blood-blood_96


title: subject_383-Blood-blood_88


title: subject_178-Blood-blood_89


title: subject_47-Blood-blood_99


title: subject_62-Blood-blood_87


title: subject_384-Blood-blood_85


title: subject_83-Blood-blood_84


title: subject_211-Blood-blood_86


title: HeLa_SCR_gene_rep2

source_name: HeLa, SCR, rep2


title: subject_41-Blood-blood_95


title: subject_344-Blood-blood_80


title: subject_365-Blood-blood_77


title: subject_315-Blood-blood_81


title: subject_78-Blood-blood_83


title: subject_380-Blood-blood_79


title: subject_16-Blood-blood_82


title: subject_73-Blood-blood_75


title: subject_151-Blood-blood_73


title: subject_352-Blood-blood_78


title: subject_99-Blood-blood_76


title: subject_343-Blood-blood_70


title: subject_190-Blood-blood_8


title: subject_13-Blood-blood_74


title: subject_95-Blood-blood_71


title: subject_281-Blood-blood_7


title: subject_221-Blood-blood_62


title: subject_216-Blood-blood_65


title: subject_269-Blood-blood_68


title: subject_156-Blood-blood_67


title: subject_226-Blood-blood_66


title: subject_309-Blood-blood_63


title: subject_80-Blood-blood_72


title: subject_102-Blood-blood_64


title: subject_312-Blood-blood_61


title: subject_369-Blood-blood_60


title: subject_257-Blood-blood_6


title: subject_228-Blood-blood_59


title: subject_66-Blood-blood_51


title: subject_43-Blood-blood_58


title: subject_324-Blood-blood_53


title: subject_372-Blood-blood_49


title: subject_334-Blood-blood_5


title: subject_263-Blood-blood_54


title: subject_127-Blood-blood_56


title: subject_243-Blood-blood_48


title: subject_373-Blood-blood_44


title: subject_159-Blood-blood_57


title: subject_30-Blood-blood_45


title: subject_172-Blood-blood_52


title: subject_387-Blood-blood_55


title: subject_97-Blood-blood_50


title: subject_124-Blood-blood_46


title: subject_42-Blood-blood_47


title: HeLa_SCR_alt-splice_rep1


title: subject_93-Blood-blood_40


title: subject_238-Blood-blood_41


title: subject_249-Blood-blood_69


title: HeLa_PPIH77_alt-splice_rep2


title: subject_260-Blood-blood_43


title: HeLa_PPIH77_alt-splice_rep3


title: HeLa_SCR_alt-splice_rep2


title: HeLa_PPIH77_alt-splice_rep1


title: subject_217-Blood-blood_35


title: subject_239-Blood-blood_42


title: subject_259-Blood-blood_33


title: subject_340-Blood-blood_36


title: subject_339-Blood-blood_30


title: subject_215-Blood-blood_31


title: subject_67-Blood-blood_28


title: subject_318-Blood-blood_23


title: subject_191-Blood-blood_37


title: subject_123-Blood-blood_26


title: subject_40-Blood-blood_29


title: subject_244-Blood-blood_32


title: subject_386-Blood-blood_38


title: subject_185-Blood-blood_3


title: subject_129-Blood-blood_4


title: subject_317-Blood-blood_25


title: subject_272-Blood-blood_39


title: subject_326-Blood-blood_34


title: subject_328-Blood-blood_204


title: subject_192-Blood-blood_27


title: subject_194-Blood-blood_202


title: subject_170-Blood-blood_24


title: subject_314-Blood-blood_199


title: subject_27-Blood-blood_20


title: subject_169-Blood-blood_2


title: subject_51-Blood-blood_203


title: HeLa_SCR_alt-splice_rep3


title: subject_152-Blood-blood_201


title: subject_210-Blood-blood_198


title: subject_104-Blood-blood_200


title: subject_77-Blood-blood_196


title: subject_291-Blood-blood_194


title: subject_370-Blood-blood_22


title: subject_289-Blood-blood_187


title: subject_55-Blood-blood_192


title: subject_118-Blood-blood_197


title: subject_59-Blood-blood_183


title: subject_382-Blood-blood_182


title: subject_327-Blood-blood_195


title: subject_53-Blood-blood_191


title: subject_96-Blood-blood_185


title: subject_296-Blood-blood_190


title: subject_311-Blood-blood_186


title: subject_187-Blood-blood_184


title: subject_275-Blood-blood_189


title: subject_31-Blood-blood_19


title: subject_333-Blood-blood_181


title: subject_224-Blood-blood_193


title: subject_64-Blood-blood_188


title: subject_201-Blood-blood_21


title: subject_37-Blood-blood_178


title: subject_92-Blood-blood_18


title: subject_180-Blood-blood_176


title: subject_236-Blood-blood_179


title: subject_284-Blood-blood_171


title: subject_198-Blood-blood_174


title: subject_56-Blood-blood_175


title: subject_358-Blood-blood_173


title: subject_182-Blood-blood_170


title: subject_323-Blood-blood_168


title: subject_86-Blood-blood_162


title: subject_183-Blood-blood_166


title: subject_220-Blood-blood_167


title: subject_32-Blood-blood_172


title: subject_197-Blood-blood_156


title: subject_336-Blood-blood_180


title: subject_143-Blood-blood_177


title: subject_371-Blood-blood_17


title: subject_137-Blood-blood_169


title: subject_82-Blood-blood_159


title: subject_235-Blood-blood_165


title: subject_278-Blood-blood_163


title: subject_119-Blood-blood_161


title: subject_248-Blood-blood_155


title: subject_63-Blood-blood_157


title: subject_105-Blood-blood_150


title: subject_72-Blood-blood_160


title: subject_68-Blood-blood_149


title: subject_313-Blood-blood_16


title: subject_268-Blood-blood_153


title: subject_76-Blood-blood_154


title: subject_17-Blood-blood_144


title: subject_245-Blood-blood_164


title: subject_285-Blood-blood_142


title: subject_287-Blood-blood_143


title: subject_148-Blood-blood_138


title: subject_132-Blood-blood_141


title: subject_46-Blood-blood_145


title: subject_290-Blood-blood_152


title: subject_306-Blood-blood_148


title: subject_219-Blood-blood_151


title: subject_283-Blood-blood_147


title: subject_29-Blood-blood_14


title: subject_135-Blood-blood_146


title: subject_164-Blood-blood_137


title: subject_101-Blood-blood_136


title: subject_255-Blood-blood_133


title: subject_294-Blood-blood_134


title: subject_65-Blood-blood_158


title: subject_166-Blood-blood_15


title: subject_300-Blood-blood_130


title: subject_117-Blood-blood_140


title: subject_246-Blood-blood_139


title: subject_179-Blood-blood_125


title: subject_109-Blood-blood_127


title: subject_360-Blood-blood_120


title: subject_188-Blood-blood_119


title: subject_71-Blood-blood_132


title: subject_116-Blood-blood_135


title: subject_142-Blood-blood_126


title: subject_21-Blood-blood_123


title: subject_237-Blood-blood_124


title: subject_69-Blood-blood_122


title: subject_5-Blood-blood_129


title: subject_331-Blood-blood_13


title: subject_150-Blood-blood_121


title: subject_250-Blood-blood_131


title: subject_39-Blood-blood_12


title: subject_181-Blood-blood_113


title: subject_367-Blood-blood_117


title: subject_176-Blood-blood_107


title: subject_3-Blood-blood_111


title: subject_94-Blood-blood_112


title: subject_100-Blood-blood_110


title: subject_160-Blood-blood_118


title: subject_88-Blood-blood_109


title: subject_264-Blood-blood_115


title: subject_74-Blood-blood_128


title: subject_295-Blood-blood_108


title: subject_128-Blood-blood_114


title: subject_34-Blood-blood_11


title: subject_288-Blood-blood_106


title: subject_286-Blood-blood_116


title: subject_18-Blood-blood_104


title: subject_225-Blood-blood_102


title: subject_305-Blood-blood_101


title: subject_337-Blood-blood_103


title: subject_364-Blood-blood_100


title: subject_85-Rectum-biopsy_95

source_name: Rectum

value: Rectum

value: Non-involved area


title: subject_61-Rectum-biopsy_96

value: Inflamed area


title: subject_115-Blood-blood_1


title: subject_43-Terminal Ileum-biopsy_97

source_name: Terminal Ileum

value: Terminal Ileum


title: subject_85-Blood-blood_105


title: subject_21-Rectum-biopsy_94


title: subject_219-Rectum-biopsy_98


title: subject_23-Terminal Ileum-biopsy_93


title: subject_62-Not Collected-biopsy_9

source_name: Not Collected

value: Not Collected

value: N/A (Sample not received)


