title: Subject_AF0010_SE_T9

description:
Blood_31.5hrsAwake_at17:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 17:45 following 31.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0010_SR_T7

status: Public on Feb 27 2013

type: RNA

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description:
Blood_25.5hrsAwake_at10:41afterSleepRestriction_Per3_4\4genotype_Subject_AF0010
Blood taken at 10:41 following 25.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0010)

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37°C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalized using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

tag: subject

tag: tissue

value: Blood

tag: sleepprotocol

value: Sleep Restriction

tag: genotype/variation

tag: hoursawake

tag: timesampletaken

tag: circadianphase


title: Subject_AF0010_SR_T3

description:
Blood_13.5hrsAwake_at22:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0010
Blood taken at 22:40 following 13.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0033_SE_T9

description:
Blood_31.5hrsAwake_at17:03afterSleepExtension_Per3_4\4genotype_Subject_AF0033
Blood taken at 17:03 following 31.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0033)

value: Sleep Extension


title: Subject_AF0010_SE_T5

description:
Blood_19.5hrsAwake_at05:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 05:45 following 19.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0010_SE_T4

description:
Blood_16.5hrsAwake_at02:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 02:45 following 16.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0010_SE_T2

description:
Blood_10.5hrsAwake_at20:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 20:45 following 10.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0010_SE_T6

description:
Blood_22.5hrsAwake_at08:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 08:45 following 22.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0033_SE_T1

description:
Blood_ 7.5hrsAwake_at17:00afterSleepExtension_Per3_4\4genotype_Subject_AF0033
Blood taken at 17:00 following  7.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0033)


title: Subject_AF0010_SE_T3

description:
Blood_13.5hrsAwake_at23:45afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 23:45 following 13.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0010_SE_T8

description:
Blood_28.5hrsAwake_at14:47afterSleepExtension_Per3_4\4genotype_Subject_AF0010
Blood taken at 14:47 following 28.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0010)


title: Subject_AF0004_SR_T10

description:
Blood_34.5hrsAwake_at21:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 21:15 following 34.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T5

description:
Blood_19.5hrsAwake_at06:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 06:15 following 19.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T8

description:
Blood_28.5hrsAwake_at15:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 15:15 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T1

description:
Blood_ 7.5hrsAwake_at18:19afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 18:19 following  7.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T9

description:
Blood_31.5hrsAwake_at18:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 18:15 following 31.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T3

description:
Blood_13.5hrsAwake_at00:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 00:15 following 13.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: BGSmallRNASeq

status: Public on Aug 03 2012

type: SRA

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

library_source: transcriptomic

data_processing:
Base-calling were finished by Illumina.
Adapters were removed and the small RNA sequences were extracted from the raw reads.
The unique sequences and their counts were calculated from the extracted sequences.
Supplementary_files_format_and_content: unique sequences and their counts

organism: Lagenaria siceraria

source_name: mixed tissues

extract_protocol: Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. lanatus) (PI 438676 Charleston Grey) by pooling equimolar amounts of total RNA from the aforesaid tissues. Construction of small RNA libraries from size fractionated RNA was carried out as described previously. In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels and sequentially ligated to 5′ and 3′ RNA adapters. Small RNAs ligated with adapters were converted to DNA by RT-PCR following Solexa protocol.

tag: strain

value: mixed tissues (leaf, stem and flesh, rind and placenta of the fruits)


title: MoschataSmallRNASeq

organism: Cucurbita moschata

value: accession Grif 14244 Early Butternut


title: Subject_AF0004_SR_T4

description:
Blood_16.5hrsAwake_at03:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 03:15 following 16.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: PepoSmallRNASeq

organism: Cucurbita pepo

value: accession NSL98075 Table King


title: WatermelonSmallRNASeq

organism: Citrullus lanatus

value: PI 438676 Charleston Grey


title: Subject_AF0004_SE_T10

description:
Blood_34.5hrsAwake_at21:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 21:15 following 34.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T2

description:
Blood_10.5hrsAwake_at21:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 21:15 following 10.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T9

description:
Blood_31.5hrsAwake_at18:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 18:15 following 31.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SR_T7

description:
Blood_25.5hrsAwake_at12:15afterSleepRestriction_Per3_4\4genotype_Subject_AF0004
Blood taken at 12:15 following 25.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T7

description:
Blood_25.5hrsAwake_at12:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 12:15 following 25.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T8

description:
Blood_28.5hrsAwake_at15:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 15:15 following 28.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T3

description:
Blood_13.5hrsAwake_at00:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 00:15 following 13.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T5

description:
Blood_19.5hrsAwake_at06:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 06:15 following 19.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T2

description:
Blood_10.5hrsAwake_at21:20afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 21:20 following 10.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T6

description:
Blood_22.5hrsAwake_at09:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 09:15 following 22.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: MMTV-Cre:p53 primary tumor TP53-1

status: Public on Aug 09 2012

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

description:
TP53-1
Gene expression data from primary MMTV-Cre:p53 tumor

hyb_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek Genomics Suite (v.5.6) and absolute expression values were obtained

label: biotin

organism: Mus musculus

source_name: MMTV-Cre:p53 primary tumor

growth_protocol: Samples from independent primary mammary tumors from MMTV-Neu,MMTV-Cre:p53, MMTV-Cre:PTEN, MMTV-Cre:PTEN:p53, WAP-Cre:PTEN, and WAP-Cre:PTEN:p53 models were frozen and kept in -80 degree.

