title: scMNase-seq_T_GB1842

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9217

status: Public on Jul 23 2018

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

country: USA

institute: NHLBI,NIH

description: scMNase-seq

library_source: genomic

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Paired-end sequencing reads for 48 scMNase-seq datasets were mapped to mouse genome (mm9) using Bowtie2. Reads with mapping quality (MAPQ) ≤ 10 were removed from further analysis. Discordantly aligned pairs were removed and paired reads were concatenated into fragments. Redundant fragments that mapped to the same location (both ends of fragments) were further removed.
We selected the longest fragments (³140 bp) as nucleosomes and the shortest (≤78 bp) as subnucleosome-sized particles.
The midpoints of nucleosomes/subnucleosomes-sized particles were defined as their positions.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plain text file. Each line is one fragment. The six columns are chrom, start position, end position, length, alignment score and strand.

molecule: genomic DNA

organism: Mus musculus

source_name: NIH/3T3 tet-on 3G cells

growth_protocol: NIH/3T3 cells were maintained in culture medium DMEM (Invitrogen cat# 10566-016) supplemented with 10% FBS (Sigma cat# F4135-500ML) and 100U/ml Penicillin-Streptomycin (Invitrogen cat# 15140-122).

extract_protocol:
For Micrococcal Nuclease (MNase) digestion, 8 ml diluted MNase (1:3000 in lysis buffer) was added to the sorted single cells and incubated at 37°C for 5 min. The reaction was stopped by addition of 80 ml of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), 1 ml of 20mg/ml Proteinase K and 5 ml of 6ng/ml circular carrier DNA. Following incubation at 55°C for 1 hour, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 160bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.

treatment_protocol: Single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).

tag: cell line

tag: cell type

value: fibroblast cell line

tag: cell number

value: Single cell


title: scMNase-seq_NIH3T3_GA9214

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9219

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9212

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9205

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9210

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9207

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9209

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9203

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9204

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9202

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9201

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8332

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8329

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8328

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8326

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9213

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8325

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9211

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9206

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8327

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8319

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8318

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8322

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8316

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8317

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8315

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA8321

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA5875

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA5877

description: scMNase-seq


title: 6520_CONTROL (bisulfite-seq)

status: Public on Jul 17 2018

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description: bisulfite converted genomic DNA

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4)
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version: 0.17.0).
Mapping sequencing reads: a maximum of 1 mismatch was allowed during seed alignment.
The tool deduplicate_bismark was used to remove duplicate alignments.
Methylation calls were performed for the alinment files with the use of Bismark methylation extractor.
Genome_build: Cow genome assembly: ARS-UCD1.2
Supplementary_files_format_and_content: Tab-delimited text files including chromosome name, genomic start position, genomic end position, percentage of methylation at that position, number of C bases that are methylated and number of C bases that are unmethylated

organism: Bos taurus

source_name: Longissimus dorsi

extract_protocol:
Total DNA was extracted from the muscle tissue for whole genome bisulfite sequencing analysis. Extraction, library construction, bisulfite treatment and sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijin, China). DNA was tested for purity using Nanodrop (OD260/OD280), DNA degradation and RNA contamination through an agarose gel electrophoresis and was quantified through Qubit.
DNA was fragmented into 200-300bp strands through the use of Covaris S220. Terminal repairing, A-ligation and adapters ligation were performed to the resulting fragments. The resulting DNA library was treated with bisulfite with the use of the EZ DNA Methylation Gold Kit from Zymo Research. Library concentration was quantified twice, first with Quibit 2.0 and after diluting to 1ng/ul, it was re-quantified with qPCR.

tag: breed

value: Brangus-Angus

tag: ID

tag: treatment

value: CONTROL

tag: tissue

value: Longissimus dorsi


title: 6254_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: scMNase-seq_NIH3T3_GA5879

description: scMNase-seq


title: 6157_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6125_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: scMNase-seq_NIH3T3_GA8314

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA5878

description: scMNase-seq


title: 6419_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA

value: METHIONINE


title: 6126_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6197_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6472_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6226_CONTROL (bisulfite-seq)

description: bisulfite converted genomic DNA


title: scMNase-seq_NIH3T3_GA8323

description: scMNase-seq


title: 6453_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6152_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6415_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6412_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6153_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6485_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6438_METHIONINE (bisulfite-seq)

description: bisulfite converted genomic DNA


title: 6226_CONTROL (rna-seq)

status: Public on Jul 13 2018

library_source: transcriptomic

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4)
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using the software package Hisat2 (version: 2.1.0).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Cow genome assembly: ARS-UCD1.2
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

molecule: total RNA

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini kit. RNA yield and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries from individual samples were sequenced with Illumina's HiSeq 3000 at University of Florida Interdisciplinary Center for Biotechnology Research using 100-pb paired-end sequencing reads.


title: 6520_CONTROL (rna-seq)


title: 6126_CONTROL (rna-seq)


title: 6254_CONTROL (rna-seq)


title: 6157_CONTROL (rna-seq)


title: 6482_CONTROL (rna-seq)


title: 6125_CONTROL (rna-seq)


title: 6197_METHIONINE (rna-seq)


title: 6472_CONTROL (rna-seq)


title: 6419_METHIONINE (rna-seq)


title: 6412_METHIONINE (rna-seq)


title: 6133_CONTROL (rna-seq)


title: 6485_METHIONINE (rna-seq)


title: 6228_METHIONINE (rna-seq)


title: 6152_METHIONINE (rna-seq)


title: A10

status: Public on Mar 29 2018

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: Single-cell RNA-Seq

data_processing:
Data were analyzed using Cell Ranger™ v1.3 pipelines and were visualized by Loupe™ Cell Browser. Both are available in 10x Genomics website.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: csv format: Files include mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the identified cell clusters.
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: Leukocytes

extract_protocol:
We sorted total viable CD45+ leukocytes from the aortas of male Ldlr-/- mice. Three samples were tested: control, after 11 and 20 weeks of a high fat, high cholesterol diet.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10x Genomics). The detailed protocol was provided by 10x Genomics.

tag: strain/background

tag: genotype/variation

value: Ldlr-/-

tag: Sex

value: male

value: aorta

value: leukocytes

tag: cell marker

value: control diet


title: 6153_METHIONINE (rna-seq)


title: A9

description: Single-cell RNA-Seq

value: 11 weeks high fat, high cholesterol diet


title: P56_neun_neg_ATAC_rep2

status: Public on Jan 27 2018

city: La Jolla

first: Rongxin

last: Fang

state: CA

institute: Ludwig Institute for Cancer Research

data_processing:
1) Reads were mapped to the mm10 reference genome using Bowtie2 in paired-end mode; 2) poorly mapped, improperly paired and mitochondrial reads were filtered; 3) PCR duplications were further removed using Picards MarkDuplicates; 4) Mapping positions of reads were adjusted accounting for Tn5 insertion; ATAC-seq signal was normalized into RPKM using deepTools for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, normalized read coverage file

source_name: adult mouse forebrain

extract_protocol:
Nuclei were isolated from snap frozen forebrain tissues and stained with antibodies against NeuN. 20,000 NeuN nuclei were sorted.
Pelleted nuclei were resuspended in the tagmentation buffer. Tagmented DNA was PCR amplified for 8-10 cycles.

tag: strain

tag: developmental stage

value: postnatal day 56


title: 6415_METHIONINE (rna-seq)


title: 6438_METHIONINE (rna-seq)


title: 6453_METHIONINE (rna-seq)


title: P56_neun_neg_ATAC_rep1


title: P56_Forebrain_scATAC_Rep1_Rep2

data_processing:
Alignment: reads were mapped to the mm10 genome assembly using BWA in pair-end mode with default parameters. Alignment filtering: non-uniquely mapped (MAPQ < 10) and improperly paired (flag = 1804) alignments were filtered. Barcode correction: every barcode combination has 4 indexes (i7, p7, p5, i5) with length of 8 bp for each. Reads with barcode combination containing more than 1 mismatch for any index were filtered. Barcodes with allowed mismatches were changed to its closest barcode. Split Reads: Reads were separated into individual cell based on the barcode combination. Mark and remove PCR duplication: for individual cell, we sorted reads based on the genomic coordinates using “samtools sort”, then marked and removed PCR duplication using Picard tools (MarkDuplicate). Remove mitochondria reads: for each cell, reads mapped to mitochondria sequence were filtered. Tn5 insertion position adjustment: all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the - strand were offset -5 bp. Calculate coverage of active promoters (promoters overlapping with aggregate scATAC-seq peaks), coverage of distal elements and “reads in peaks” ratio for each cell. Cell selection: we kept cells that passed our threshold (1) active promoter coverage > 5%; 2) number of reads > 1,000; 3) reads in peak ratio greater than corresponding bulk ATAC-seq level. Selected cells were separated into two replicates based on barcode combination. Insert size distribution was estimated by Picard (CollectInsertSizeMetrics).
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: .mat: binary accessible matrix; xgi: row names for the matrix representing cell barcodes; ygi: column names for the matrix representing genomic elements (features); .qc: Quality metrics for cells that passed quality filtering (column 1: cell barcodes, column 2: number of reads, column 3: promoter coverage, column 4: fraction of reads in peaks.