title: subject_71-Rectum-biopsy_99


title: subject_371-Rectum-biopsy_89


title: subject_33-Descending colon-biopsy_92

source_name: Descending colon

value: Descending colon


title: subject_100-Rectum-biopsy_91


title: subject_288-Descending colon-biopsy_85


title: subject_289-Descending colon-biopsy_90


title: subject_181-Sigmoid colon-biopsy_87

source_name: Sigmoid colon

value: Sigmoid colon


title: subject_84-Terminal Ileum-biopsy_84


title: subject_24-Rectum-biopsy_88


title: subject_32-Ascending colon-biopsy_86

source_name: Ascending colon

value: Ascending colon


title: subject_72-Rectum-biopsy_80


title: subject_69-Rectum-biopsy_81


title: subject_24-Ascending colon-biopsy_8


title: subject_98-Terminal Ileum-biopsy_78


title: subject_83-Terminal Ileum-biopsy_79


title: subject_94-Terminal Ileum-biopsy_83


title: subject_95-Terminal Ileum-biopsy_82


title: subject_2-Blood-blood_10


title: subject_39-Sigmoid colon-biopsy_77


title: subject_38-Transverse colon-biopsy_72

source_name: Transverse colon

value: Transverse colon


title: subject_45-Terminal Ileum-biopsy_76


title: subject_286-Rectum-biopsy_71


title: subject_368-Terminal Ileum-biopsy_70


title: subject_41-Transverse colon-biopsy_66


title: subject_179-Rectum-biopsy_74


title: subject_281-Rectum-biopsy_67


title: subject_36-Rectum-biopsy_73


title: subject_1-Terminal Ileum-biopsy_69


title: subject_232-Descending colon-biopsy_68


title: subject_127-Ascending colon-biopsy_7


title: subject_53-Terminal Ileum-biopsy_64


title: subject_59-Ascending colon-biopsy_62


title: subject_12-Rectum-biopsy_61


title: subject_5-Rectum-biopsy_65


title: subject_32-Rectum-biopsy_59


title: subject_219-Sigmoid colon-biopsy_58


title: subject_13-Rectum-biopsy_60


title: subject_53-Transverse colon-biopsy_63


title: subject_220-Sigmoid colon-biopsy_57


title: subject_229-Terminal Ileum-biopsy_6


title: subject_235-Sigmoid colon-biopsy_55


title: subject_54-Terminal Ileum-biopsy_75


title: subject_235-Descending colon-biopsy_54


title: subject_71-Descending colon-biopsy_56


title: subject_34-Ascending colon-biopsy_5


title: subject_235-Rectum-biopsy_52


title: subject_221-Sigmoid colon-biopsy_47


title: subject_30-Ascending colon-biopsy_45


title: subject_101-Transverse colon-biopsy_46


title: subject_291-Transverse colon-biopsy_48


title: subject_291-Rectum-biopsy_50


title: subject_291-Rectum-biopsy_49


title: subject_235-Terminal Ileum-biopsy_53


title: subject_290-Transverse colon-biopsy_44


title: subject_290-Rectum-biopsy_42


title: subject_70-Transverse colon-biopsy_39


title: subject_290-Ascending colon-biopsy_40


title: subject_16-Transverse colon-biopsy_38


title: subject_290-Terminal Ileum-biopsy_43


title: subject_371-Ascending colon-biopsy_4


title: subject_368-Descending colon-biopsy_36


title: subject_219-Terminal Ileum-biopsy_326


title: subject_286-Transverse colon-biopsy_35


title: subject_83-Ascending colon-biopsy_322


title: subject_125-Transverse colon-biopsy_324


title: subject_98-Ascending colon-biopsy_327


title: subject_66-Transverse colon-biopsy_315


title: subject_130-Ascending colon-biopsy_320


title: subject_76-Ascending colon-biopsy_321


title: subject_179-Ascending colon-biopsy_328


title: subject_76-Transverse colon-biopsy_323


title: subject_291-Ascending colon-biopsy_37


title: subject_99-Ascending colon-biopsy_329


title: subject_13-Transverse colon-biopsy_32


title: subject_12-Transverse colon-biopsy_33


title: subject_35-Ascending colon-biopsy_325


title: subject_76-Descending colon-biopsy_318


title: subject_5-Descending colon-biopsy_34


title: subject_290-Descending colon-biopsy_41


title: subject_76-Rectum-biopsy_319


title: subject_66-Rectum-biopsy_316


title: subject_372-Rectum-biopsy_308


title: subject_66-Terminal Ileum-biopsy_314


title: subject_31-Terminal Ileum-biopsy_311


title: subject_31-Rectum-biopsy_317


title: subject_372-Transverse colon-biopsy_310


title: subject_372-Terminal Ileum-biopsy_309


title: subject_31-Ascending colon-biopsy_312


title: subject_82-Transverse colon-biopsy_304


title: subject_31-Transverse colon-biopsy_313


title: subject_34-Terminal Ileum-biopsy_306


title: subject_41-Rectum-biopsy_31


title: subject_130-Rectum-biopsy_303


title: subject_372-Sigmoid colon-biopsy_300


title: subject_130-Terminal Ileum-biopsy_301


title: subject_40-Terminal Ileum-biopsy_307


title: subject_53-Sigmoid colon-biopsy_30


title: subject_130-Descending colon-biopsy_302


title: subject_373-Transverse colon-biopsy_297


title: subject_373-Ascending colon-biopsy_296


title: subject_183-Rectum-biopsy_287


title: subject_128-Terminal Ileum-biopsy_298


title: subject_183-Ascending colon-biopsy_290


title: subject_30-Terminal Ileum-biopsy_305


title: subject_17-Rectum-biopsy_285


title: subject_55-Terminal Ileum-biopsy_29


title: subject_181-Ascending colon-biopsy_3


title: subject_183-Transverse colon-biopsy_291


title: subject_373-Rectum-biopsy_293


title: subject_102-Rectum-biopsy_288


title: subject_373-Sigmoid colon-biopsy_292


title: subject_88-Terminal Ileum-biopsy_294


title: subject_183-Sigmoid colon-biopsy_286


title: subject_183-Terminal Ileum-biopsy_289


title: subject_373-Terminal Ileum-biopsy_295


title: subject_128-Rectum-biopsy_299


title: subject_88-Rectum-biopsy_284


title: subject_229-Transverse colon-biopsy_51


title: subject_122-Ascending colon-biopsy_278


title: subject_94-Terminal Ileum-biopsy_283


title: subject_17-Ascending colon-biopsy_281


title: subject_17-Ascending colon-biopsy_279


title: subject_220-Terminal Ileum-biopsy_276


title: subject_17-Terminal Ileum-biopsy_280


title: subject_73-Ascending colon-biopsy_277


title: subject_36-Ascending colon-biopsy_273


title: subject_18-Descending colon-biopsy_28


title: subject_18-Rectum-biopsy_269


title: subject_124-Ascending colon-biopsy_275


title: subject_12-Descending colon-biopsy_265


title: subject_5-Transverse colon-biopsy_267


title: subject_72-Sigmoid colon-biopsy_260


title: subject_59-Rectum-biopsy_262


title: subject_37-Transverse colon-biopsy_26


title: subject_32-Descending colon-biopsy_268


title: subject_41-Terminal Ileum-biopsy_259


title: subject_53-Rectum-biopsy_258


title: subject_88-Sigmoid colon-biopsy_282


title: subject_55-Terminal Ileum-biopsy_257


title: subject_38-Sigmoid colon-biopsy_274


title: subject_289-Terminal Ileum-biopsy_270


title: subject_54-Descending colon-biopsy_272


title: subject_37-Descending colon-biopsy_263


title: subject_5-Sigmoid colon-biopsy_266


title: subject_45-Ascending colon-biopsy_271


title: subject_32-Transverse colon-biopsy_27


title: subject_69-Descending colon-biopsy_261


title: subject_13-Sigmoid colon-biopsy_264


title: subject_229-DELETED-biopsy_256

source_name: DELETED

value: DELETED


title: subject_71-Sigmoid colon-biopsy_253


title: subject_369-Ascending colon-biopsy_255


title: subject_230-Terminal Ileum-biopsy_254


title: subject_220-Rectum-biopsy_252


title: subject_221-Rectum-biopsy_251


title: subject_231-Descending colon-biopsy_250


title: subject_282-Descending colon-biopsy_244


title: subject_1-Rectum-biopsy_247


title: subject_54-Rectum-biopsy_243


title: subject_281-Descending colon-biopsy_245


title: subject_232-Transverse colon-biopsy_246


title: subject_97-Rectum-biopsy_241


title: subject_286-Descending colon-biopsy_249


title: subject_122-Descending colon-biopsy_237


title: subject_74-Descending colon-biopsy_234


title: subject_73-Descending colon-biopsy_242


title: subject_368-Rectum-biopsy_248


title: subject_1-Ascending colon-biopsy_24


title: subject_70-Ascending colon-biopsy_235


title: subject_39-Sigmoid colon-biopsy_239


title: subject_287-Descending colon-biopsy_231