extract_protocol: Total RNA was extracted with Trizol reagent twice. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

tag: strain background

value: mixed

value: primary mammary tumor less than 1.0 cm diameter


title: MMTV-Cre:p53 primary tumor C53-25

description:
C53-25
Gene expression data from primary MMTV-Cre:p53 tumor

scan_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: MMTV-Cre:p53 primary tumor C53-18

description:
C53-18
Gene expression data from primary MMTV-Cre:p53 tumor

label_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: Subject_AF0004_SE_T4

description:
Blood_16.5hrsAwake_at03:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 03:15 following 16.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: Subject_AF0004_SE_T1

description:
Blood_ 7.5hrsAwake_at18:15afterSleepExtension_Per3_4\4genotype_Subject_AF0004
Blood taken at 18:15 following  7.5 hours awake after following a Sleep Extension protocol from a Per3 4\4 genotype subject (Subject AF0004)


title: fascia-hernia-RH14

status: Public on Jun 01 2012

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

country: USA

institute: AbbVie

hyb_protocol: The chips were hybridized at 48°C for 20 hrs in the hybridization buffer provided by the manufacturer. After hybridization, the chips were washed and stained with streptavidin-C3.

scan_protocol: The chips were scanned on the BeadArray Reader, as described by Illumina at http://www.illumina.com. The Illumina Beadstudio software was used to assess fluorescent hybridization signals.

data_processing: The Illumina Beadstudio software was used to assess fluorescent hybridization signals. The data were background adjusted in lumi ('forcePositive' method, equivalent to BeadStudio default method), and then transformed using VST method in R (lumi package). The data were then normalized using quantile normalization with lumi in R. Skin samples and fascia samples were normalized independently.

source_name: fascia, trochar site, away from hernia, at beginning of operation

label_protocol: Total RNA was amplified using the WT-Ovation™ Pico RNA Amplification System protocol (NuGen, San Carlos, CA). 40 ng of total RNA was used as starting material to generate at least 6μg of cDNA. Amplified cDNA was purified using Zymo Research Clean and Concentrator™-25 (Zymo Research, Orange, CA). 3μg of amplified and purified cDNA was incubated at 50°C for 30 minutes with 5μl of UNG buffer and 5μl UNG enzyme and 60 minutes with 5μl labeling buffer and 5μl ARP (biotin) solution as described in NuGen’s labeling protocol for the Illumina Beadarray platform. All samples (total RNA, amplified cDNA, and biotin labeled amplified cDNA) were quantitated using a Nanodrop™ (Thermo Fisher Scientific, Waltham, MA) spectrophotometer. RNA quality and integrity was assessed on selected samples with the Experion™ automated electrophoresis system (Bio-Rad, Hercules, CA).

extract_protocol: Total RNA was isolated from the skin and fascia specimens by following the manufacturer’s protocol from the RNeasy® Lipid Tissue Mini Kit (Qiagen) using a rotor homogenizer and on-column DNase treatment.

tag: group

value: hernia

value: fascia

tag: Sex

value: F

tag: age

tag: bmi

tag: smoker

value: no

tag: diabetes

value: yes

tag: steroids

tag: hernias


title: fascia-normal-NC6

value: normal


title: fascia-normal-NC4


title: fascia-normal-NC14


title: fascia-normal-NC12

value: M


title: fascia-normal-NC13


title: fascia-hernia-RH12


title: fascia-hernia-RH6


title: fascia-hernia-RH2


title: skin-hernia-RH12

source_name: skin, trochar site, away from hernia, at beginning of operation

value: skin


title: skin-normal-NC6


title: fascia-hernia-RH8


title: skin-normal-NC12


title: fascia-normal-NC9


title: fascia-hernia-RH11


title: skin-normal-NC13


title: skin-hernia-RH13


title: fascia-hernia-RH10


title: fascia-normal-NC10


title: fascia-hernia-RH13


title: skin-normal-NC14


title: fascia-normal-NC11


title: skin-normal-NC4


title: skin-hernia-RH10


title: skin-hernia-RH11


title: skin-normal-NC11


title: fascia-hernia-RH3


title: skin-hernia-RH14


title: skin-normal-NC9


title: skin-hernia-RH3


title: skin-normal-NC10


title: CD4+ naive T cell MIRA-Seq in patients with Psoriasis

status: Public on Mar 17 2012

city: Seoul

first: Sin-Gi

last: Park

address: 19, Sadang-ro, Dongjak-Gu

department: Department of Bioinformatics & Life science

country: South Korea

institute: Soongsil univ.