source_name: mouse forebrain

extract_protocol:
Nuclei were isolated from snap frozen forebrain tissues or GM12878 cells.  Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode wqas introduced by PCR.
Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination (p7 and p5 barcodes). After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode (i7 and i5 barcodes) was introduced by PCR. In general, libraries were sequenced on a HiSeq2500 with following read lengths:  50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). The human mouse mixtures was sequenced on a Miseq with this read lengths: 44 + 43 + 37 + 44 (Read1 + Index1 + Index2 + Read2). The first 8 bp of Index1 correspond to the p7 barcode and the last 8 bp to the i7 barcode. The first 8 bp of Index2 correspond to the i5 barcode and the last 8 bp to the p5 barcode. PLease note that the barcode information was integrated into the read name.
combinatorial ATAC-seq

tag: barcodes

value: Set_1 for Replicate 1; Set_2 for Replicate 2


title: E15.5_Forebrain_scATAC_Rep1_Rep2

value: embryonic day 15.5


title: E13.5_Forebrain_scATAC_Rep1_Rep2

value: embryonic day 13.5


title: E14.5_Forebrain_scATAC_Rep1_Rep2

value: C57BL/6NCrl x C57BL/6NTac

value: embryonic day 14.5


title: P0_Forebrain_scATAC_Rep1_Rep2

value: postnatal day 0


title: E16.5_Forebrain_scATAC_Rep1_Rep2

value: embryonic day 16.5


title: E12.5_Forebrain_scATAC_Rep1_Rep2

value: embryonic day 12.5


title: E11.5_Forebrain_scATAC_Rep1_Rep2

value: embryonic day 11.5

value: Set_1 for Replicate 1; Set_2 for Replicate 2; p5 only 7 bp called


title: EpiSC_ZIC2_ChIPseq

status: Public on May 01 2017

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

country: Japan

institute: Biohistory Research Hall

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2.
ChIP-seq peaks were called using MACS1.4, input DNA without ChIP as reference, and the default settings except for band width, which was adjusted to 150 bases.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using SraTailor

source_name: Epiblast stem cells

growth_protocol: Feeder-free epiblast stem cell culture in N2/B27-supplemented DMEM/F12 with 20 ng/ml activin and 10 ng/ml Fgf2. EpiSCA cultures were freed from activin for 18 hr before harvest, without significant changes in microarray data and called ChIP-seq peaks.

extract_protocol:
After 24 h, the cultures were fixed with 1% formalin for 10 min at room temperature, and then the cells were scraped from dishes, washed, collected in a tube and lysed using the lysis buffer containing 1% SDS. Cell lysates were sonicated in a 1–ml vial using COVARIS M220, which produced an average DNA fragment size of approximately 150 bp. The lysate was mixed with streptavidin beads overnight and washed with a series of solutions described in Matsuda K et al. (submitted).
The DNA fragments were ligated with adapters and amplified by PCR using TruSeq ChIP Sample Prep Kit (Illumina), according to the manufacturer’s directions, except that we terminated the PCR reaction at 10 cycles.

treatment_protocol: A suspension of EpiSCs following Accutase treatment was plated on a 10 cm diameter dish and immediately transfected with 5 mg of pCAGGS-BLRP-BirA plasmid to express BLRP-tagged plasmid and Lipofectamine 2000 (Thermo Fisher). After 8 h, the culture medium was refreshed and 5 mM biotin was added.

tag: chip target

tag: chip reagent

value: Streptavidine

tag: tag

value: biotin


title: L1700166

description: Single-cell RNA-Seq

value: Ldlr-/-

value: male

value: aorta

value: 20 weeks high fat, high cholesterol diet


title: EpiSC_OTX2_ChIPseq


title: EpiSC_POU5F1_ChIPseq


title: GM12878_E15.5_Forebrain_scATAC

organism:
Homo sapiens
Mus musculus

source_name: Mixture of nuclei from E15.5 mouse forebrain and lymphoblastoid cell line (GM12878)

value: mixture of mouse embryonic forebrain and human GM12878 immortalized  lymphoblastoid cell line


title: EpiSCA_ZIC2_ChIPseq

source_name: Epiblast stem cells_freed from Activin


title: EpiSCA_OTX2_ChIPseq


title: EpiSC_POU3F1_ChIPseq


title: MV4-11_PROseq rep2

status: Public on Apr 20 2017

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
Library strategy: PRO-seq
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
Reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was calculated for each strand separately and reported in bedGraph format.

molecule: nuclear RNA

organism: Homo sapiens

source_name: MV4-11 cells

growth_protocol: RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine

extract_protocol:
Nuclei isolation by douncing in isotonic buffer with 0.1% Triton X-100. Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: EpiSCA_POU3F1_ChIPseq


title: EpiSC_SOX2_ChIPseq


title: EpiSC_control


title: EpiSCA_POU5F1_ChIPseq


title: U936_PROseq rep2

source_name: U936 cells


title: MV4-11_PROseq rep1


title: Kasumi-1_PROseq rep5

source_name: Kasumi-1 cells


title: Ly-1_PROseq rep3

source_name: Ly-1 cells


title: U936_PROseq rep1


title: Ly-1_PROseq rep2


title: Ly-1_PROseq rep1


title: Kasumi-1_PROseq rep4


title: Kasumi-1_PROseq rep2


title: EpiSCA_SOX2_ChIPseq


title: Kasumi-1_PROseq rep1


title: Daudi_PROseq

source_name: Daudi cells

value: Daudi


title: Kasumi-1_PROseq rep3


title: Kasumi-1_PROseq rep6


title: antiH3K27ry-2

status: Public on Apr 01 2016

city: North Bethesda

first: sandip

last: de

address: 6 center drive

department: rm 3B-331, bldg 6B

institute: NICHD/NIH

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the Drosophila reference genome (release 5.22/6.02).
.tdf files were generated from .bam files via IGV tools.
Genome_build: Release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format.

organism: Drosophila melanogaster

source_name: 3rd instar brains and imaginal disks, H3K27me3 ChIP

growth_protocol: All flies were grown at 25°C. 3rd instar larvae were dissected for brains and imaginal discs.

extract_protocol:
Fixed brains and imaginal discs were dissected from 10 third instar larvae. Sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Pho (custom made), anti-Ph (a kind gift from Donna Arndt-Jovin), and anti-Engrailed (custom made) antibodies, and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies.
Input ChIP DNA (30 ng) was blunt-ended and phosphorylated. A single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products were purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA was purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated before cluster generation.

value: ry

value: 3rd instar larvae

value: CNS and imaginal disks

tag: chip antibody


title: antiH3K27ry-1


title: 477b

status: Public on Feb 27 2014

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

description: Sample 196

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh3 using tophat v2.0.8
FPKM values were obtained from the tophat output
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for genes and transcript isoforms, and read counts per gene.