title: subject_123-Sigmoid colon-biopsy_233


title: subject_230-Transverse colon-biopsy_25


title: subject_284-Descending colon-biopsy_232


title: subject_12-Ascending colon-biopsy_230


title: subject_370-Sigmoid colon-biopsy_236


title: subject_13-Ascending colon-biopsy_240


title: subject_230-Rectum-biopsy_23


title: subject_45-Rectum-biopsy_238


title: subject_94-Rectum-biopsy_228


title: subject_35-Rectum-biopsy_223


title: subject_84-Rectum-biopsy_229


title: subject_80-Terminal Ileum-biopsy_227


title: subject_36-Transverse colon-biopsy_214


title: subject_36-Sigmoid colon-biopsy_222


title: subject_83-Rectum-biopsy_225


title: subject_82-Terminal Ileum-biopsy_226


title: subject_98-Rectum-biopsy_224


title: subject_291-Terminal Ileum-biopsy_21


title: subject_99-Terminal Ileum-biopsy_220


title: subject_70-Descending colon-biopsy_217


title: subject_281-Ascending colon-biopsy_209


title: subject_369-Transverse colon-biopsy_22


title: subject_179-Sigmoid colon-biopsy_219


title: subject_125-Rectum-biopsy_216


title: subject_179-Transverse colon-biopsy_211


title: subject_125-Terminal Ileum-biopsy_218


title: subject_38-Ascending colon-biopsy_210


title: subject_35-Transverse colon-biopsy_215


title: subject_73-Transverse colon-biopsy_208


title: subject_98-Sigmoid colon-biopsy_213


title: subject_54-Ascending colon-biopsy_204


title: subject_39-Transverse colon-biopsy_206


title: subject_97-Transverse colon-biopsy_207


title: subject_45-Descending colon-biopsy_205


title: subject_38-Rectum-biopsy_221


title: subject_99-Rectum-biopsy_212


title: subject_69-Transverse colon-biopsy_202


title: subject_231-Ascending colon-biopsy_199


title: subject_68-Ascending colon-biopsy_200


title: subject_59-Descending colon-biopsy_203


title: subject_281-Transverse colon-biopsy_20


title: subject_72-Transverse colon-biopsy_201


title: subject_56-Terminal Ileum-biopsy_198


title: subject_80-Rectum-biopsy_197


title: subject_84-Descending colon-biopsy_191


title: subject_82-Rectum-biopsy_193


title: subject_95-Sigmoid colon-biopsy_195


title: subject_232-Terminal Ileum-biopsy_194


title: subject_83-Transverse colon-biopsy_192


title: subject_100-Transverse colon-biopsy_2


title: subject_40-Transverse colon-biopsy_184


title: subject_101-Rectum-biopsy_183


title: subject_24-Sigmoid colon-biopsy_188


title: subject_34-Transverse colon-biopsy_180


title: subject_100-Descending colon-biopsy_187


title: subject_94-Sigmoid colon-biopsy_196


title: subject_181-Transverse colon-biopsy_186


title: subject_282-Transverse colon-biopsy_19


title: subject_16-Descending colon-biopsy_182


title: subject_288-Transverse colon-biopsy_185


title: subject_30-Transverse colon-biopsy_178


title: subject_371-Sigmoid colon-biopsy_189


title: subject_68-Sigmoid colon-biopsy_181


title: subject_33-Ascending colon-biopsy_18


title: subject_289-Transverse colon-biopsy_190


title: subject_127-Descending colon-biopsy_179


title: subject_284-Transverse colon-biopsy_177


title: subject_287-Transverse colon-biopsy_176


title: subject_74-Transverse colon-biopsy_171


title: subject_124-Terminal Ileum-biopsy_172


title: subject_370-Transverse colon-biopsy_175


title: subject_221-Terminal Ileum-biopsy_17


title: subject_122-Transverse colon-biopsy_174


title: subject_61-Sigmoid colon-biopsy_169


title: subject_123-Transverse colon-biopsy_173


title: subject_33-Transverse colon-biopsy_165


title: subject_85-Descending colon-biopsy_168


title: subject_21-Descending colon-biopsy_167


title: subject_21-Descending colon-biopsy_166


title: subject_24-Terminal Ileum-biopsy_162


title: subject_40-Sigmoid colon-biopsy_161


title: subject_181-Rectum-biopsy_160


title: subject_43-Rectum-biopsy_170


title: subject_21-Rectum-biopsy_164


title: subject_288-Rectum-biopsy_159


title: subject_85-Ascending colon-biopsy_16


title: subject_68-Terminal Ileum-biopsy_156


title: subject_127-Terminal Ileum-biopsy_153


title: subject_71-Terminal Ileum-biopsy_154


title: subject_34-Sigmoid colon-biopsy_157


title: subject_371-Terminal Ileum-biopsy_163


title: subject_70-Terminal Ileum-biopsy_155


title: subject_16-Terminal Ileum-biopsy_151


title: subject_289-Rectum-biopsy_158


title: subject_287-Rectum-biopsy_150


title: subject_30-Rectum-biopsy_152


title: subject_43-Descending colon-biopsy_15


title: subject_61-Terminal Ileum-biopsy_143


title: subject_122-Rectum-biopsy_147


title: subject_123-Rectum-biopsy_146


title: subject_370-Rectum-biopsy_149


title: subject_56-Terminal Ileum-biopsy_148


title: subject_284-Rectum-biopsy_145


title: subject_74-Rectum-biopsy_144


title: subject_21-Terminal Ileum-biopsy_139


title: subject_100-Terminal Ileum-biopsy_141


title: subject_33-Rectum-biopsy_138


title: subject_21-Ascending colon-biopsy_14


title: subject_287-Terminal Ileum-biopsy_135


title: subject_21-Terminal Ileum-biopsy_140


title: subject_284-Terminal Ileum-biopsy_136


title: subject_36-Terminal Ileum-biopsy_134


title: subject_73-Terminal Ileum-biopsy_132


title: subject_123-Terminal Ileum-biopsy_137


title: subject_370-Terminal Ileum-biopsy_131


title: subject_85-Terminal Ileum-biopsy_142


title: subject_181-Terminal Ileum-biopsy_129


title: subject_33-Terminal Ileum-biopsy_130


title: subject_39-Rectum-biopsy_133


title: subject_71-Ascending colon-biopsy_126


title: subject_74-Terminal Ileum-biopsy_127


title: subject_288-Terminal Ileum-biopsy_128


title: subject_286-Terminal Ileum-biopsy_123


title: subject_370-Ascending colon-biopsy_13


title: subject_232-Rectum-biopsy_120


title: subject_5-Terminal Ileum-biopsy_122


title: subject_80-Ascending colon-biopsy_125


title: subject_282-Terminal Ileum-biopsy_124


title: subject_287-Ascending colon-biopsy_12


title: subject_72-Terminal Ileum-biopsy_116


title: subject_179-Terminal Ileum-biopsy_115


title: subject_72-Ascending colon-biopsy_117


title: subject_12-Terminal Ileum-biopsy_118


title: Diploid_20

status: Public on Jul 06 2017

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Library strategy: HiC-seq
Standard Illumina base-calling pipeline.
Sequence processing pipeline  Paired-end reads of sequencing batches were de-multiplexed to single cell datasets based on the two 8 bp unique identification tags attached to each cell during the Tn5-transposase tagmentation. Reads lacking a perfect match were discarded. Reads were broken down to segments on their matches to the MboI recognition site (GATC), concatenating segments shorter than 16 bp with their adjacent segment. Each segment was independently mapped to the Mus Musculus genome (assembly mm9) using Bowtie2 in end-to-end alignment mode. The uniquely mapped (MAPQ > 36) segments from each paired-end read were consolidated into a chain of segments by merging segments mapped to overlapping genomic regions. Next, the segments chain was translated to a chain of fragment-ends (fends) by associating each segment with its downstream fend. Finally, adjacent fend pairs from all chains were used to comprise the contact map of the cell. All the analysis following used the distinct contacts, ignoring the number of times each contact appeared in the map.
Genome_build: mm9

source_name: Diploid F1 Mus musculus hybrid ESC cell line from an intercross of 129/SV-Jae and castaneus

growth_protocol: Two mouse ESC lines were used. One diploid F1 hybrid ESC from an intercross of Mus musculus 129/SV-Jae and Mus musculus castaneus (129 x Castaneus, a gift from Joost Gribnau) and one haploid ESC20 (H129-1; ECACC 14040203, gift from Martin Leeb and Anton Wutz) were grown either in 2i medium without feeder cells or ES-DMEM with fetal bovine serum (FBS) on feeder cells21. Both cells lines were tested for mycoplasma contamination.