description:
Based on the affinity of the MBD2b/MBD3L1 complex (MIRA technique)
MES_processed_data_file : Psoriasis_naive_CD4+_T_cell_MES.wig
Final_processed_data_file : Psoriasis_processed_data.table

library_source: genomic

data_processing: The sequence tags were mapped to the human genome with UCSC hg18 (http://genome.ucsc.edu/) assembly based on NCBI build 36.1 through the Solexa Analysis Pipeline (version 0.3.0). Those reads that were mapped to multiple locations were discarded and only those uniquely mapped are retained in the analysis. We obtained about 15~20 million Illumina sequencing reads at every 200 base pair (bp) interval, across the whole genome from MIRA-Seq. As a result, 34 bp reading sequences were obtained. The first and last nucleotides were excluded for exact sequence match. The 34 bp reading sequence was extended toward the 3‘end to cover DNA fragments bound by the MBD proteins. To visualize the data, the readout was converted to browser extensible data (BED) and wiggle (WIG) files compatible with the UCSC Genome Browser (http://genome.ucsc.edu).Tagged overlapping sequences were counted with 200 bp resolution. To find enriched genomic regions, numbers of mapped reads in window of 1 kb were compared with the total number of reads in the genome. MES was calculated as log2 average of gene methylation count in 200 bp interval divided by promoter size (8*200 bp) which is normalized by background total methylation count divided by genome size (15005528*200 bp). The genomic coordinates of promoters and genebodies were downloaded from UCSC Genome Browser database build hg18.

molecule: genomic DNA

source_name: CD4+ naive T cell

extract_protocol: To obtain naïve CD4+ T cells, peripheral blood mononuclear cells (PBMCs) from blood were isolated by Ficoll-paqueTM PLUS (GE Healthcare bio-Science) density gradient centrifugational method and naïve CD4+ T cells were purified by naïve CD4+ T cells isolation kit II (Miltenyi Biotec). The purity of naïve CD4+ T cells was over 90 % by flow cytometric analysis. For epigenetic analysis, genomic DNA of all the samples was isolated with DNA blood mini kit (QIAGEN). The individual DNAs were pooled and purified using 3M NaOAc (pH 5.2) along with ethanol precipitation method. In each experiment set, genomic DNAs of 12~20 individual sample were pooled to reduce individual variation in further analysis. First, for preparation of DNA for Solexa sequencing, glutathione S-transferase (GST)-tagged with methyl-CPG-binding domain (MBD)-2b and His-tagged MBD-3L1 proteins were prepared. Briefly, the purified genomic DNA was sonicated into 100 to 500 bp fragments and incubated with GST-MBD-2b protein, His-MBD-3L1 protein, and the JM110 bacterial RNA. MagneGST beads (Promega) were pre-blocked with the JM110 bacterial RNA to block nonspecific interaction between nucleic acid and MBD proteins, and incubated in the MIRA binding buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 3 mM MgCl2, 0.1% Triton X-100, 5% glycerol, 25 μg/ml bovine serum albumin) and washed with washing buffer (10 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 mM EDTA, 3 mM MgCl2, 0.1% Triton X-100) at 4°C. Second, for preparation of DNA for confirm the Solexa sequencing, DNA (2 μg) was dissolved in 50 μl of the appropriate buffer and 10 U of MseI (NEB), and incubated at 37 °C overnight. After purification of DNA, pull-down of methylated DNA fragments (restricted using MseI) was performed using the Methylcollector kit (Active Motif) according to the manufacturers' protocols. All DNA was eluted and purified with QIAquick PCR Purification Kit (QIAGEN). To apply Solexa sequencing, the DNAs were ligated to a pair of Solexa adaptors for Illumina Genome Analyzer Sequencing. The ligation products were eluted from 175 to 225 bp fragments on an agarose gel after PCR amplification. Cluster generation and 36 cycles of sequencing were done according to the manufacturer's instructions.

tag: disease state

value: Psoriasis

tag: cell type

value: CD4+ naive T cell


title: CD4+ naive T cell MIRA-Seq in healthy controls.

description:
Based on the affinity of the MBD2b/MBD3L1 complex (MIRA technique)
MES_processed_data_file : HC_naive_CD4+_T_cell_MES.wig
final_processed_data_file : HC_processed_data.table

value: healthy control


title: skin-hernia-RH2

tag: tissue


title: skin-hernia-RH6


title: skin-hernia-RH8


title: FAR1OE, ethanol, biological rep3

status: Public on Sep 29 2011

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

hyb_protocol: cRNA was generated by using the Affymetrix One-Cycle Target Labeling and Control Reagent kit (Affymetrix Inc., Santa Clara, California, USA), following the manufacturer’s protocol. The biotinylated cRNA was hybridized to the YG_S98 Affymetrix DNA chips, containing 9335 probe sets which represent approximately 7000 genes and open reading frames from S. cerevisiae Genome database. Chips were washed and scanned on the Affymetrix Complete GeneChip Instrument System, generating digitized image data (DAT) files.