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood, and depleted of rRNA and globin RNA (ScriptSeq™ Complete Gold Kit:Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: post-infection

value: whole blood

tag: infectious agent

value: Plasmodium falciparum (Pf)

tag: class

value: Delayed Fever

tag: age

tag: gender

value: Female

tag: anemia status at baseline

tag: s. haematobium at baseline

tag: pf infection status

value: I

tag: parasite density

tag: temp max

tag: extraction date

tag: sequencing date


title: 391b

description: Sample 182

tag: tissue

tag: ID

value: Male


title: 487b

description: Sample 198


title: 468b

description: Sample 192


title: 475a

description: Sample 193

value: pre-infection

value: U


title: 468a

description: Sample 191


title: 391a

description: Sample 181


title: 475b

description: Sample 194


title: 433b

description: Sample 188


title: 464b

description: Sample 190

value: Early Fever


title: 396a

description: Sample 185


title: 433a

description: Sample 187


title: 392a

description: Sample 183


title: 487a

description: Sample 197


title: 382a

description: Sample 179


title: 382b

description: Sample 180


title: 477a

description: Sample 195


title: 380b

description: Sample 178


title: 380a

description: Sample 177


title: 370b

description: Sample 176


title: 392b

description: Sample 184


title: EM-KCs from KC-DTR WT littermate control mouse, 15 days after DT treatment, biological replicate 2

status: Public on Nov 21 2015

type: RNA

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Kupffer cells from WT DT-receptor mice, treated with DT on day 15

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_WT, DT15

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 WT


title: 396b

description: Sample 186


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 15 days after DT treatment, biological replicate 2

description: Kupffer cells from transgenic DT-receptor mice, treated with DT on day 15

source_name: KC_DTR_Tg, DT15

value: DTR Tg


title: EM-KCs from KC-DTR WT littermate control mouse, 15 days after DT treatment, biological replicate 1


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 30 days after DT treatment, biological replicate 1

description: Kupffer cells from transgenic DT-receptor mice, treated with DT on day 30

source_name: KC_DTR_Tg, DT30


title: 464a

description: Sample 189


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 15 days after DT treatment, biological replicate 3


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 15 days after DT treatment, biological replicate 1


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 30 days after DT treatment, biological replicate 2


title: 321a

description: Sample 167


title: 353b

description: Sample 174


title: 353a

description: Sample 173


title: 322b

description: Sample 170


title: 340b

description: Sample 172


title: 322a

description: Sample 169


title: 321b

description: Sample 168


title: 255a

description: Sample 159

value: Immune


title: 294b

description: Sample 164


title: 245a

description: Sample 157


title: 262b

description: Sample 162


title: 245b

description: Sample 158


title: 307a

description: Sample 165


title: 262a

description: Sample 161


title: 294a

description: Sample 163


title: 233b

description: Sample 156


title: 340a

description: Sample 171


title: 255b

description: Sample 160


title: 233a

description: Sample 155


title: 226b

description: Sample 154


title: 226a

description: Sample 153


title: 218b

description: Sample 152


title: 307b

description: Sample 166


title: 218a

description: Sample 151


title: 370a

description: Sample 175


title: 215a

description: Sample 149


title: 215b

description: Sample 150


title: 214a

description: Sample 147


title: 212b

description: Sample 146


title: 214b

description: Sample 148


title: 210a

description: Sample 143


title: 212a

description: Sample 145


title: 184b

description: Sample 142


title: 158a

description: Sample 137


title: 182a

description: Sample 139


title: 210b

description: Sample 144


title: 154b

description: Sample 136


title: 120b

description: Sample 130


title: 153b

description: Sample 134


title: 154a

description: Sample 135


title: 158b

description: Sample 138


title: 111b

description: Sample 128


title: 184a

description: Sample 141


title: 135a

description: Sample 131


title: 135b

description: Sample 132


title: 120a

description: Sample 129


title: 111a

description: Sample 127


title: 081b

description: Sample 126


title: 080a

description: Sample 123


title: 080b

description: Sample 124


title: 079b

description: Sample 122


title: 076b

description: Sample 120


title: 079a

description: Sample 121


title: 076a

description: Sample 119


title: 065a

description: Sample 117


title: 064b

description: Sample 116


title: 182b

description: Sample 140


title: 065b

description: Sample 118


title: 059b

description: Sample 114


title: 064a

description: Sample 115


title: 054a

description: Sample 111


title: 014a

description: Sample 109


title: 054b

description: Sample 112


title: 153a

description: Sample 133


title: 478a

status: Public on Nov 08 2013

tag: time-point

value: Pre-infection


title: 490a


title: 482a


title: 505a


title: 505b

value: Post-infection


title: 482b


title: 488a


title: 478b


title: 490b


title: 454a


title: 488b


title: 059a

description: Sample 113


title: 428a


title: 429a


title: 427b


title: 428b


title: 425b


title: 429b


title: 014b

description: Sample 110


title: 081a

description: Sample 125


title: 427a


title: 422b


title: Parent 3

status: Public on Feb 06 2014

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description:
cDNA, from amplified total RNA
BRAF mutated

hyb_protocol: Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing:
Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); Anova

source_name: WM164 Melanoma cell Line

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Cells were grown RPMI media supplimented with 5% FCS, 2mM L –Glutamine and 2x Penstrep .

extract_protocol: mRNA was  extracted  using RNeasy mini kit Qiagen

treatment_protocol: Cells were treated with 500nM PLX4032 for 16 days period with media containing inhibitor being changed every 3 days

value: Melanoma Lymph node Metastasis

tag: cell line

tag: treatment

value: DMSO


title: 422a

tag: infectious agent


title: 454b

tag: class


title: Parent 2


title: 413b

tag: age


title: 400b

tag: gender


title: 397a

tag: anemia status at baseline


title: 390b

tag: s. haematobium at baseline


title: 425a

tag: pf infection status


title: 400a

tag: parasite density


title: 397b

tag: temp max


title: 387b

tag: extraction date


title: 390a

tag: sequencing date


title: 383a


title: 387a


title: Parent 1

tag: tissue


title: 373b


title: 379b


title: 379a


title: 373a

tag: ID


title: 371b


title: 418b


title: 311a


title: 356a


title: 383b


title: 356b


title: 310b


title: 371a


title: 310a


title: 413a


title: 292b


title: 292a


title: 283b


title: 277a


title: 277b


title: 276b


title: 265a


title: 418a


title: 311b


title: 273b


title: 264b


title: 283a


title: 264a


title: 263b


title: 263a


title: 171a


title: 273a


title: 171b


title: 250a


title: 216a


title: 250b


title: 148b


title: 168a


title: 148a


title: 142a


title: 274a


title: 142b


title: 265b


title: 276a


title: 123a


title: 123b


title: 122b


title: 122a


title: 089a


title: 108a


title: 108b


title: 216b


title: 070a


title: 089b


title: 070b


title: 062b


title: 062a


title: 049b


title: 168b


title: 049a


title: 047a


title: 039b


title: 047b


title: 132b


title: 029a


title: 025a


title: 132a


title: 018b


title: 005b


title: 025b


title: 019b


title: 019a


title: 018a


title: 005a


title: Baf53b+/- Homecage - Replicate 2400

status: Public on Mar 24 2013

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description:
MUHC_2400
Tissue harvested directly from home cage

data_processing:
Basecalling performed using RTA version 1.13.48
Demultiplexing performed using CASAVA version 1.8.2
Alignments to reference assembly mm9 performed using ELAND v2e and bowtie version 0.12.8
Filtering and selection performed using in-house tools
Expression analysis performed using CASAVA version 1.8.2
Differential analysis performed using CyberT: http://cybert.ics.uci.edu
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for each replicate have been combined in a single text file (RPKM_Values.txt), the differential analysis results from CyberT have been summarized and annotated in a single excel file (Differential_Analysis.xls)

source_name: Baf53b_Het_Homecage_dosal hippocampus

extract_protocol:
RNA was isolated from bilateral, dorsal hippocampus using the using RNeasy minikit (Qiagen, 74104).
cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).
Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and sequenced on an IlluminaHiSeq 2000 instrument during a single-end 50 cycles sequencing run by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine.

tag: strain background

tag: genotype/variation

value: Baf53b+/- mutant

tag: sample group

value: homecage; sacrificed directly from the animal's cage

value: dorsal hippocampus


title: 029b

tag: time-point

value: Plasmodium falciparum (Pf)


title: 039a

tag: infectious agent


title: 274b


title: MF.103-11b+.SI#5

status: Public on Dec 28 2011

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: MF.103-11b+.SI#5, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: intestine