extract_protocol:
For harvesting ESCs from cultures on feeder cells, the feeder cells were depleted using Feeder Removal MicroBeads (Miltenyi Biotec), followed by fixation and permeabilisation of the enriched ESCs and staining for Oct-3/4-immunoreactivity as described below, and Oct-3/4-positive cells were collected by Fluorescence-activated cell sorting (FACS), were ready for subsequent Hi-C processing.    To fix the cells, 50 to 200 million ESCs were suspended in relevant medium and fixed for 10 min by adding formaldehyde at a final concentration of 2% at room temperature before quenching with 127 mM glycine for 5 min on ice. The cells were washed with PBS and permeabilised in 10 mM Tris-HCl (pH 8), 10 mM NaCl, 0.2% IGEPAL CA-630 with cOmplete EDTA-free protease inhibitor cocktail (Roche) for 30 min on ice with intermittent agitation, and spun to collect the nuclei pellet, which was ready for Hi-C processing.    To enrich for specific cell types before the Hi-C process, cells were blocked with PBS-FT (5% FBS, 0.1% Tween-20 in PBS) at room temperature for 1 hr, incubated with a primary antibody in PBS-FT as required (anti-Oct3/4, Santa-Cruz sc-5279, at 1:100 dilution; or anti-Geminin, Abcam 175799 at 1:400 dilution) for 1 hr on ice. Samples were then washed with PBS-FT, and incubated with the secondary antibodies (Alexa Fluor 647-anti-mouse IgG, Thermo Fisher A-31571, or Alexa Fluor 555-anti-rabbit IgG, Thermo Fisher A-21428) for 30 min on ice, washed with 2% FBS in PBS, stained with Hoechst 33342 at the final concentration of 15 µg/ml and subjected to FACS by Influx (BD Biosciences) to collect nuclei cells of interest.
Hi-C processing  The cells (approximately half million to several million) were washed with 1.24 x NEBuffer 3 (New England Biolabs; 62 mM Tris-HCl [pH 7.9], 124 mM NaCl, 12.4 mM MgCl2, 1.24 mM DTT) and suspended in 400 µl of 1.24 x NEBuffer 3. Six µl of 20% SDS was added and incubated at 37˚C for 60 min with constant agitation, then 40 µl of 20% Triton X-100 was added and incubated at 37˚C for 60 min with constant agitation. Next, 50 µl of 25 U/µl Mbo I (New England Biolabs) was added and incubated at 37˚C overnight with constant agitation. To label the digested DNA ends, 1.56 µl of 10 mM dCTP, 1.56 µl of 10 mM dGTP, 1.56 µl of 10 mM dTTP, 39 µl of 0.4 mM biotin-14-dATP (Thermo Fisher) and 10.4 µl of 5 U/µl DNA polymerase I, large (Klenow) fragment (New England Biolabs) were added and incubated at 37˚C for 45 min with occasional mixing. The sample was then spun and supernatant partially removed leaving 50 µl with cells, followed by addition of 100 µl of 10x T4 DNA ligase reaction buffer (New England Biolabs), 10 µl of 100x BSA (New England Biolabs), water and 10 µl of 1 U/µl T4 DNA ligase (Thermo Fisher) were added to make the total volume 1 ml, and incubated at 16˚C overnight. Then the nuclei were passed through a 30 µm cell strainer and single nuclei were sorted into individual empty wells in 96 well plates using an Influx cell sorter. The plates were sealed and stored at -80˚C until further processing.    Single-cell Hi-C library preparation  To prepare single-cell Hi-C libraries from single nuclei in 96 well plate, 5 µl of PBS was added to each well, the plate was sealed and crosslinks reversed by incubating at 65˚C overnight. Hi-C concatemer DNA was fragmented and linked with sequencing adapters using the Nextera XT DNA Library Preparation Kit (Illumina), by adding 10 µl of Tagment DNA Buffer and 5 µl of Amplicon Tagment Mix, incubating at 55˚C for 5 min, then cooling down to 10˚C, followed by addition 5 µl of Neutralize Tagment Buffer and incubation for 5 min at room temperature. Hi-C ligation junctions were then captured by Dynabeads M-280 streptavidin beads (Thermo Fisher; 20 µl of original suspension per single-cell sample). Beads were prepared by washing with 1 x BW buffer (5 mM Tris-Cl pH 7.5, 0.5 mM EDTA, 1 M NaCl), resuspended in 4 x BW buffer (20 mM Tris-Cl pH 7.5, 2 mM EDTA, 4 M NaCl; 8 µl per sample), and then mixed with the 25 µl sample and incubated at room temperature overnight with gentle agitation. Using a Bravo automated liquid handling system (Agilent Technologies), the beads were then washed four times with 200 µl of 1 x BW buffer, twice with 200 µl of 10 mM Tris-Cl pH 7.5 at room temperature, and resuspended in 25 µl of 10 mM Tris-Cl pH 7.5. Single-cell Hi-C libraries were amplified from the beads by adding 15 µl of Nextera PCR Master Mix, 5 µl of Index 1 primer of choice and 5 µl of Index 2 primer of choice. Samples were then incubated at 72˚C for 3 min, 95˚C for 30 sec followed by the thermal cycling at 95˚C for 10 sec, 55˚C for 30 sec and 72˚C for 30 sec for 12 or 18 cycles, then incubated at 72˚C for 5 min. The supernatant was separated from the beads, and the 96 supernatants from a 96 well plate that had 12 cycles of amplification were combined together whereas the supernatants from 18 cycles of amplification were processed uncombined. The combined or uncombined supernatant was purified with AMPure XP beads (Beckman Coulter; 0.6 times volume of the supernatant) according to manufacturer's instructions and eluted with 10 mM Tris-Cl pH 8.5 (100 µl when 96 samples were combined; 30 µl when sample was uncombined). The eluate was purified once more with AMPure XP beads (equal volume to the previous eluate) and eluted with 11 µl of 10 mM Tris-Cl pH 8.5.


title: subject_281-Terminal Ileum-biopsy_119


title: subject_30-Descending colon-biopsy_110


title: subject_37-Terminal Ileum-biopsy_112


title: subject_231-Terminal Ileum-biopsy_121


title: subject_34-Descending colon-biopsy_106


title: subject_68-Rectum-biopsy_104


title: subject_231-Rectum-biopsy_101


title: subject_40-Descending colon-biopsy_107


title: mirMM.375-MM95db

status: Public on Feb 10 2017

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: microRNA expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Newly-diagnosed MM patient 375

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: multiple myeloma

value: primary tumor

tag: t(4;14) translocation

value: y


title: mirMM.310-MM95db

source_name: Newly-diagnosed MM patient 310

value: n


title: mirMM.313-MM95db

source_name: Newly-diagnosed MM patient 313


title: mirMM.335-MM95db

source_name: Newly-diagnosed MM patient 335


title: mirMM.392-MM95db

source_name: Newly-diagnosed MM patient 392


title: mirMM.302-MM95db

source_name: Newly-diagnosed MM patient 302


title: mirMM.406-MM95db

source_name: Newly-diagnosed MM patient 406


title: subject_74-Ascending colon-biopsy_10

value: inflammatory bowel disease


title: subject_32-Terminal Ileum-biopsy_113

value: F


title: subject_127-Rectum-biopsy_105

value: Rectum


title: subject_70-Rectum-biopsy_100

value: M

value: Non-involved area


title: subject_101-Terminal Ileum-biopsy_109

value: Terminal Ileum

value: Inflamed area


title: subject_21-Ascending colon-biopsy_11


title: subject_16-Rectum-biopsy_108


title: mirMM.431-MM95db

source_name: Newly-diagnosed MM patient 431


title: subject_13-Terminal Ileum-biopsy_114


title: subject_73-Rectum-biopsy_111

source_name: Rectum


title: subject_229-Rectum-biopsy_103


title: subject_289-Ascending colon-biopsy_1


title: subject_369-Terminal Ileum-biopsy_102

source_name: Terminal Ileum


title: mirMM.295-MM95db

source_name: Newly-diagnosed MM patient 295


title: mirMM.268-MM95db

source_name: Newly-diagnosed MM patient 268


title: mirMM.269-MM95db

source_name: Newly-diagnosed MM patient 269


title: mirMM.263-MM95db

source_name: Newly-diagnosed MM patient 263


title: mirMM.213-MM95db

source_name: Newly-diagnosed MM patient 213


title: mirMM.154-MM95db

source_name: Newly-diagnosed MM patient 154


title: mirMM.206-MM95db

source_name: Newly-diagnosed MM patient 206


title: mirMM.179-MM95db

source_name: Newly-diagnosed MM patient 179


title: mirMM.123-MM95db

source_name: Newly-diagnosed MM patient 123


title: mirMM.078-MM95db

source_name: Newly-diagnosed MM patient 078


title: mirMM.069-MM95db

source_name: Newly-diagnosed MM patient 069


title: mirMM.055-MM95db

source_name: Newly-diagnosed MM patient 055


title: mirMM.115-MM95db

source_name: Newly-diagnosed MM patient 115


title: mirMM.052-MM95db

source_name: Newly-diagnosed MM patient 052


title: mirMM.104-MM95db

source_name: Newly-diagnosed MM patient 104


title: mirMM.049-MM95db

source_name: Newly-diagnosed MM patient 049


title: mirMM.056-MM95db

source_name: Newly-diagnosed MM patient 056


title: mirMM.035-MM95db

source_name: Newly-diagnosed MM patient 035


title: mirMM.040-MM95db

source_name: Newly-diagnosed MM patient 040


title: mirMM.030-MM95db

source_name: Newly-diagnosed MM patient 030


title: mirMM.021-MM95db

source_name: Newly-diagnosed MM patient 021


title: mirMM.025-MM95db

source_name: Newly-diagnosed MM patient 025


title: Embryonic Kupffer cells (EM-KCs) from KC-DTR mouse, no DT treatment, biological replicate 3

status: Public on Nov 21 2015

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

description: Kupffer cells from transgenic DT-receptor mice, no treatment with DT

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
probe_group_file:  = MoGene-1_0-st-v1.r4.pgf
meta-probeset_file:  = MoGene-1_0-st-v1.r4.mps

label: Biotin

source_name: KC_DTR_Tg, noDT

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Livers were isolated from the mice between 6-12 weeks of age

extract_protocol: Livers were perfused with PBS and subsequently digested with 1mg/ml Collagenase A and 10U/ul DNase (20mins at 37oC). Kupffer cells were isolated from single cell suspensions by FACS.

treatment_protocol: Indicated KC-DTR mice received 50ng DT at the designated time prior to FACS-purification of liver Kupffer cells

value: Liver

tag: genotype

value: DTR Tg


title: intensive-care unit patient [27_03_2013_C10_2313]

status: Public on Jul 06 2015

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: blood gene expression data from healthy subjects and critically-ill patients.

hyb_protocol: Standard Affymetrix GeneAtlas® Hybridization, Wash, and Stain Kit.

scan_protocol: Standard GeneTitan® multi channel instrument.

data_processing: Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 2.15.1; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Affy package version 1.36.1. Array data were background corrected by Robust Multi-array Average, quantiles-normalized and summarized by medianpolish using the expresso function. The resultant 49,386 probe intensities were filtered by means of a 0.5 variance cutoff using the genefilter method to recover 24,646 expressed probes. The occurrence of non-experimental chip effects was evaluated by means of the Surrogate Variable Analysis (R package version 3.4.0) and corrected by the empirical Bayes method ComBat.

source_name: whole blood

label_protocol: 100ng total RNA was labeled using standard GeneChip® 3' IVT Express Kit (Affymetrix)

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood RNA isolation (QIAGEN) procedure using the QIAcube workstation.