scan_protocol: Chips were washed and scanned on the Affymetrix Complete GeneChip Instrument System, generating digitized image data files.

data_processing: GeneChip operating system (GCOS).

organism: Saccharomyces cerevisiae

source_name: FAR1OE, ethanol

label_protocol: cRNA was generated by using the Affymetrix One-Cycle Target Labeling and Control Reagent kit (Affymetrix Inc., Santa Clara, CA) following the protocol of the manufacturer.

growth_protocol: Yeast strains were collected from glycerol stocks stored at -80°C with a hot sterile rod, without letting the stock to thaw. These cells were grown o/n and used to inoculate fresh synthetic complete medium at a density of about 2*10^5 cell/ml. Cells were then collected during exponential growth (beteween) 3*10^6 e 7*10^6 and used for RNA extraction as described in extract protocol.

extract_protocol: Typically 1*10^9 cells/sample were collected by filtration, washed two times with cold water and immediately freezed at –80°C. For RNA extraction, samples were kept on ice till they were completely thawed. Cells were resuspended in LETS 2X buffer (0.2M LiCl, 0.02M EDTA, 0.4% SDS, 0.02M Tris-HCl, pH=7.4) and phenol/chloroform/isoamylalcohol (PCI) (25:24:1, v/v). After the addition of acid-washed glass beads (Sigma), cells were broken by three vortex/ice cycles of 45 sec each on ice. Suspension was centrifuged (30’, 13000 rpm) and the upper phase was extracted twice with about one volume of PCI. The acqueous layer was collected and precipitated with LiCl (0.5M final concentration) and ethanol at -80°C. Total RNA was purified using the RNeasy RNA purification kit (Quiagen) and stored in RNase-free water.

tag: genotype

tag: carbon source

value: ethanol


title: WT, ethanol, biological rep1

source_name: Wild-type, ethanol


title: far1Δ, ethanol, biological rep3

source_name: far1Δ, ethanol


title: FAR1OE, ethanol, biological rep2


title: far1Δ, ethanol, biological rep2


title: FAR1OE, glucose, biological rep3

source_name: FAR1OE, glucose

value: glucose


title: WT, ethanol, biological rep2


title: WT, glucose, biological rep2

source_name: Wild-type, glucose


title: WT, ethanol, biological rep3


title: FAR1OE, glucose, biological rep1


title: WT, glucose, biological rep3


title: FAR1OE, ethanol, biological rep1


title: far1Δ, glucose, biological rep1

source_name: far1Δ, glucose


title: FAR1OE, glucose, biological rep2


title: far1Δ, ethanol, biological rep1


title: WT, glucose, biological rep1


title: far1Δ, glucose, biological rep2


title: far1Δ, glucose, biological rep3


title: PBMC from pTOL group (W64_pTOL)

status: Public on Jan 09 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: PBMC from pTOL group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'frma' function of the Bioconductor package (v2.6) 'frma' in R.2.11.1

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted from peripheral blood using the TRIzol method (Invitrogen, Cergy Pontoise, France). Genomic DNA was removed by DNase treatment (Roche, Indianapolis, IN, USA). RNA quality and quantity was determined using an Agilent 2100 BioAnalyzer (Palo Alto, CA, USA). RNA was reverse transcribed into cDNA using polydT oligonucleotide and Maloney leukemia virus reverse transcription (Invitrogen).

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: tolerance group

value: pTOL

tag: gender [0=male;1=female]

tag: months from transplant

value: PBMC


title: H3K36me3_ChIPSeq (rep2)

status: Public on Jul 25 2011

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Chromatin IP against H3K36me3

data_processing: DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the HG18 genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described in (Koch et al, Nat Struct Mol Biol (2011), advance online doi:10.1038/nsmb.2085) . As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

source_name: H1299 Cell line

growth_protocol: H1299 cells were grown in DMEM, supplemented with 10% FCS, 100 U ml-1 penicillin-streptomycin and 2mM L-glutamine. Cells were crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). Aliquots of 5x107 cells were snap-frozen in liquid nitrogen and stored at -80C for later use.

extract_protocol: Library were prepared in accordance with the Illumina protocol for ChIP-Seq experiments.

treatment_protocol:
EDTA-free protease inhibitors (Roche, France) were added to all buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 12 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.
All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody (santa cruz N-20, ref sc-899x for RNA polymerase II and Abcam ab9050 for H3k36me3), the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.
Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input.