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Standard (Re-purified: 99% pure)

value: 7 weeks

tag: exclusion markers

value: PI CD3 B220

tag: genetic background

tag: phenotype markers

tag: separation method

value: dissection/trimming

tag: Sex

value: male


title: MF.Medl.SLN#1

description: MF.Medl.SLN#1, Medullary macrophages from skin draining lymph nodes

source_name: Skin-draining LN

extract_protocol: Digested with Liberase for 20 minutes

tag: age

value: 6 weeks

value: B220 CD90 Ly-6G CD103 SiglecF CD11c


title: MF.II+480lo.PC#1

description: MF.II+480lo.PC#1, Peritoneal Lavage

source_name: Peritoneal Cavity

extract_protocol: Peritoneal Lavage

value: 8 weeks

value: F4/80lo MHC II+ CD11c+ CD115+


title: MF.BM#1

description: MF.BM#1, B220neg CD3neg  Ly-6C/Glo CD115int F4/80+

source_name: Bone marrow

extract_protocol: Flushed femurs and tibias; RBC lysed with ACK buffer


title: MF.103-11b+.SI#2

description: MF.103-11b+.SI#2, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF

extract_protocol: Standard (No re-purification: 94% pure)


title: MF.Medl.SLN#2

description: MF.Medl.SLN#2, Medullary macrophages from skin draining lymph nodes


title: MF.II+480lo.PC#3

description: MF.II+480lo.PC#3, Peritoneal Lavage


title: MF.II+480lo.PC#2

description: MF.II+480lo.PC#2, Peritoneal Lavage


title: MF.103-11b+.SI#3

description: MF.103-11b+.SI#3, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF

extract_protocol: Standard (Re-purified: 98% pure)


title: MF.103-11b+.SI#7

description: MF.103-11b+.SI#7, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF

extract_protocol: Standard (Re-purified: 99.3% pure)


title: MF.BM#2

description: MF.BM#2, B220neg CD3neg  Ly-6C/Glo CD115int F4/80+


title: MF.BM#3

description: MF.BM#3, B220neg CD3neg  Ly-6C/Glo CD115int F4/80+


title: MF.103-11b+.SI#1

description: MF.103-11b+.SI#1, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF


title: DC.LC.Sk#4

status: Public on Apr 29 2010

description: DC.LC.Sk#4, epidermal langerhans cells

source_name: skin

extract_protocol: Disruption using syringe

value: MHCII+ CD11b+ CD45+


title: MF.103-11b+.SI#4

description: MF.103-11b+.SI#4, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF


title: DC.LC.Sk#5

description: DC.LC.Sk#5, epidermal langerhans cells


title: MF.Sbcaps.SLN#3

description: MF.Sbcaps.SLN#3, Subcapsular sinus macrophages from skin draining lymph nodes


title: MF.Sbcaps.SLN#2

description: MF.Sbcaps.SLN#2, Subcapsular sinus macrophages from skin draining lymph nodes


title: MF.103-11b+.SI#6

description: MF.103-11b+.SI#6, Small Intestinal Lamina Propria CD11c-hi CD103- CD11b+ MF


title: Macrophages_mock-infected_12h_rep3

status: Public on Apr 15 2009

last: Bok

address: 50 South drive

department: NIAID

institute: NIH

description: The macrophage cell line RAW264.7 was infected with mouse norovirus MNV-1. The cells were harvested 12 hours post infection, and the expression profile of infected cells was compared to the expression profile of mock-infected cells.

hyb_protocol: As described in Affymetrix's Eukaryotic Sample and Array Processing manual

data_processing: Data were analysed using GeneSpring GX 7.3.1 (Agilent, Santa Clara, CA). Signal values from the probe sets were calculated using micro array suite 5 (MAS5). Each chip was independently normalized to the median expression level of all genes on the chip. Each gene was then normalized to the median expression levels of that gene. Each of the 45,101 genes was filtered by the call of “present or marginal” Affymetrix flag in 3 of the sample replicates.  The remaining genes were analyzed by 1-way ANOVA to identify those with statistically significant differences between samples infected with MNV-1 (3 replicates) and uninfected samples (3 replicates). Variances were calculated using the parametric test with p-value cutoff 0.05.

label: biotin

source_name: RAW264.7 cells, mock-infected, 12hours

extract_protocol: RNA was extracted using Qiagen RNeasy kit as described in the manufacturer's protocol.

tag: Murine macrophage cell line, RAW 264.7


title: Macrophages_mock-infected_12h_rep1

scan_protocol: As described in Affymetrix's Eukaryotic Sample and Array Processing manual


title: Macrophages_mock-infected_12h_rep2

label_protocol: As described in Affymetrix's Eukaryotic Sample and Array Processing manual


title: Macrophages_MNVinfected_12h_rep3

source_name: RAWcells, MNV-1 infected, 12hours

tag: MNV-1, mouse norovirus


title: Macrophages_MNVinfected_12h_rep1

tag: Mouse Norovirus (MNV-1)


title: Macrophages_MNVinfected_12h_rep2


title: Zc3h12aKO_macrophages_0h

status: Public on Feb 19 2009

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

institute: Kyoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using the arrayassist program (Stratagene).

source_name: Zc3h12a KO macrophages unstimulated

label_protocol: Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufactuerer's inscrution.

growth_protocol: peritoneal macrophages were preprared from thioglycollate-injected mice.

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

treatment_protocol: stimulated with 100 ng/ml LPS for indicated periods

tag: strain

value: Zc3h12a KO


title: Wild-type macrophages 0h

source_name: wild-type macrophages unstimulated

value: wild-type


title: Wild-type macrophages 1h

source_name: wild-type macrophages stimulated with LPS for 1 h


title: Zc3h12aKO_macrophages_4h

source_name: Zc3h12a KO macrophages stimulated with LPS for 4 h


title: RAW264.7 macrophages stably expressing LXRalpha and treated with DMSO for 24h

status: Public on Aug 01 2009

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

description: RAW264.7 macrophages stably expressing murine LXRalpha by Chemical Transfection and treated with DMSO for 24h

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

label_protocol: standard Affymetrix protocol

extract_protocol: RNAeasy mini-kit

tag: cell line


title: Wild-type macrophages 2h

source_name: wild-type macrophages stimulated with LPS for 2 h


title: RAW264.7 macrophages stably expressing LXRalpha and treated with LXR and RXR ligands for 24h

description: RAW264.7 macrophages stably expressing murine LXRalpha generated by Chemical Transfection were treated with LXR ligand (GW3965, 1uM) and RXR ligand (LG268 100nM) for 24h.


title: Zc3h12aKO_macrophages_1h

source_name: Zc3h12a KO macrophages stimulated with LPS for 1 h


title: Wild-type macrophages 4h

source_name: wild-type macrophages stimulated with LPS for 4 h


title: Zc3h12aKO_macrophages_2h

source_name: Zc3h12a KO macrophages stimulated with LPS for 2 h


title: Sample_UI2_BMDMs_not_infected_24h_rep2

status: Public on Jan 01 2009

city: Paris

first: Eric

last: Prina

address: 25 rue du Dr Roux

department: Parasitology and Mycology

country: France

institute: Institut Pasteur

hyb_protocol: Affymetrix EukGE-WS2v5 Hybridization

scan_protocol: Standard Affymetrix protocol

data_processing:
Data processing, background correction, normalization and signal quantification were carried out with GC-Robust Multiarray Analysis (GC-RMA) algorithm using all samples (I1, I2, UI1 and UI2).
Unreliable probe-sets called “Absent” by Affymetrix GeneChip Operating Software (GCOS, www.affymetrix.com/support/technical/manual/expression_manual.affx) for at least 3 out of 4 GeneChips were discarded from subsequent analyses, as well as probe-sets called “Absent” once within samples plus once within controls (total number of probe-sets filtered out: 25,994 out of 45,101, i.e. 57.64%; see online supplementary material).
Local pooled error (LPE) tests were performed to identify significant differences in gene expression between parasite-free and parasite-harboring MΦs.
Benjamini-Hochberg (BH) multiple-test correction was applied to control for the number of false positives with an adjusted 5% statistical significance threshold.
We used GC-RMA algorithm, LPE tests and BH multiple-test correction as implemented in Splus ArrayAnalyzer® module (www.insightful.com/products/s-plus_arrayanalyzer/).
A total of 1,248 probe-sets showed significant differential expression, and were input into Ingenuity Pathway Analysis software 5.5.1 (www.ingenuity.com) to perform a biological interaction network analysis.

source_name: BALB/c mouse bone marrow-derived macrophages

label_protocol:
Affymetrix standard protocol:
www.affymetrix.com/support/technical/other/oncecyle_presentation.pdf

growth_protocol: Bone marrow cell suspensions recovered from tibias and femurs of BALB/c mice were suspended in RPMI 1640 medium (Seromed) supplemented with 10% FCS, antibiotics and 20% L-929 fibroblast-conditioned medium. Cells were distributed in bacteriologic Petri dishes (Greiner, Germany) and incubated at 37 °C in a 5% CO2 air atmosphere. Six days later, bone marrow-derived smoothly adherent macrophages (BMDMs) were washed with Dulbecco’s phosphate buffered solution (PBS) and resuspended in prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG, Berlin, Germany). Recovered BMDMs were deposited in flat-bottom 24-well plates (Tanner, Switzerland) at a density of 5 * 10e-05 cells per well (reference time: t=0h).