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (4 hours) while mixing by inversion.

tag: gender

value: male

tag: age

tag: pneumonia diagnoses

tag: thrombocytopenia

value: discovery

value: ICUA


title: ΔsigBCDE_standard_biol.rep2

status: Public on Sep 15 2015

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing:
The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.
Normalized signal intensity calculated with Chipster v3.1 analysis software

organism: Synechocystis sp. PCC 6803

source_name: cells from ΔsigBCDE_standard growth conditions

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

value: ΔsigBCDE

tag: phenotype

value: glucose tolerant


title: ΔsigBCDE_standard_biol.rep1


title: ΔsigBCDE_standard_biol.rep3


title: ctrl28_2

status: Public on Dec 27 2016

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

country: Japan

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

source_name: hippocampus

label_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cDNA.

value: hippocampus

tag: treatment

value: Control 28 days


title: intensive-care unit patient [27_03_2013_F09_3393]


title: Embryonic Kupffer cells (EM-KCs) from KC-DTR mouse, no DT treatment, biological replicate 1


title: intensive-care unit patient [27_03_2013_D10_2849655]

value: hap

value: validation


title: intensive-care unit patient [27_03_2013_G02_935]

value: female


title: Embryonic Kupffer cells (EM-KCs) from KC-DTR mouse, no DT treatment, biological replicate 2


title: intensive-care unit patient [27_03_2013_D05_2836701]


title: ctrl28_1

tag: strain


title: IH28D_3

tag: tissue

value: intermittent hypoxia 28 days


title: ctrl28_3


title: intensive-care unit patient [27_03_2013_H02_3283]


title: intensive-care unit patient [27_03_2013_E01_2437188]


title: intensive-care unit patient [27_03_2013_D09_2539575]


title: intensive-care unit patient [27_03_2013_E06_2977805]


title: intensive-care unit patient [27_03_2013_E07_1073]

value: DM


title: intensive-care unit patient [27_03_2013_F02_2904613]


title: intensive-care unit patient [27_03_2013_D11_2307892]


title: intensive-care unit patient [27_03_2013_F01_2968378]


title: intensive-care unit patient [27_03_2013_G07_499]


title: intensive-care unit patient [27_03_2013_G08_3316.1]


title: intensive-care unit patient [27_03_2013_C12_2563256]


title: intensive-care unit patient [27_03_2013_E11_2989698]


title: intensive-care unit patient [27_03_2013_E10_2922677]


title: intensive-care unit patient [27_03_2013_E04_2575353]


title: intensive-care unit patient [27_03_2013_C03_2803146]


title: intensive-care unit patient [27_03_2013_B04_2890]


title: intensive-care unit patient [27_03_2013_B07_2839]


title: intensive-care unit patient [27_03_2013_C02_171]


title: intensive-care unit patient [26_03_2013_E04_2716]


title: intensive-care unit patient [27_03_2013_B08_2866326]


title: intensive-care unit patient [22_01_2013_H11_2750964]


title: intensive-care unit patient [26_03_2013_H06_3128]


title: intensive-care unit patient [27_03_2013_B10_2869]


title: intensive-care unit patient [26_03_2013_C06_2972]


title: intensive-care unit patient [26_03_2013_B08_2542360]


title: intensive-care unit patient [27_03_2013_A09_2915]


title: intensive-care unit patient [26_03_2013_G06_3018]


title: intensive-care unit patient [26_03_2013_G04_3016]


title: intensive-care unit patient [26_03_2013_F07_3073]


title: intensive-care unit patient [26_03_2013_C02_2542638]


title: intensive-care unit patient [27_03_2013_A12_329]


title: intensive-care unit patient [26_03_2013_A03_2792222]


title: intensive-care unit patient [26_03_2013_D05_2795]


title: intensive-care unit patient [27_03_2013_A02_3128.1]


title: intensive-care unit patient [27_03_2013_C09_1206]


title: intensive-care unit patient [26_03_2013_D06_2741]


title: intensive-care unit patient [27_03_2013_A05_2887.1]


title: intensive-care unit patient [26_03_2013_F04_2042]


title: intensive-care unit patient [27_03_2013_A07_2914]


title: intensive-care unit patient [26_03_2013_F02_2973085]


title: intensive-care unit patient [27_03_2013_C01_1626]


title: intensive-care unit patient [26_03_2013_B02_2077005]


title: intensive-care unit patient [22_01_2013_H08_2079564]


title: intensive-care unit patient [22_01_2013_H05_2417828]


title: intensive-care unit patient [22_01_2013_H04_2712378]


title: intensive-care unit patient [26_03_2013_E03_2717.1]


title: intensive-care unit patient [22_01_2013_F08_2330273]


title: intensive-care unit patient [22_01_2013_H09_2095014]


title: intensive-care unit patient [22_01_2013_G10_2206690]


title: intensive-care unit patient [22_01_2013_G04_2506984]


title: intensive-care unit patient [22_01_2013_C12_2219502]


title: intensive-care unit patient [22_01_2013_D08_2453929]


title: intensive-care unit patient [22_01_2013_E06_1151]


title: intensive-care unit patient [22_01_2013_D04_2641079]


title: intensive-care unit patient [22_01_2013_D05_2512541]


title: intensive-care unit patient [22_01_2013_C07_1692]


title: intensive-care unit patient [22_01_2013_C05_1550]


title: intensive-care unit patient [22_01_2013_C10_1438]


title: intensive-care unit patient [22_01_2013_H01_1708]


title: intensive-care unit patient [22_01_2013_F06_2337277]


title: intensive-care unit patient [22_01_2013_D10_893]


title: intensive-care unit patient [22_01_2013_C01_2062249]


title: intensive-care unit patient [22_01_2013_B10_2739656]


title: intensive-care unit patient [22_01_2013_D01_2308334]


title: intensive-care unit patient [22_01_2013_B05_966]


title: intensive-care unit patient [22_01_2013_B07_774]


title: intensive-care unit patient [22_01_2013_E05_2512233]


title: intensive-care unit patient [22_01_2013_D11_2091020]


title: intensive-care unit patient [22_01_2013_B09_2624919]


title: intensive-care unit patient [22_01_2013_F07_2329751]


title: intensive-care unit patient [22_01_2013_G01_2661366]


title: intensive-care unit patient [22_01_2013_C02_2295511]


title: intensive-care unit patient [22_01_2013_E08_1311]


title: intensive-care unit patient [22_01_2013_A10_2412748]


title: intensive-care unit patient [22_01_2013_B02_2143801]


title: intensive-care unit patient [22_01_2013_B04_2063277]


title: intensive-care unit patient [22_01_2013_A12_2273467]


title: intensive-care unit patient [22_01_2013_B01_2047406]


title: intensive-care unit patient [22_01_2013_A01_2435440]


title: intensive-care unit patient [21_03_2013_H07_2995]


title: intensive-care unit patient [22_01_2013_A06_2068847]


title: intensive-care unit patient [21_03_2013_H08_2994]


title: intensive-care unit patient [21_03_2013_H09_2919]


title: intensive-care unit patient [21_03_2013_H04_2977]


title: intensive-care unit patient [21_03_2013_F08_2448]


title: intensive-care unit patient [21_03_2013_H02_2921]


title: intensive-care unit patient [21_03_2013_G11_2937]


title: intensive-care unit patient [21_03_2013_H06_2978]


title: intensive-care unit patient [21_03_2013_F10_2442]


title: intensive-care unit patient [22_01_2013_A09_2168597]


title: intensive-care unit patient [21_03_2013_G12_2947]


title: intensive-care unit patient [21_03_2013_G04_2392]


title: intensive-care unit patient [21_03_2013_F05_2465]


title: intensive-care unit patient [21_03_2013_F09_2444]


title: intensive-care unit patient [21_03_2013_F03_2029]


title: intensive-care unit patient [21_03_2013_F07_2455]


title: intensive-care unit patient [21_03_2013_G10_2951]