tag: tumor stage

value: Immortalized

value: Lung carcinoma

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#


title: H3K36me3_ChIPSeq (rep1)

description: Chromatin IP against H3K36me3


title: PolII_N20_ChIPSeq

description: Chromatin IP against Total PolII

value: anti-RNA polymerase II

value: Santa Cruz


title: GnRH, biological rep6

status: Public on Aug 17 2011

city: New York

first: Tony

last: Yuen

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set III)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Expression Array 230 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

label_protocol: Affymetrix two round T7 amplification.

growth_protocol: Anterior pituitaries (13-15/experiment) from rats ovariectomized for two weeks were enzymatically dispersed with trypsin and resuspended in Ca2+-free Minimum Essential Medium (MEM) containing 0.5% BSA and loaded into a unit gravity sedimentation chamber containing a gradient of 1.0-3.0% BSA in Ca2+-free MEM. After equilibration, cells were collected from the bottom of the gradient in 20x50 ml fractions. Fractions 17-20 contained large cells and were combined; this pool represented ~6% of the total cells recovered from the sedimentation chamber. As determined by subsequent immunocytochemistry, LH-positive cells in this pool ranged from 40-60% compared to < 7% for unfractionated cells. The gonadotrope-enriched pool was pelleted and resuspended in supplemented MEM culture medium [MEM plus 200 µM kanamycin sulfate, 0.2 nM E2, and 10% fetal bovine serum (FBS) that had been charcoal-treated to remove endogenous steroids].

extract_protocol: Cell lysates were processed for total RNA using a Qiagen RNeasy mini kit (Qiagen, Valencia, CA) and included an on-column DNase I digestion step.

treatment_protocol: On day 3 of culture, GnRH was added to experimental wells to achieve a final concentration of 10 nM; control wells received an equivalent volume of vehicle medium.  After 40 min, cells were rinsed with ice-cold PBS, lysis buffer containing guanidinium thiocyanate was added, cells were scraped, triturated, and stored at -70ºC.

value: enriched gonadotropes

tag: strain

value: Sprague-Dawley

tag: gender

value: Female

tag: age

value: adult

tag: agent

value: 10 nM GnRH


title: Vehicle, biological rep6

description: Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set III)

value: vehicle


title: Vehicle, biological rep4

description: Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set II)


title: Vehicle, biological rep5

source_name: Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set III)


title: GnRH, biological rep3

description: Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set II)


title: Vehicle, biological rep2

description:
Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set I)
CEL file is missing (backup storage was lost)


title: GnRH, biological rep2

description:
Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set I)
CEL file is missing (backup storage was lost)


title: GnRH, biological rep5

source_name: Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set III)


title: GnRH, biological rep4

source_name: Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set II)


title: Vehicle, biological rep1

source_name: Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set I)


title: Vehicle, biological rep3

source_name: Primary rat gonadotrope cells, vehicle, 40 min (Enrichment set II)


title: Rabbit_IG_ChIPSeq

status: Public on May 20 2011

description: Chromatin IP against Rabbit IG.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: IG_mm9_136_NoArtefacts_Scaled.wig

source_name: Primary T-cells

extract_protocol:
EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1ug/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x10^7 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4C. Chromatin was collected by centrifugation for 5 minutes at 4C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 10 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80C until use and 50ul aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G, with the exception of sheep alpha-rabbit coated beads (M-280) for the ETS1 ChIP. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250ul of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100ul of blocking solution, extracts were added and the mix was incubated overnight at 4C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1ug/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65C for 15 and 10 minutes in 110ul and 100ul of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65C overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input.

CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.

value: thymus

value: T cells

tag: developmental stage

value: CD4+/CD8+ double-positive (DP)


title: PolII_Ser2P_ChIPSeq

description: Chromatin IP against Ser2P form of PolII.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: Ser2P_190_210_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): Ser2P_210_190_merged__no_artefacts_Scaled_BGSub.area.gff

tag: antibody (clone)


title: PolII_Ser5P_ChIPSeq

description: Chromatin IP against Ser5P form of PolII.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: Ser5P_175_155_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): Ser5P_175_155_merged__no_artefacts_Scaled_BGSub.area.gff

tag: cell type

value: Ser5P (3E8)


title: H3K36me3_ChIPSeq

description: Chromatin IP against H3K36me3.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: H3K36me3_230_220_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): H3K36me3_230_220_merged__no_artefacts_Scaled_BGSub.area.gff

tag: tissue

tag: antibody vendor

tag: antibody catalog number


title: TBP_ChIPSeq

description: Chromatin IP against TBP.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TBP_130_115_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TBP_130_115_merged__no_artefacts_Scaled_BGSub.area.gff

value: TBP

value: Diagenode


title: Input_ChIPSeq

description: Chromatin IP against sonicated genomic DNA.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: Input_all_merged_Scaled.wig
Input enriched regions: artefacts+-500_extended_bin50.sgr