extract_protocol: Total RNA extraction directly from living Macrophages(RNeasy+ Mini-Kit, Qiagen), RNA quality control and concentration were determined using the NanoDrop ND-1000 microspectrophotometer. RNA integrity was assessed using the Agilent-2100 Bioanalyzer (RNA Integrity Numbers ≥ 9/10).

treatment_protocol: At t=24h, amastigotes were NOT added to bone marrow-derived macrophages. Parasite-free macrophages were cultured at 34°C for 24h.


title: macrophages

status: Public on Mar 22 2010

city: Shinjuku-ku

first: Takeshi

last: Miyamoto

state: Tokyo

address: 35 Shinanomachi

department: School of Medicine

institute: Keio University

description: Gene expression data from macrophages

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Mouse Genome 430 2.0 Array. GeneChip® Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips® Arrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip®Operating Software using Affymetrix default analysis settings.

source_name: macrophages cultured in the presence of M-CSF for six days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, one-cycle, from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow cells were isolated from 8 weeks old mouse and cultured in the presence of M-CSF for three days. Then M-CSF-dependent adherent cells were harvested as macrophage and osteoclast common progenitor cells.

extract_protocol: RLT extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Common progenitor cells were cultured with M-CSF alone for macrophages and M-CSF plus RANKL for osteoclasts, respectively. After six days of cultivation, cells were lysed in RLT solution (RNeasy, QIAGEN).

tag: cell type

value: Bone marrow derived macrophages


title: Sample_I2_BMDMs_infected_24h_rep2

description: Leishmania RNA did not interfere with BALB/c mouse RNA hybridization onto GeneChips by increasing the fluorescence signal (data not shown). Indeed, FC values for a technical replicate of mouse RNA were comparable to those for mouse RNA “contaminated” with up to 10% of L. amazonensis RNA taking the “non-contaminated” mouse RNA as a reference (P-value ~ 0, one-sided paired Student’s t-test for FC increases).

treatment_protocol: At t=24h, amastigotes were added at a multiplicity of 4 amastigotes per bone marrow-derived macrophage. Parasite-housing macrophages (>98%) were cultured at 34°C for 24h.

tag: Female Swiss nu/nu mice , between 8 and 12-week old were used for L. amazonensis strain LV79 (MPRO/BR/1972/M1841) propagation.


title: Sample_UI1_BMDMs_not_infected_24h_rep1


title: Sample_I1_BMDMs_infected_24h_rep1


title: Myd88-/-Trif-/-, Lp03, T=4 hours

status: Public on Nov 15 2008

city: New Haven

first: Sunny

last: Shin

state: CT

address: 295 Congress Ave.

department: Section of Microbial Pathogenesis

institute: Yale University School of Medicine

description: Myd88-/-Trif-/- bone marrow derived macrophages, Lp03, T=4 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station and stained with streptavidin phycoerythrin.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzedusing Affymetrix GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: bone marrow-derived macrophages

label_protocol: Biotinylated cRNA were prepared according to the recommended Affymetrix protocol from 5 ug total RNA.

growth_protocol: Macrophages were derived from bone marrow treated with  M-CSF for 7 days

extract_protocol: RNAbee reagent extraction of total RNA was performed according to manufactuer's protocol. RNA was further purified using the Qiagen RNeasy kit. Quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on the Agilent Bioanalyzer.

treatment_protocol: Macrophages were infected with WT (Lp02) or dotA mutant (Lp03) L. pneumophila for 4 hours at an MOI=25

tag: Myd88-/-Trif-/- bone marrow-derived macrophages, Lp03, T=4 hours


title: Myd88-/-Trif-/-, Lp02, T=4 hours

description: Myd88-/-Trif-/- bone marrow derived macrophages, Lp02, T=4 hours

tag: Myd88-/-Trif-/- bone marrow-derived macrophages, Lp02, T=4 hours


title: Myd88-/-Rip2-/-, Lp03, T=4 hours

description: Myd88-/-Rip2-/- bone marrow derived macrophages, Lp03, T=4 hours

tag: Myd88-/-Rip2-/- bone marrow-derived macrophages, Lp03, T=4 hours


title: WT IL-4

status: Public on Oct 10 2008

city: Munchen

first: Laura

last: Helming

address: Trogerstr. 30

institute: Institut für medizinische Mikrobiologie, Immunologie und Hygiene

description: Gene expression of macrophages after 18 hours exposure to IL-4

hyb_protocol: 15µg of biotinylated cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

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

data_processing: All data analyses were performed by using Bioconductor version 1.5 for the statistical software R. RMA was used as measurement

source_name: WT IL-4

label_protocol: Biotinylated antisense cRNA was prepared by using two cycles of in vitro amplification according to the Affymetrix Small Sample Labeling Protocol II.

growth_protocol: Cells were harvested from the peritoneal cavity of thioglycolate treated mice.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit.

treatment_protocol: Cells were treated for 18 hours on permanox slides.

tag: Mice used in this study were on a C57BL/6J background, 10-30 weeks old and housed at specific-pathogen free conditions.

tag: Peritoneal macrophages from C57BL/6J


title: WT_BoneMarrowMacrophages_LPS-stimulated_4hours_rep1

status: Public on Jun 25 2008

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

description: no additional description

scan_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001 Affymetrix 11 µm feature parameter settings: alpha 1 = 0.05, alpha 2 = 0.065, tau = 0.15

data_processing: Affymetrix MAS 5.0, trimmed mean (trimming off the top and bottom 2%) set to 150

label: biotin/SAPE

source_name: WT mouse bone marrow macrophages, LPS stimulated, 4 hours

label_protocol: NuGEN Ovation protocol following the manufacturer's recommendations

growth_protocol: cells were grown in macrophage-SFM medium (Gibco) containing 10% FCS and 30% L-929R-cell-conditioned medium at 37°C in a humidified CO2 (5%) incubator

extract_protocol: Qiagen RNeasy protocol following the manufacturer's recommendations

treatment_protocol: stimulation with 1 ug/ml LPS for 4 hours

tag: bone marrow macrophages from 1 female and 2 male wild type Balb/c mice


title: WT_BoneMarrowMacrophages_LPS-stimulated_4hours_rep2

description: no additional description

hyb_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001


title: IRAK4-KD_BoneMarrowMacrophages_LPS-stimulated_1hour_rep1

description: no additional description

source_name: IRAK4 kinase dead mouse bone marrow macrophages, LPS stimulated, 1 hour

treatment_protocol: stimulation with 1 ug/ml LPS for 1 hour

tag: bone marrow macrophages from 1 female and 1 male IRAK4 kinase dead Balb/c mouse


title: Dap12-KO untreated

description: Gene expression of resting macrophages

source_name: Dap12-KO untreated

tag: Peritoneal macrophages from DAP12 KO


title: WT_BoneMarrowMacrophages_unstimulated_4hours_rep2

description: no additional description

source_name: WT mouse bone marrow macrophages, unstimulated, 4 hours

treatment_protocol: no treatment


title: IRAK4-KD_BoneMarrowMacrophages_LPS-stimulated_4hours_rep2

description: no additional description

source_name: IRAK4 kinase dead mouse bone marrow macrophages, LPS stimulated, 4 hours


title: WT_BoneMarrowMacrophages_unstimulated_4hours_rep1

description: no additional description


title: WT untreated

description: Gene expression of resting macrophages

source_name: WT untreated


title: WT_BoneMarrowMacrophages_LPS-stimulated_1hour_rep2

description: no additional description

source_name: WT mouse bone marrow macrophages, LPS stimulated, 1 hour


title: IRAK4-KD_BoneMarrowMacrophages_unstimulated_4hours_rep1

description: no additional description

source_name: IRAK4 kinase dead mouse bone marrow macrophages, unstimulated, 4 hours


title: IRAK4-KD_BoneMarrowMacrophages_LPS-stimulated_4hours_rep1

description: no additional description


title: Myd88-/-Rip2-/-, Lp02, T=4 hours

description: Myd88-/-Rip2-/- bone marrow derived macrophages, Lp02, T=4 hours

tag: Myd88-/-Rip2-/- bone marrow-derived macrophages, Lp02, T=4 hours


title: IRAK4-KD_BoneMarrowMacrophages_LPS-stimulated_1hour_rep2

description: no additional description


title: BMDM_Pam3CSK4-MDP_3h_rep2

status: Public on Mar 15 2008

city: Ann Arbor

first: Yun-Gi

last: Kim

state: MI

address: 1500 E. Medical Center Dr. 4111 CCGC

institute: University of Michigan

description: Gene expression data from bone marrow derived macrophages

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 7G.