title: intensive-care unit patient [21_03_2013_F06_2461]


title: intensive-care unit patient [21_03_2013_E07_2507]


title: intensive-care unit patient [21_03_2013_G01_2409]


title: intensive-care unit patient [21_03_2013_E06_2514]


title: intensive-care unit patient [21_03_2013_F12_2407]


title: intensive-care unit patient [21_03_2013_E04_2526]


title: intensive-care unit patient [21_03_2013_G09_2950]


title: intensive-care unit patient [21_03_2013_H11_2805]


title: intensive-care unit patient [21_03_2013_H03_2963.1]


title: intensive-care unit patient [21_03_2013_E11_2491]


title: intensive-care unit patient [21_03_2013_E10_2472.2]


title: intensive-care unit patient [21_03_2013_D08_2608]


title: intensive-care unit patient [21_03_2013_E03_2532]


title: intensive-care unit patient [21_03_2013_D09_2562]


title: intensive-care unit patient [21_03_2013_C07_2656]


title: intensive-care unit patient [21_03_2013_D06_2569]


title: intensive-care unit patient [21_03_2013_C11_2639]


title: intensive-care unit patient [21_03_2013_C01_1124]


title: intensive-care unit patient [21_03_2013_C09_2657]


title: intensive-care unit patient [21_03_2013_C10_2643]


title: intensive-care unit patient [21_03_2013_D12_2505.1]


title: intensive-care unit patient [21_03_2013_D03_2632]


title: intensive-care unit patient [21_03_2013_C03_651]


title: intensive-care unit patient [21_03_2013_D07_2583]


title: intensive-care unit patient [21_03_2013_C12_2613]


title: intensive-care unit patient [21_03_2013_B08_1645.1]


title: intensive-care unit patient [21_03_2013_B11_1318]


title: intensive-care unit patient [21_03_2013_B12_1176]


title: intensive-care unit patient [21_03_2013_A06_2229]


title: intensive-care unit patient [21_03_2013_D02_2622]


title: intensive-care unit patient [21_03_2013_B06_1939]


title: intensive-care unit patient [21_03_2013_B02_2035]


title: intensive-care unit patient [21_03_2013_A08_2201.2]


title: intensive-care unit patient [21_03_2013_B05_2009]


title: intensive-care unit patient [21_03_2013_A02_2291]


title: intensive-care unit patient [21_03_2013_A05_2259]


title: intensive-care unit patient [21_03_2013_B01_2118]


title: intensive-care unit patient [20_03_2013_H09_2296]


title: intensive-care unit patient [20_03_2013_H11_2272.1]


title: intensive-care unit patient [20_03_2013_H07_2304]


title: intensive-care unit patient [20_03_2013_H08_2302]


title: intensive-care unit patient [21_03_2013_C06_221]


title: intensive-care unit patient [20_03_2013_H05_2233720]


title: intensive-care unit patient [20_03_2013_H06_2306]


title: intensive-care unit patient [20_03_2013_H04_882.1]


title: intensive-care unit patient [20_03_2013_F05_922]


title: intensive-care unit patient [20_03_2013_H03_2319]


title: intensive-care unit patient [20_03_2013_F08_2688463]


title: intensive-care unit patient [20_03_2013_G11_2345]


title: intensive-care unit patient [20_03_2013_G07_2363]


title: intensive-care unit patient [20_03_2013_E06_1861]


title: intensive-care unit patient [20_03_2013_G08_2358]


title: intensive-care unit patient [20_03_2013_G04_2368.1]


title: intensive-care unit patient [20_03_2013_F07_1202]


title: intensive-care unit patient [20_03_2013_E11_2111361]


title: intensive-care unit patient [20_03_2013_E12_2403959]


title: intensive-care unit patient [20_03_2013_E03_2919602]


title: intensive-care unit patient [20_03_2013_E01_364]


title: intensive-care unit patient [20_03_2013_D09_2348773]


title: intensive-care unit patient [20_03_2013_G06_2367]


title: intensive-care unit patient [20_03_2013_E04_2666347]


title: intensive-care unit patient [20_03_2013_C12_2897831]


title: intensive-care unit patient [20_03_2013_D08_2025044]


title: intensive-care unit patient [20_03_2013_C06_1590]


title: intensive-care unit patient [20_03_2013_E02_2148523]

value: cap


title: intensive-care unit patient [20_03_2013_D06_2060094]


title: intensive-care unit patient [20_03_2013_E09_663]


title: intensive-care unit patient [20_03_2013_B07_2801914]


title: intensive-care unit patient [20_03_2013_B05_797]


title: intensive-care unit patient [20_03_2013_B08_1152]


title: intensive-care unit patient [20_03_2013_E05_866]


title: intensive-care unit patient [20_03_2013_A10_1579]


title: intensive-care unit patient [20_03_2013_A07_1707]


title: intensive-care unit patient [20_03_2013_C09_2316460]


title: intensive-care unit patient [20_03_2013_B12_1326]


title: intensive-care unit patient [19_03_2013_H06_1772]


title: intensive-care unit patient [20_03_2013_A09_2381906]


title: intensive-care unit patient [19_03_2013_H10_2296377]


title: intensive-care unit patient [20_03_2013_B04_2559525]


title: intensive-care unit patient [19_03_2013_H02_2193207]


title: intensive-care unit patient [20_03_2013_B03_2130323]


title: intensive-care unit patient [19_03_2013_G06_2690766]


title: intensive-care unit patient [19_03_2013_G09_2866838]


title: intensive-care unit patient [19_03_2013_G07_2833571]


title: intensive-care unit patient [19_03_2013_G10_231]


title: intensive-care unit patient [20_03_2013_A05_2081]


title: intensive-care unit patient [19_03_2013_G04_1070]


title: intensive-care unit patient [19_03_2013_G02_1004]


title: intensive-care unit patient [19_03_2013_H09_2327068]


title: intensive-care unit patient [19_03_2013_G05_2138509]


title: intensive-care unit patient [20_03_2013_D12_1382]


title: intensive-care unit patient [19_03_2013_F12_516]


title: intensive-care unit patient [19_03_2013_F10_1598]


title: intensive-care unit patient [19_03_2013_G11_423]


title: intensive-care unit patient [20_03_2013_B01_2593636]


title: intensive-care unit patient [20_03_2013_A04_1259]


title: intensive-care unit patient [19_03_2013_F09_2197135]


title: intensive-care unit patient [19_03_2013_F06_219]


title: intensive-care unit patient [19_03_2013_E06_823]


title: intensive-care unit patient [19_03_2013_E03_2124]


title: intensive-care unit patient [19_03_2013_D09_1992]


title: intensive-care unit patient [19_03_2013_B02_2147]


title: intensive-care unit patient [19_03_2013_C09_434]


title: intensive-care unit patient [19_03_2013_D11_1532]


title: intensive-care unit patient [19_03_2013_F04_1451.1]


title: intensive-care unit patient [19_03_2013_A08_2078363]


title: intensive-care unit patient [19_03_2013_E05_2796089]


title: intensive-care unit patient [19_03_2013_C05_855]


title: intensive-care unit patient [19_03_2013_A12_2360467]


title: intensive-care unit patient [19_03_2013_A09_2096625]


title: intensive-care unit patient [19_03_2013_A10_2210087]


title: intensive-care unit patient [19_03_2013_B08_1674]


title: intensive-care unit patient [19_03_2013_B10_1456]


title: intensive-care unit patient [19_03_2013_C08_980]


title: intensive-care unit patient [19_03_2013_C06_775]


title: intensive-care unit patient [19_03_2013_B03_2106]


title: intensive-care unit patient [19_03_2013_A05_2768950]


title: intensive-care unit patient [14_03_2013_H08_2858074]


title: intensive-care unit patient [19_03_2013_A07_2152708]


title: intensive-care unit patient [14_03_2013_H07_2455809]


title: intensive-care unit patient [14_03_2013_H10_2613389]


title: intensive-care unit patient [14_03_2013_H09_2337626]


title: intensive-care unit patient [14_03_2013_H05_2630414]


title: intensive-care unit patient [14_03_2013_H06_1603]


title: intensive-care unit patient [19_03_2013_B04_2027]


title: intensive-care unit patient [19_03_2013_A01_2391003]


title: intensive-care unit patient [14_03_2013_H02_467]


title: intensive-care unit patient [14_03_2013_G10_1628]


title: intensive-care unit patient [19_03_2013_F01_398]


title: intensive-care unit patient [14_03_2013_G04_790]


title: intensive-care unit patient [19_03_2013_D08_2647417]


title: intensive-care unit patient [14_03_2013_F02_879]


title: intensive-care unit patient [14_03_2013_E02_2402211]


title: intensive-care unit patient [14_03_2013_E07_1437]


title: intensive-care unit patient [14_03_2013_D05_1624]


title: intensive-care unit patient [14_03_2013_D01_1908]


title: intensive-care unit patient [14_03_2013_C10_2396220]


title: intensive-care unit patient [14_03_2013_D06_1464]


title: intensive-care unit patient [14_03_2013_F09_2859676]


title: intensive-care unit patient [14_03_2013_F01_653]


title: intensive-care unit patient [14_03_2013_D12_2095177]


title: intensive-care unit patient [14_03_2013_F07_2716673]