extract_protocol:
EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1ug/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x10^7 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4C. Chromatin was collected by centrifugation for 5 minutes at 4C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 10 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80C until use and 50ul aliquots were taken to serve as input controls.  Inputs were combined with an equal volume of 2x elution buffer (100mM Tris pH 8, 10mM EDTA pH 8, 2% SDS) and incubated overnight in a water bath at 65C for 13-15 hours. SDS was then diluted by the addition of an equal volume of TE (10mM Tris pH8, 1mM EDTA pH 8) and RNA was digested by RNase A at a final concentration of 0.2ug/ml at 37C for 2 hours. Samples were subsequently Proteinase K treated at 55C for two hours at a final concentration of 0.2ug/ml. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions and followed by a Qiaquick purification (PCR purification columns, Qiagen, Germany). To ensure greater DNA purity, columns were washed twice in PE buffer and eluted in 50ul H2O. DNA concentration was measured using a Nanodrop 1000 (Thermo Scientific, France) and 500ng were run on 2% agarose gels to verify sonication efficiencies or alternatively 2ng using High Sensitivity DNA chips on a 2100 Bioanalyzer.

CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.


title: FAIRE_Seq

description: FAIRE.

data_processing:
All sequence reads were aligned using SOLiD pipeline to the mouse 2007 (mm9, NCBI Build 37) genome. The output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: FAIRE_140_140_merged_.wig
Peak (GFF): FAIRE_merged_peaks.area.gff

extract_protocol:
For each biological replicate, cells were sorted and 4x106 aliquots were crosslinked and lyzed as described for ChIP-Seq. Sonication was also performed as described, except that 14 on/off cycles were used. The soluble DNA fraction was isolated by performing three consecutive phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions. Samples were then similarly reverse-crosslinked overnight and purified using Minelute (Qiagen) purification columns. DNA was quantified on a Nanodrop 1000 and the size distribution was verified using High Sensitivity DNA chips on a 2100 Bioanalyzer. Samples were subsequently treated similarly to ChIP samples for sequencing.
CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: H3K4me3_166_156_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): H3K4me3_166_156_merged__no_artefacts_Scaled_BGSub.area.gff


title: H3K4me1_ChIPSeq

description: Chromatin IP against H3K4me1.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: H3K4me1_166_156_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): H3K4me1_166_156_merged__no_artefacts_Scaled_BGSub.area.gff


title: GnRH, biological rep1

source_name: Primary rat gonadotrope cells, 10 nM GnRH, 40 min (Enrichment set I)


title: RIP using IgG antibody, biological replicate 1

status: Public on Jul 13 2011

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
01_ConigG-1_10-21-10_S2.CEL

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST array, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing: The Partek Genomics Suite was used to perform microarray data analysis and to generate graphics (Partek GS, St. Louis, MO). Affymetrix array raw fluorescence intensity measures of gene expression were normalized and quantified using robust multi-array analysis. To identify genes differentially expressed between groups, we employed an ANOVA between the groups of interest.

source_name: Hec50co endometrial cancer cells untreated

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility. Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN. Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Hec50co cell lines were cultured in DMEM medium containing 10% fetal bovine serum and 1% penicillin/streptomycin (Gibco BRL)  at 37°C in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol: The Magna RIP Kit (Millipore, MA, USA) was used to immunoprecipitate MTDH and IgG and isolate immunoprecipitated RNA, and was performed according to the manufacturer's instructions.

treatment_protocol: Hec50co cells were maintained in culture without treatment or with 100nM BEZ treatment prior to RIP procedures.

value: Grade 3 endometrioid adenocarcinoma - low differentiation

tag: genotype

value: p53 large deletion - null phenotype

tag: ip antibody

value: IgG [Santa Cruz Biotechnology, normal rabbit IgG, catalog # sc-2027]


title: RIP using MTDH antibody - untreated, biological replicate 2

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
05_ConMTDH-2_10-21-10_S2.CEL

value: MTDH [Sigma, rabbit, HPA010932]


title: RIP using MTDH antibody - untreated, biological replicate 3

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
06_ConMTDH-3_10-21-10_S2.CEL


title: RIP using MTDH antibody - untreated, biological replicate 1

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
04_ConMTDH-1_10-21-10_S2.CEL


title: RIP using MTDH antibody - 100nM BEZ, biological replicate 3

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
09_BEZMTDH-3_10-21-10_S2.CEL

source_name: Hec50co endometrial cancer cells treated with 100nM BEZ (dual PI3K/mTOR inhibitor)


title: RIP using IgG antibody, biological replicate 3

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
03_ConigG-3_10-21-10_S2.CEL

value: p53 large


title: RIP using IgG antibody, biological replicate 2

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
02_ConigG-2_10-21-10_S2.CEL


title: RIP using MTDH antibody - 100nM BEZ, biological replicate 2

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
08_BEZMTDH-2_10-21-10_S2.CEL