data_processing: The data were analyzed using the affy package of Bioconductor. Raw probe-level data were converted to expression measures using the Robust Multi-array Average (RMA) method.

source_name: Mus musculus bone marrow derived macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: Total RNA was purified with RNeasy Mini Kit (Qiagen).

treatment_protocol: BMDMs were stimulated with 1 mg/ml Pam3CSK4 for 24 h and given 10 mg/ml MDP for 3 h


title: BMDM_Pam3CSK4-Pam3CSK4_3h_rep2

treatment_protocol: BMDMs were stimulated with 1 mg/ml Pam3CSK4 for 24 h and given 1 mg/ml Pam3CSK4 for 3 h


title: BMDM_MDP-MDP_3h_rep2

treatment_protocol: BMDMs were stimulated with 10 mg/ml MDP for 24 h and given 10 mg/ml MDP for 3 h


title: Dap12-KO IL-4

source_name: Dap12-KO IL-4


title: BMDM_MDP-Pam3CSK4_3h_rep2

treatment_protocol: BMDMs were stimulated with 10 mg/ml MDP for 24 h and given 1 mg/ml Pam3CSK4 for 3 h


title: BMDM_unpretreated-Pam3CSK4_3h_rep2

treatment_protocol: BMDMs were left untreated for 24 h and given 1 mg/ml Pam3CSK4 for 3 h


title: IRAK1/IRAK2 KO_macrophages_0h

status: Public on Mar 08 2008

description: Gene expression data from unstimulated IRAK1/IRAK2 KO macrophages

scan_protocol: slides were scanned using the Affymetrix GeneChip scanner 3000.

source_name: IRAK1/IRAK2 KO macrophages unstimulated

treatment_protocol: stimulated with 100 ng/ml MALP-2 for indicated periods

tag: IRAK1/IRAK2 KO macrophages unstimulated


title: IRAK1/IRAK2 KO_macrophages_4h

description: Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 4h

source_name: IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 4 h


title: IRAK2 KO_macrophages_4h

description: Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 4h

source_name: IRAK2 KO macrophages stimulated with MALP-2 for 4 h


title: BMDM_untreated_3h_rep2

treatment_protocol: BMDMs were left untreated for 24 h and unstimulated for 3 h

tag: bone marrow derived macrophages from C57BL/6


title: BMDM_unpretreated-MDP_3h_rep2

treatment_protocol: BMDMs were left untreated for 24 h and stimulated with 10 mg/ml MDP for 3 h


title: IRAK2 KO_macrophages_2h

description: Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 2h

source_name: IRAK2 KO macrophages stimulated with MALP-2 for 2 h


title: IRAK1/IRAK2 KO_macrophages_2h

description: Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 2h

source_name: IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 2 h


title: Wild-type_macrophages_8h

description: Gene expression data from wild-type macrophages stimulated with MALP-2 for 8h

source_name: wild-type macrophages stimulated with MALP-2 for 8 h


title: WT_BoneMarrowMacrophages_LPS-stimulated_1hour_rep1

description: no additional description


title: Wild-type_macrophages_4h

description: Gene expression data from wild-type macrophages stimulated with MALP-2 for 4h

source_name: wild-type macrophages stimulated with MALP-2 for 4 h


title: Wild-type_macrophages_0h

description: Gene expression data from unstimulated wild-type macrophages

source_name: wild-type macrophages unstimulated

tag: wild-type macrophages unstimulated


title: IRAK2 KO_macrophages_0h

description: Gene expression data from unstimulated IRAK2 KO macrophages

source_name: IRAK2 KO macrophages unstimulated

tag: IRAK2 KO macrophages unstimulated


title: IRAK1/IRAK2 KO_macrophages_8h

description: Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 8h

source_name: IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 8 h


title: Wild-type_macrophages_2h

description: Gene expression data from wild-type macrophages stimulated with MALP-2 for 2h

source_name: wild-type macrophages stimulated with MALP-2 for 2 h


title: LPS plus IL-10, 30 min, Rep_1

status: Public on Dec 01 2007

city: Memphis

first: Peter

middle: J

last: Murray

address: 332 Nth Lauderdale

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

description: Macrophages treated with LPS plus IL-10, 30 min, Replicate 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (GCOS v1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) plus IL-10 (10 ng/ml) for 30 minutes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Macrophages were isolated from the bone marrow of IL-10 -/- mice and cultured in complete DMEM containing CSF-1 (source: conditioned media from L cells)  and 10% fetal bovine serum for 7 days until mature macrphages constituted >95% of the viable cells. Macrophages were scraped and re-plated under identical conditions for each replicate sample. For each replicate, a complete independent experiment was performed using mice of the same age and sex. Each replicate was performed sequentially.

treatment_protocol: Macrophages were treated for the indicated times with LPS (100 ng/ml) or with LPS (100 ng/ml) plus IL-10 (10 ng/ml) in the presence of complete DMEM/10% FBS without CSF-1.

tag: Genotype


title: LPS plus IL-10, 30 min, Rep_2

description: Macrophages treated with LPS plus IL-10, 30 min, Replicate 2


title: LPS, 30 min, Rep_2

description: Macrophages treated with LPS, 30 min, Replicate 2

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) for 30 minutes


title: LPS plus IL-10, 30 min, Rep_3

description: Macrophages treated with LPS plus IL-10, 30 min, Replicate 3


title: LPS plus IL-10, 20 min, Rep_1

description: Macrophages treated with LPS plus IL-10, 20 min, Replicate 1

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) plus IL-10 (10 ng/ml) for 20 minutes


title: LPS, 20 min, Rep_3

description: Macrophages treated with LPS, 20 min, Replicate 3

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) for 20 minutes


title: LPS plus IL-10, 20 min, Rep_2

description: Macrophages treated with LPS plus IL-10, 20 min, Replicate 2


title: LPS, 30 min, Rep_3

description: Macrophages treated with LPS, 30 min, Replicate 3


title: LPS, 20 min, Rep_1

description: Macrophages treated with LPS, 20 min, Replicate 1


title: LPS, 30 min, Rep_1

description: Macrophages treated with LPS, 30 min, Replicate 1


title: LPS plus IL-10, 10 min, Rep_2

description: Macrophages treated with LPS plus IL-10, 10 min, Replicate 2

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) plus IL-10 (10 ng/ml) for 10 minutes


title: LPS, 10 min, Rep_2

description: Macrophages treated with LPS, 10 min, Replicate 2

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) for 10 minutes


title: LPS plus IL-10, 10 min, Rep_1

description: Macrophages treated with LPS plus IL-10, 10 min, Replicate 1


title: LPS, 10 min, Rep_1

description: Macrophages treated with LPS, 10 min, Replicate 1


title: WT macrophage LPS

status: Public on Aug 17 2007

city: Suita

first: Masahiro

last: Yamamoto

address: 2-2, Yamada-oka

institute: Osaka University

description: Successfully analyzed

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Genechip Mouse Genome array.