title: intensive-care unit patient [14_03_2013_G02_2905183]


title: intensive-care unit patient [14_03_2013_G09_490]


title: intensive-care unit patient [14_03_2013_E01_2254503]


title: intensive-care unit patient [14_03_2013_E06_1391]


title: intensive-care unit patient [14_03_2013_F10_160]


title: intensive-care unit patient [14_03_2013_F08_2458860]


title: intensive-care unit patient [14_03_2013_C01_2647680]


title: intensive-care unit patient [14_03_2013_A07_1751]


title: intensive-care unit patient [14_03_2013_B12_2502387]


title: intensive-care unit patient [14_03_2013_B08_2290568]


title: intensive-care unit patient [14_03_2013_B11_2423113]


title: intensive-care unit patient [14_03_2013_C09_2210219]


title: intensive-care unit patient [14_03_2013_G01_2646192]


title: intensive-care unit patient [14_03_2013_A06_2935946]


title: intensive-care unit patient [14_03_2013_C06_2555715]


title: intensive-care unit patient [14_03_2013_A04_1822]


title: intensive-care unit patient [14_03_2013_A05_1797]


title: intensive-care unit patient [14_03_2013_A03_2440481]


title: intensive-care unit patient [14_03_2013_A01_1153]


title: intensive-care unit patient [14_03_2013_D04_2002]


title: intensive-care unit patient [14_03_2013_E03_2394591]


title: intensive-care unit patient [13_03_2013_H05_2832620]


title: intensive-care unit patient [13_03_2013_H09_496]


title: intensive-care unit patient [13_03_2013_H08_2423724]


title: intensive-care unit patient [13_03_2013_G11_1266]


title: intensive-care unit patient [13_03_2013_G12_2015183]


title: intensive-care unit patient [13_03_2013_F03_427]


title: intensive-care unit patient [13_03_2013_F07_2939065]


title: intensive-care unit patient [13_03_2013_F10_2805753]


title: intensive-care unit patient [13_03_2013_G02_933]


title: intensive-care unit patient [13_03_2013_G08_2092988]


title: intensive-care unit patient [13_03_2013_F06_290]


title: intensive-care unit patient [13_03_2013_G03_2401944]


title: intensive-care unit patient [13_03_2013_G01_1251]


title: intensive-care unit patient [13_03_2013_G07_2610361]


title: intensive-care unit patient [13_03_2013_G06_2671849]


title: intensive-care unit patient [13_03_2013_H01_1866]


title: intensive-care unit patient [13_03_2013_E09_2841476]


title: intensive-care unit patient [13_03_2013_F02_2716785]


title: intensive-care unit patient [13_03_2013_F04_2873858]


title: intensive-care unit patient [13_03_2013_E12_2180867]


title: intensive-care unit patient [19_03_2013_A06_2788315]


title: intensive-care unit patient [13_03_2013_E10_2152430]


title: intensive-care unit patient [13_03_2013_G09_1551]


title: intensive-care unit patient [13_03_2013_E07_2260580]


title: intensive-care unit patient [13_03_2013_E04_2784251]


title: intensive-care unit patient [13_03_2013_E01_2727912]


title: intensive-care unit patient [13_03_2013_E02_2855460]


title: intensive-care unit patient [13_03_2013_E06_2158239]


title: intensive-care unit patient [13_03_2013_D12_2799039]


title: intensive-care unit patient [13_03_2013_D03_2528458]


title: intensive-care unit patient [13_03_2013_C11_2931020]


title: intensive-care unit patient [13_03_2013_D11_2441106]


title: intensive-care unit patient [13_03_2013_D02_2041720]


title: intensive-care unit patient [13_03_2013_D05_2061687]


title: intensive-care unit patient [13_03_2013_C06_474]


title: intensive-care unit patient [13_03_2013_C08_357]


title: intensive-care unit patient [13_03_2013_B04_1611]


title: intensive-care unit patient [13_03_2013_B11_880]


title: intensive-care unit patient [13_03_2013_C01_816]


title: intensive-care unit patient [13_03_2013_B01_2232]


title: intensive-care unit patient [13_03_2013_C09_304]


title: intensive-care unit patient [13_03_2013_B06_1481]


title: intensive-care unit patient [13_03_2013_B02_2003]


title: intensive-care unit patient [13_03_2013_D01_2465607]


title: intensive-care unit patient [13_03_2013_B12_834]


title: intensive-care unit patient [13_03_2013_A12_2473497]


title: intensive-care unit patient [13_02_2013_H07_1901]


title: intensive-care unit patient [13_02_2013_H09_175]


title: intensive-care unit patient [13_02_2013_H10_394]


title: intensive-care unit patient [13_03_2013_D10_2755346]


title: intensive-care unit patient [13_03_2013_A06_2577185]


title: intensive-care unit patient [13_02_2013_H08_2329914]


title: intensive-care unit patient [13_03_2013_A09_2578388]


title: intensive-care unit patient [13_02_2013_H06_638]


title: intensive-care unit patient [13_03_2013_A11_2464900]


title: intensive-care unit patient [13_02_2013_H12_2479926]


title: intensive-care unit patient [13_02_2013_H11_956]


title: intensive-care unit patient [13_02_2013_F07_1967]


title: intensive-care unit patient [13_02_2013_F02_2080847]


title: intensive-care unit patient [13_02_2013_H03_1249]


title: intensive-care unit patient [13_02_2013_E03_2469217]


title: intensive-care unit patient [13_02_2013_D04_1106]


title: intensive-care unit patient [13_02_2013_D09_2712753]


title: intensive-care unit patient [13_02_2013_E09_2276373]


title: intensive-care unit patient [13_02_2013_G12_2004]


title: intensive-care unit patient [13_02_2013_G10_2537801]


title: intensive-care unit patient [13_02_2013_G04_299]


title: intensive-care unit patient [13_02_2013_G08_2014]


title: intensive-care unit patient [13_02_2013_B12_1906]


title: intensive-care unit patient [13_02_2013_D01_2139889]


title: intensive-care unit patient [13_02_2013_C06_2245]


title: intensive-care unit patient [13_02_2013_F10_2284122]


title: intensive-care unit patient [13_02_2013_E07_262]


title: intensive-care unit patient [13_02_2013_G01_1192]


title: intensive-care unit patient [13_02_2013_D02_2452268]


title: intensive-care unit patient [13_02_2013_C11_2254575]


title: intensive-care unit patient [13_02_2013_F09_554]


title: intensive-care unit patient [13_02_2013_F01_2033946]


title: intensive-care unit patient [13_02_2013_F04_2286989]


title: intensive-care unit patient [13_02_2013_D03_2245555]


title: intensive-care unit patient [13_02_2013_D07_2685636]


title: intensive-care unit patient [13_02_2013_G05_2197127]


title: intensive-care unit patient [13_02_2013_B09_1474]


title: intensive-care unit patient [13_02_2013_C03_1246]


title: intensive-care unit patient [13_02_2013_E12_1388]


title: intensive-care unit patient [13_02_2013_C10_396]


title: intensive-care unit patient [13_02_2013_B11_1738]


title: intensive-care unit patient [13_02_2013_B08_2540647]


title: intensive-care unit patient [13_02_2013_B07_2392914]


title: intensive-care unit patient [13_02_2013_A07_2071168]


title: intensive-care unit patient [12_03_2013_H07_2279]


title: intensive-care unit patient [13_02_2013_A04_1234.1]


title: intensive-care unit patient [12_03_2013_H05_2675425]


title: intensive-care unit patient [13_02_2013_B03_2774321]


title: intensive-care unit patient [13_02_2013_A10_2789759]


title: intensive-care unit patient [13_02_2013_A05_2318175]


title: intensive-care unit patient [13_02_2013_A11_2440861]


title: intensive-care unit patient [12_03_2013_G09_2008]


title: intensive-care unit patient [12_03_2013_H02_2791031]


title: intensive-care unit patient [12_03_2013_H08_2190]


title: intensive-care unit patient [12_03_2013_G04_1056]


title: intensive-care unit patient [12_03_2013_H01_2060742]


title: intensive-care unit patient [13_02_2013_B05_2518579]


title: intensive-care unit patient [12_03_2013_E04_1317]


title: intensive-care unit patient [12_03_2013_F10_2224]


title: intensive-care unit patient [12_03_2013_G01_1521.1]


title: intensive-care unit patient [12_03_2013_F01_2933729]


title: intensive-care unit patient [12_03_2013_F07_1165]


title: intensive-care unit patient [12_03_2013_F05_950]


title: intensive-care unit patient [12_03_2013_G08_2131]


title: intensive-care unit patient [12_03_2013_F12_2121352]


title: intensive-care unit patient [12_03_2013_F04_2888440]


title: intensive-care unit patient [12_03_2013_G06_2914265]


title: intensive-care unit patient [12_03_2013_F08_1818]


title: intensive-care unit patient [12_03_2013_G02_2895821]


title: intensive-care unit patient [12_03_2013_G07_2599222]


title: intensive-care unit patient [12_03_2013_E01_1669]


title: intensive-care unit patient [12_03_2013_E11_2166952]


title: intensive-care unit patient [12_03_2013_C09_2612272]


title: intensive-care unit patient [12_03_2013_C08_312]


title: intensive-care unit patient [12_03_2013_D12_176]


title: intensive-care unit patient [12_03_2013_E02_2477033]


title: intensive-care unit patient [12_03_2013_E03_291.1]


title: intensive-care unit patient [12_03_2013_C04_2108553]


title: intensive-care unit patient [12_03_2013_B11_2920851]


title: intensive-care unit patient [12_03_2013_D01_2927001]


title: intensive-care unit patient [12_03_2013_B12_2328205]


title: intensive-care unit patient [12_03_2013_C05_2367719]


title: intensive-care unit patient [12_03_2013_D03_1442.1]


title: intensive-care unit patient [12_03_2013_B02_2101232]


title: intensive-care unit patient [12_03_2013_B07_2788747]


title: intensive-care unit patient [12_03_2013_C07_2809703]


title: intensive-care unit patient [12_03_2013_B06_2531925]


title: intensive-care unit patient [12_03_2013_B01_2123380]


title: intensive-care unit patient [12_03_2013_B08_2459317]


title: intensive-care unit patient [12_03_2013_B10_2310586]


title: intensive-care unit patient [12_03_2013_A11_2332187]


title: intensive-care unit patient [12_03_2013_A09_2601184]


title: intensive-care unit patient [12_03_2013_A12_2024940]