title: RIP using MTDH antibody - 100nM BEZ, biological replicate 1

description:
RNA-binding protein Immunoprecipitated RNA (RIP)
07_BEZMTDH-1_10-21-10_S2.CEL


title: MTDH control, biological replicate 2

status: Public on Dec 17 2010

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
5_MTDHplus2_4-13-10_s2.CEL

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Gene 1.0 ST array (Part No. 901085), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

source_name: Hec50co human endometrial cancer cells with a control scrambled ShRNA

growth_protocol: These cell lines were cultured in DMEM medium containing 10% fetal bovine serum and 1% penicillin/streptomycin (Gibco BRL)  at 37°C in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol: mirVana miRNA Isolation Kit (Ambion, Austin, TX) RNA extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: We transfected cells with MTDH short hairpin RNA  interference constructs provided from ORIGENE (Rockville, MD). Individual cell clones resistant to puromycin were expanded and subjected to screening of the expression of the targeted protein by Western blotting.

tag: cell line

value: Hec50co endometrial cancer cell line

tag: cell line traits

value: Loss of p53, loss of hormone receptors ER and PR

tag: disease state

value: Grade 3 endometrioid adenocarcinoma

tag: genotype/variation

value: control


title: MTDH knockdown, biological replicate 2

status: Public on May 01 2011

description: Gene expression data resulting from the knockdown of MTDH in Ishikawa H endometrial cancer cells

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Gene 1.0 ST array (Part No. 901085), and incubated at 45C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

source_name: MTDH knockdown

value: Ishikawa H endometrial cancer cells

value: Grade 1 endometrioid adenocarcinoma - high differentiation

value: p53 mutation G186T


title: MTDH control, biological replicate 3

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
6_MTDHplus3_4-13-10_s2.CEL


title: MTDH knockdown, biological replicate 1


title: MTDH control, biological replicate 3

description: Gene expression data from control Ishikawa H endometrial cancer cells

source_name: MTDH control


title: MTDH knockdown, biological replicate 2

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
2_MTDH-2_4-13-10_s2.CEL

source_name: Hec50co human endometrial cancer cells with MTDH knocked down using ShRNA

value: MTDH knockdown


title: MTDH control, biological replicate 1


title: MTDH knockdown, biological replicate 3


title: MTDH control, biological replicate 1

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
4_MTDHplus1_4-13-10_s2.CEL


title: MTDH knockdown, biological replicate 3

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
3_MTDH-3_4-13-10_s2.CEL


title: Normal prostate tissue adjacent to tumor from patient No.36 PN36U95C

status: Public on Jan 16 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

description: Gene expression data from normal prostate tissue adjacent to tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95C array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: PN36, normal prostate tissue adjacent to tumor from patient No.36

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 minutes of excision and stored in -80C until RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. For prostate tissues adjacent to tumor, samples free of cancer cells, high-grade prostatic neoplasia, or any obvious neoplastic alterations, containing at least 60% glandular cells were selected.

tag: Tissue:normal prostate tissue adjacent to tumor


title: Cultured Dendritic Cells, CD8+ subset - Expt #2

status: Public on Jun 15 2003

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description:
This dataset contains the gene expression profile of a CD11c high, CD8 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen

source_name: Sorted CD11c high, CD8+ Splenic Dendritic Cell population, cultivated 2 hours


title: MTDH knockdown, biological replicate 1

description:
Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
1_MTDH-1_4-13-10_s2.CEL


title: Cultured Dendritic Cells, CD4- CD8- subset - Expt #2

description:
This dataset contains the gene expression profile of a CD11c high, CD4 negative and CD8 negative ("Double Negative") splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen

source_name: Sorted CD11c high, CD8-, CD4- Splenic Dendritic Cell population, cultivated 2 hours


title: Cultured Dendritic Cells, CD8+ subset - Expt #1


title: MTDH control, biological replicate 2


title: Cultured Dendritic Cells, CD4+ subset - Expt #2

description:
This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen

source_name: Sorted CD11c high, CD4+ Splenic Dendritic Cell population, cultivated 2 hours


title: Dendritic Cells, CD8- CD4-  subset - Expt #1

status: Public on Jun 13 2003

description:
This dataset contains the gene expression profile of a CD11c high, CD4 negative, CD8 negative ("Double negative") splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen

source_name: Sorted CD11c high, CD8-, CD4- Splenic Dendritic Cell population


title: Dendritic Cells, CD8- CD4-  subset - Expt #2


title: Cultured Dendritic Cells, CD4+ subset - Expt #1


title: Dendritic Cells, CD8+ subset - Expt #1

description:
This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen

source_name: Sorted CD11c high, CD8+ Splenic Dendritic Cell population


title: Dendritic Cells, CD4+ subset - Expt #2

source_name: Sorted CD11c high, CD4+ Splenic Dendritic Cell population


title: Macrophages, Exposed to Toxoplasma gondii - Repeat #2

status: Public on Mar 27 2003

description:
CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation.  Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of MΦ, rhMCSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation.
Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors.
Keywords = Infectious diseases, Parasites, Infection, Innate immunity