scan_protocol: Gene chip scanner 3000 OB

data_processing: MAS5.0 was used

label: Biotinylated RNA

source_name: Wild type macrophages were treated with LPS

label_protocol: Biotinylated cRNA were prepared according to Affymetryx protocol

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

tag: 129/B6 background


title: IRAK4-KD_BoneMarrowMacrophages_unstimulated_4hours_rep2

description: no additional description

source_name: IRAK4 kinase dead mouse bone marrow macrophages, unstimulated, 4 hours


title: Trib1 #2 KO macrophage LPS

description: Successfully analyzed

source_name: Trib1 #2 KO macrophages were treated with LPS

tag: 129/B6 background, 6-10 weeks


title: LPS plus IL-10, 10 min, Rep_3

description: Macrophages treated with LPS plus IL-10, 10 min, Replicate 3


title: LPS, 10 min, Rep_3

description: Macrophages treated with LPS, 10 min, Replicate 3


title: LPS, 20 min, Rep_2

description: Macrophages treated with LPS, 20 min, Replicate 2


title: Wild-type macrophage medium

description: Successfully analyzed

source_name: WT macrophages are treated with medium


title: Trib1 #2 Wild-type macrophage LPS

description: Successfully analyzed

source_name: Trib1 #2 Wild-type macrophages were treated with LPS


title: Intestine CD11b(+)11c(-)_BP21

status: Public on Aug 24 2007

city: La Jolla

first: Tim

last: Denning

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description: Gene expression data from macrophages

data_processing: As per Vanderbilt Microarray Shared Resource Standard Protocol, Algorithm: 5.0 ExpressionStat; MAS5.0

source_name: Intestine (freshly isolated)

growth_protocol: Freshly isolated, then FACS-sorted for CD11b+11c- cells

extract_protocol: Qiagen Rneasy Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment involved


title: Intestine CD11b(+)11c(-)_BP04

description: Gene expression data from macrophages

hyb_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol


title: Spleen CD11b(+)11c(-)_BP03

description: Gene expression data from macrophages

scan_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

source_name: Spleen (freshly isolated)


title: Spleen CD11b(+)11c(-)_BP20

description: Gene expression data from macrophages

label_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol


title: LPS_pre_LPS_restimulation_rep_C

status: Public on Aug 10 2007

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

description: Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether.

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: rma background correction and normalization. Linear values.

label: biotin, PE

source_name: macrophages with 1_1 stimulation with LPS

label_protocol: Affymetrix standard procedure

extract_protocol: Cells were lysed in TriFast for RNA isolation as recommended by the manufacturer

tag: strain

tag: cells

value: bone marrow cells differentiated in M-CSF


title: Trib1 #1 KO macrophage treated with LPS

description: Successfully analyzed

source_name: Trib1 #1 KO macrophages were treated with LPS


title: LPS_pre_no_restimulation_rep_B

source_name: macrophages with 1_0 stimulation with LPS


title: LPS_pre_no_restimulation_rep_C


title: no_pre_no_restimulation_rep_B

source_name: macrophages with 0_0 stimulation with LPS


title: no_pre_LPS_restimulation_rep_B

source_name: macrophages with 0_1 stimulation with LPS


title: IRAK2 KO_macrophages_8h

description: Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 8h

source_name: IRAK2 KO macrophages stimulated with MALP-2 for 8 h


title: no_pre_LPS_restimulation_rep_A


title: no_pre_no_restimulation_rep_C


title: no_pre_no_restimulation_rep_A


title: LPS_pre_no_restimulation_rep_A


title: Macrophage 14smi122

status: Public on Jul 19 2007

city: Cleveland

first: Jonathan

middle: David

last: Smith

state: OH

address: 9500 Euclid Avenue

department: Cell Biology

institute: Cleveland Clinic

description: Gene expression data from mouse bone marrow macrophages

hyb_protocol: Following fragmentation, 12 ug of cRNA was hybridized to Affymetrix 430v2 arrays according to Affymetric protocols

scan_protocol: Arrays were scanned using the Hewlet-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Affymetrix Microarray Suite version 5.0 (MAS 5.0) using Refiner software (Genedata) using default settings. The normalization target was set to 500.

source_name: 16 week old apoE-deficient F2 male mouse from an AKRxDBA/2 intercross

label_protocol: Biotin labeled cRNA was prepared from 1 ug RNA using the BioARray High Yield RNA Transcript labeling kit (Enzo)

growth_protocol: Cells were cultured for 2 weeks in DMEM containing 10% FBS and 20% L-cell conditioned medium

extract_protocol: RNA extracted with RNAeasy minikit (Qiagen)

tag: Male


title: no_pre_LPS_restimulation_rep_C


title: Macrophage 14smi117


title: Macrophage 14smi114


title: Macrophage 14smi119


title: Macrophage 14smi116


title: Macrophage 14smi118


title: Macrophage 14smi121


title: Macrophage 14smi110


title: Macrophage 14smi115


title: Macrophage 14smi112


title: Macrophage 14smi120


title: Macrophage 14smi109


title: Macrophage 14smi108


title: Macrophage 14smi105


title: Macrophage 14smi107


title: Macrophage 14smi113


title: Macrophage 14smi111


title: Macrophage 14smi104


title: Macrophage 14smi106


title: LPS_pre_LPS_restimulation_rep_B


title: Macrophage 14smi102


title: Macrophage 14smi101


title: Macrophage 14smi100


title: Macrophage 14smi097


title: Macrophage 14smi098


title: Macrophage 14smi103


title: Macrophage 14smi099


title: Macrophage 14smi095


title: Macrophage 14smi096


title: Macrophage 14smi093


title: Macrophage 14smi090


title: Macrophage 14smi089


title: Macrophage 14smi087


title: Macrophage 14smi092


title: Macrophage 14smi088


title: Macrophage 14smi094


title: Macrophage 14smi086


title: Macrophage 14smi083


title: Macrophage 14smi082


title: Macrophage 14smi084


title: Macrophage 14smi085


title: Macrophage 14smi077


title: Macrophage 14smi081


title: LPS plus IL-10, 20 min, Rep_3

description: Macrophages treated with LPS plus IL-10, 20 min, Replicate 3

source_name: IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) plus IL-10 (10 ng/ml) for 20 minutes


title: Macrophage 14smi078


title: Macrophage 14smi079


title: Macrophage 14smi080


title: Macrophage 14smi076


title: Macrophage 14smi091


title: Macrophage 14smi069


title: Macrophage 14smi071


title: Macrophage 14smi075


title: Macrophage 14smi066


title: Macrophage 14smi065


title: Macrophage 14smi062


title: Macrophage 14smi068


title: Macrophage 14smi072


title: Macrophage 14smi073


title: Macrophage 14smi063


title: Macrophage 14smi061


title: Macrophage 14smi074


title: Macrophage 14smi057


title: Macrophage 14smi060


title: Macrophage 14smi070


title: Macrophage 14smi056


title: Macrophage 14smi064


title: Macrophage 14smi067


title: Macrophage 14smi058


title: Macrophage 14smi055


title: Macrophage 14smi052


title: Macrophage 14smi053


title: Macrophage 14smi054


title: Macrophage 14smi059


title: Macrophage 14smi050


title: Macrophage 14smi049


title: Macrophage 14smi051


title: Macrophage 14smi047


title: LPS_pre_LPS_restimulation_rep_A


title: Macrophage 14smi044


title: Macrophage 14smi040


title: Macrophage 14smi033


title: Macrophage 14smi036


title: Macrophage 14smi048


title: Macrophage 14smi035


title: Macrophage 14smi042


title: Macrophage 14smi045


title: Macrophage 14smi039


title: Macrophage 14smi032


title: Macrophage 14smi046


title: Macrophage 14smi029


title: Macrophage 14smi038


title: Macrophage 14smi027


title: Macrophage 14smi043


title: Macrophage 14smi025


title: Macrophage 14smi037


title: Macrophage 14smi026


title: Macrophage 14smi034


title: Macrophage 14smi041


title: Macrophage 14smi030


title: Macrophage 14smi024


title: Macrophage 14smi031


title: Macrophage 14smi023


title: Macrophage 14smi028


title: Macrophage 14smi021


title: Macrophage 14smi020


title: Macrophage 14smi022


title: Macrophage 14smi018


title: Macrophage 14smi019


title: Macrophage 14smi010


title: Macrophage 14smi014


title: Macrophage 14smi016


title: Macrophage 14smi009


title: Macrophage 14smi015


title: Macrophage smi117

source_name: 16 week old apoE-deficient F2 female mouse from an AKRxDBA/2 intercross