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title: intensive-care unit patient [12_03_2013_A08_2416144]


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title: intensive-care unit patient [12_03_2013_A10_2177162]


title: intensive-care unit patient [12_03_2013_D08_1012]


title: intensive-care unit patient [12_03_2013_B09_2311040]


title: intensive-care unit patient [12_03_2013_B03_2032265]


title: intensive-care unit patient [12_03_2013_A05_2136]


title: intensive-care unit patient [07_03_2013_H04_2222336]


title: intensive-care unit patient [12_03_2013_A03_2719005]


title: intensive-care unit patient [07_03_2013_H09_2169]


title: intensive-care unit patient [07_03_2013_H12_2150996]


title: intensive-care unit patient [07_03_2013_H02_1114]


title: intensive-care unit patient [07_03_2013_G10_2339779]


title: intensive-care unit patient [07_03_2013_G07_2494142]


title: intensive-care unit patient [07_03_2013_G09_2206431]


title: intensive-care unit patient [07_03_2013_G11_2418573]


title: intensive-care unit patient [07_03_2013_G04_2144490]


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title: intensive-care unit patient [07_03_2013_F11_2708043]


title: intensive-care unit patient [07_03_2013_E02_2771367]


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title: intensive-care unit patient [07_03_2013_E12_2291430]


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title: intensive-care unit patient [07_03_2013_G01_2014763]


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title: intensive-care unit patient [07_03_2013_F10_181]


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title: intensive-care unit patient [07_03_2013_E05_2305248]


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title: intensive-care unit patient [07_03_2013_C10_2145922]


title: intensive-care unit patient [07_03_2013_C11_293]


title: intensive-care unit patient [07_03_2013_C02_2793139]


title: intensive-care unit patient [07_03_2013_D04_714]


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title: intensive-care unit patient [06_02_2013_H08_2580909]


title: intensive-care unit patient [06_02_2013_H07_2294649]


title: intensive-care unit patient [06_02_2013_F05_220]


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title: intensive-care unit patient [06_02_2013_G06_689]


title: intensive-care unit patient [06_02_2013_H02_2580739]


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title: intensive-care unit patient [06_02_2013_G12_2351284]


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title: intensive-care unit patient [06_02_2013_E01_2268424]


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title: intensive-care unit patient [06_02_2013_B07_2016652]


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title: intensive-care unit patient [05_03_2013_H03_2039709]


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title: intensive-care unit patient [06_02_2013_A06_601.2]


title: intensive-care unit patient [05_03_2013_H06_2193]


title: intensive-care unit patient [05_03_2013_H05_2623033]


title: intensive-care unit patient [05_03_2013_H01_2198551]


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title: intensive-care unit patient [05_03_2013_G08_2662486]


title: intensive-care unit patient [05_03_2013_G11_1112]


title: intensive-care unit patient [05_03_2013_F08_182]


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title: intensive-care unit patient [05_03_2013_D06_2045301]


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title: intensive-care unit patient [03_04_2013_A02_3210]


title: intensive-care unit patient [27_03_2013_F07_3404]

value: no-cap


title: intensive-care unit patient [27_03_2013_F08_3395]


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title: intensive-care unit patient [27_03_2013_D02_2209803]


title: healthy subject [26_03_2013_H12_hv48]

value: healthy


title: intensive-care unit patient [27_03_2013_H05_3266]


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title: intensive-care unit patient [03_04_2013_A09_3172]


title: healthy subject [27_03_2013_A03_hv33]


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title: intensive-care unit patient [27_03_2013_B12_1109]


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title: intensive-care unit patient [26_03_2013_A06_579]


title: intensive-care unit patient [22_01_2013_H10_2428168]


title: intensive-care unit patient [22_01_2013_H12_2606322]


title: intensive-care unit patient [22_01_2013_B03_2764528]


title: intensive-care unit patient [22_01_2013_E11_2533256]


title: intensive-care unit patient [22_01_2013_G09_2318433]


title: intensive-care unit patient [22_01_2013_D12_2402042]


title: healthy subject [26_03_2013_A04_hv22]


title: intensive-care unit patient [27_03_2013_G01_2769]


title: intensive-care unit patient [22_01_2013_E09_1552]


title: intensive-care unit patient [26_03_2013_F08_3071]


title: intensive-care unit patient [21_03_2013_G07_2406]


title: intensive-care unit patient [22_01_2013_A05_2245624]


title: intensive-care unit patient [22_01_2013_A07_306]


title: intensive-care unit patient [21_03_2013_F01_2475]


title: intensive-care unit patient [22_01_2013_A11_2587750]


title: intensive-care unit patient [21_03_2013_H10_2924]


title: intensive-care unit patient [21_03_2013_F04_2468]


title: intensive-care unit patient [21_03_2013_G08_2955]


title: intensive-care unit patient [22_01_2013_A03_2023712]


title: intensive-care unit patient [21_03_2013_E05_2516]


title: intensive-care unit patient [21_03_2013_D05_2637]


title: intensive-care unit patient [21_03_2013_C08_2654]


title: intensive-care unit patient [22_01_2013_C11_316]


title: intensive-care unit patient [20_03_2013_H02_2329]


title: intensive-care unit patient [21_03_2013_D11_2545]


title: intensive-care unit patient [21_03_2013_G03_2384]


title: intensive-care unit patient [20_03_2013_H01_2340]


title: intensive-care unit patient [21_03_2013_E02_2536]


title: intensive-care unit patient [20_03_2013_G03_2458108]


title: intensive-care unit patient [20_03_2013_G12_2343]


title: intensive-care unit patient [20_03_2013_F03_2647363]


title: intensive-care unit patient [20_03_2013_C07_2937810]


title: healthy subject [20_03_2013_D11_hv16]


title: healthy subject [20_03_2013_C02_hv04]


title: healthy subject [20_03_2013_G02_hv36]


title: healthy subject [20_03_2013_C11_hv12]


title: intensive-care unit patient [20_03_2013_B11_1225]


title: healthy subject [20_03_2013_D03_hv54]


title: intensive-care unit patient [19_03_2013_H04_2849441]


title: healthy subject [20_03_2013_D05_hv17]


title: intensive-care unit patient [19_03_2013_F05_2047294]


title: healthy subject [20_03_2013_C04_hv08]


title: intensive-care unit patient [19_03_2013_H08_2603118]


title: healthy subject [20_03_2013_D04_hv47]


title: healthy subject [20_03_2013_C05_hv02]


title: intensive-care unit patient [20_03_2013_F11_1546]


title: intensive-care unit patient [19_03_2013_H05_2128798]


title: healthy subject [19_03_2013_E09_hv20]


title: intensive-care unit patient [20_03_2013_A03_2587517]


title: intensive-care unit patient [19_03_2013_F07_2113]


title: healthy subject [19_03_2013_E07_hv39]


title: healthy subject [19_03_2013_E01_hv14]


title: healthy subject [19_03_2013_D05_hv38]


title: healthy subject [19_03_2013_D02_hv43]


title: intensive-care unit patient [19_03_2013_C04_897]


title: intensive-care unit patient [19_03_2013_C12_725]


title: healthy subject [19_03_2013_D04_hv09]


title: healthy subject [19_03_2013_D06_hv10]


title: intensive-care unit patient [19_03_2013_C10_533]


title: healthy subject [19_03_2013_D07_hv53]


title: healthy subject [19_03_2013_E08_hv41]


title: healthy subject [14_03_2013_G11_hv55]


title: intensive-care unit patient [19_03_2013_A04_2682699]


title: intensive-care unit patient [19_03_2013_C01_1299]


title: healthy subject [19_03_2013_D03_hv23]


title: intensive-care unit patient [19_03_2013_A03_2122227]


title: healthy subject [19_03_2013_D12_hv34]


title: intensive-care unit patient [14_03_2013_E04_1257]


title: intensive-care unit patient [14_03_2013_D09_2500051]


title: healthy subject [14_03_2013_B03_hv15]