source_name: Monocyte-derived Macrophages, Exposed to the intracellular protozan parasite Toxoplasma gondii for 18 hours


title: Macrophages, Baseline - Repeat #2

source_name: Monocyte-derived Macrophages, Untreated


title: Macrophages, Exposed to Leishmania major - Repeat #2

source_name: Monocyte-derived Macrophages, Exposed to the intracellular protozan parasite Leishmania major for 18 hours


title: Macrophages, Exposed to Leishmania donovani - Repeat #2

source_name: Monocyte-derived Macrophages, Exposed to the intracellular protozan parasite Leishmania donovani for 18 hours


title: Macrophages, Exposed to Mycobacterium tuberculosis - Repeat #1

source_name: Monocyte-derived Macrophages, Exposed to the Mycobacterium tuberculosis bacilli for 18 hours


title: Cultured Dendritic Cells, CD4- CD8- subset - Expt #1


title: Dendritic Cells, CD8+ subset - Expt #2

description:
This dataset contains the gene expression profile of a CD11c high, CD8 positive splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen


title: Macrophages, Exposed to Brugia malayi (5) - Repeat #2

source_name: Monocyte-derived Macrophages, Exposed to the extracellular worm parasite Brugia malyi (5 worms/well)  for 18 hours


title: Macrophages, Exposed to Mycobacterium tuberculosis - Repeat #2


title: Macrophages, Exposed to Brugia malayi (50) - Repeat #2

source_name: Monocyte-derived Macrophages, Exposed to the extracellular worm parasite Brugia malyi (50 worms/well)  for 18 hours


title: Macrophages, Exposed to Brugia malayi (50) - Repeat #1

description:
CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation.  Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of MΦ, rhM-CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation.
Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors.
Keywords = Infectious diseases, Parasites, Infection, Innate immunity


title: Macrophages, Baseline - Repeat #1


title: Dendritic Cells, Exposed to Brugia malayi (5) - Repeat #2

description:
CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation.  Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin.  For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture.  Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation.
Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors.
Keywords = Infectious diseases, Parasites, Infection, Innate immunity

source_name: Monocyte-derived Dendritic Cells, Exposed to the extracellular worm parasite Brugia malyi (5 worms/well)  for 18 hours


title: Macrophages, Exposed to Leishmania donovani - Repeat #1


title: Macrophages, Exposed to Leishmania major - Repeat #1


title: Dendritic Cells, Exposed to Toxoplasma gondii - Repeat #2

source_name: Monocyte-derived Dendritic Cells, Exposed to the intracellular protozan parasite Toxoplasma gondii for 18 hours


title: Macrophages, Exposed to Toxoplasma gondii - Repeat #1


title: Dendritic Cells, CD4+ subset - Expt #1

description:
This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed directly upon isolation. Global scaling was applied to Avg Difference intensity values.
Keywords = mouse, dendritic cells, spleen


title: Dendritic Cells, Exposed to Leishmania major - Repeat #2

description:
CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation.  Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin.  For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture.  Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation.
Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors.

Keywords = Infectious diseases, Parasites, Infection, Innate immunity

source_name: Monocyte-derived Dendritic Cells, Exposed to the intracellular protozan parasite Leishmania major for 18 hours


title: Macrophages, Exposed to Brugia malayi (5) - Repeat #1


title: Dendritic Cells, Exposed to Brugia malayi (50) - Repeat #2

source_name: Monocyte-derived Dendritic Cells, Exposed to the extracellular worm parasite Brugia malyi (50 worms/well)  for 18 hours


title: Dendritic Cells, Exposed to Mycobacterium tuberculosis - Repeat #2

source_name: Monocyte-derived Dendritic Cells, Exposed to the Mycobacterium tuberculosis bacilli for 18 hours


title: Dendritic Cells, Exposed to Brugia malayi (50) - Repeat #1


title: Dendritic Cells, Exposed to Leishmania donovani - Repeat #2

source_name: Monocyte-derived Dendritic Cells, Exposed to the intracellular protozan parasite Leishmania donovani for 18 hours


title: Dendritic Cells, Exposed to Mycobacterium tuberculosis - Repeat #1


title: Dendritic Cells, Exposed to Leishmania major - Repeat #1


title: Dendritic Cells, Baseline - Repeat #2

source_name: Monocyte-derived Dendritic Cells, Untreated


title: Dendritic Cells, Exposed to Toxoplasma gondii - Repeat #1


title: Dendritic Cells, Exposed to Leishmania donovani - Repeat #1


title: Dendritic Cells, Baseline - Repeat #1


title: Dendritic Cells, Exposed to Brugia malayi (5) - Repeat #1