tag: Female


title: Macrophage 14smi011


title: Macrophage smi122


title: Macrophage smi121


title: Macrophage smi125


title: Macrophage 14smi013


title: Macrophage smi118


title: Macrophage 14smi012


title: Macrophage smi119_2


title: Macrophage 14smi017


title: Macrophage smi120


title: Macrophage smi123


title: Macrophage smi113


title: Macrophage smi112


title: Macrophage smi115


title: Macrophage smi114


title: Macrophage smi126


title: Macrophage smi109


title: Macrophage smi124


title: Macrophage smi116


title: Macrophage smi108


title: Macrophage smi110


title: Macrophage smi111


title: Macrophage smi107


title: Macrophage smi106_2


title: Macrophage smi105


title: Macrophage smi97


title: Macrophage smi98


title: Macrophage smi104


title: Macrophage smi96


title: Macrophage smi95


title: Macrophage smi94


title: Macrophage smi91


title: Macrophage smi102


title: Macrophage smi103


title: Macrophage smi93


title: Macrophage smi88


title: Macrophage smi99


title: Macrophage smi101


title: Macrophage smi100


title: Macrophage smi92


title: Macrophage smi83


title: Macrophage smi85


title: Macrophage smi84


title: Macrophage smi86


title: Macrophage smi80


title: Macrophage smi90


title: Macrophage smi87


title: Macrophage smi78


title: Macrophage smi77


title: Macrophage smi79


title: Macrophage smi81


title: Macrophage smi89


title: Macrophage smi76


title: Macrophage smi74


title: Macrophage smi73


title: Macrophage smi75


title: Macrophage smi66


title: Macrophage smi71


title: Macrophage smi63


title: Macrophage smi64


title: Macrophage smi82


title: Macrophage smi65


title: Macrophage smi61


title: Macrophage smi67


title: Macrophage smi68


title: Macrophage smi70


title: Macrophage smi59


title: Macrophage smi69


title: Macrophage smi57


title: Macrophage smi60


title: Macrophage smi72


title: Macrophage smi52


title: Macrophage smi56


title: Macrophage smi58


title: Macrophage smi62


title: Macrophage smi48


title: Macrophage smi55


title: Macrophage smi50


title: Macrophage smi53


title: Macrophage smi49


title: Macrophage smi47


title: Macrophage smi46


title: Macrophage smi45


title: Macrophage smi42


title: Macrophage smi38


title: Macrophage smi40


title: Macrophage smi37


title: Macrophage smi39


title: Macrophage smi41


title: Macrophage smi36


title: Macrophage smi33


title: Macrophage smi51


title: Macrophage smi34


title: Macrophage smi35


title: Naive-rep1

status: Public on Apr 22 2007

first: Simmie

middle: L

last: Foster

address: 300 Cedar St

department: Immunobiology

description:
Additional protocols:

                               cDNA SYNTHESIS

FIRST STRAND cDNA SYNTHESIS

Important notes:

• Step 1. The recommended starting amount of total RNA is 10µg per reaction. Do not use less than this. 10µg of  total RNA produces approximately 40µg to 110µg of cRNA. If you require more cRNA than this then 2 reactions for each sample should be carried out.
• Step 3 breaks the secondary structure of RNA and step 4 prevents secondary structure reformation. These steps are the key steps for successful cDNA preparation.
• The T7(dT)24  primer used in the cDNA synthesis must be of high quality and HPLC-purified. Insufficiently purified primer may appear to produce good double stranded cDNA, (since the 5’ end of the primer is not critical for the priming step), but still result in poor in vitro transcription yields if the primer is contaminated with shorter sequences, (missing the 5’ end). Affymetrix have found GENSET’s HPLC-purified T7(dT)24 primer to be very reliable. Affymetrix also sells the T7(dT)24 primer as a quality assured kit (T7-Oligo dT  Promoter  Primer Kit )
• A master mix should be prepared for step 5. Mix thoroughly, spin briefly if necesssary.

METHOD

1. Place the following in a microfuge tube:

X µl  (10µg) total RNA in DEPC treated dH2O.
2 µl  (50 µM) T7(dT)24 primer.
Y µl  DEPC treated dH2O.
11µl  Total

2. Mix by pipetting, spin briefly if necessary.
3. Incubate at 65-70 0C for 10 minutes in a heated block
4. Place tubes on ice.
5. Prepare a master mix on ice. The quantities for each reaction are:

      4µl  (5x ) First Strand Buffer (thaw at 37 0C,  keep on ice )
      2µl  DTT  (0.1M)
      1µl dNTPs  (10mM)
   7µl   Total

6. Mix by pipetting, spin briefly if necessary. Add 7µl of master mix to each reaction tube.
7. Incubate at 42 0C for 2 mins in a heated block.

8. Add 2µl Superscript II Reverse Transcriptase (200U/µl ).
9. Incubate at 42 0C for 1 hour in a heated block.
10. Place tubes on ice and proceed to ‘Second Strand Synthesis’ or freeze the samples on dry ice and store at -80 o C.

SECOND STRAND cDNA SYNTHESIS

Important notes:

• Exactly 2U of RNase H should be used per reaction. Check concentration.
• Make a master mix for step 2. Mix thoroughly and spin briefly if necessary.
• For step 5, incubate either in a water bath in the cold room or in a refrigerated block with a lid to reduce condensation.
• For step 9, store at -80 0C only if you cannot proceed to ‘Clean-up of double stranded cDNA’ immediately after the synthesis is complete.

METHOD

1. Place all reagents and the first strand reaction tubes on ice.
2. Prepare a master mix on ice in a new microfuge tube. For each reaction use:

 91µl     DEPC treated dH2O
30µl    Second Strand Buffer (5X )
                      3µl     dNTPs (10mM )
  1µl    E. coli DNA Ligase  10U/µl  (10U )
  4µl    E. coli DNA Polymerase I  10U/µl   (40U )
   1µl   E. coli RNAse H   2U/µl   (2U )
130µl Total

3. Mix by vortexing, spin briefly if necessary. Add 130µl of master mix to each of the first strand reaction tubes.
4. Mix by pipetting, spin briefly if necessary.
5. Incubate at 16 0C for 2 hours.
6.  Add 2µl (10U) T4 DNA Polymerase.
7.  Incubate at 16 0C for 5 mins
8.  Add 10µl 0.5M EDTA
9. Place tubes on ice and proceed to ‘Clean-up of double stranded cDNA’ or freeze the samples on dry ice and store at -80 0C.

CLEAN-UP OF DOUBLE STRANDED cDNA

Important points:

• The cDNA is cleaned using the GeneChip Sample Cleanup Module (Affymetrix).
• Read the kit protocol before use and follow all the safety instructions.
• The cDNA wash buffer is supplied as a concentrate. Before using for the first time, add 24ml of ethanol (96-100%) to obtain a working solution.
• Perform all steps at room temperature and work without interruption.
• Carry out centrifugation at >10,000 rpm.
• After clean-up, all of the double stranded cDNA is used for the in vitro transcription reaction.
• Do not attempt to quantify the cDNA as the primer can contribute significantly to the absorbance at 260nm.

METHOD

1. Add 600µl cDNA binding buffer to the 162µl cDNA preparation in a 1.5ml microfuge          tube and mix by vortexing for 3 seconds.
2. Check that the colour of the mixture is yellow. If the colour is orange or violet, add 10µl of 3M sodium acetate pH 5.0 and mix to turn the solution yellow.
3. Apply 500µl of the sample to the cDNA Cleanup Spin Column sitting in a 2ml collection tube and spin for 1 min in a microfuge (>10,000rpm). Discard flow-through.
4. Reload the spin column with the remaining mixture (262µl) and spin. Discard flow-through and collection tube.
5.Transfer spin column to a new 2ml collection tube (supplied).
6. Pipette 750µl cDNA Wash Buffer onto the spin column and spin for 1 min in a microfuge (>10,000rpm). Discard flow-through.
7. Cut the cap off the spin column and spin for 5 mins at maximum speed to dry the membrane. Discard flow-through and collection tube.
8. Transfer spin column to a 1.5ml collection tube and pipette 14µl of cDNA Elution Buffer directly onto the spin column membrane.
9. Incubate for 4 mins at room temperature then spin for 1 min at maximum speed to elute.
10. Re-apply eluate to the spin column and repeat step 9. The average volume of eluate is 12µl from 14µl of elution buffer.
11. Place tubes on ice and proceed to the in vitro transcription reaction or freeze the samples         on dry ice and store at -80 o C.

SYNTHESIS OF cRNA - IN VITRO TRANSCRIPTION.

Important points.

• The reagents used for the in vitro transcription are from the Enzo BioArray High Yield Transcript Labelling Kit.
• Once thawed, reagents should be kept at room temperature until the reaction is ready to be incubated at 37 0C in order to reduce precipitation of DTT.
• The reaction should be carried out in an incubator or warm room to reduce condensation on the inside of the lid.

METHOD

1. Thaw all reagents and double stranded cDNA at room temperature.
2. Prepare a master mix at room temperature. For each reaction use:

10µl  DEPC treated dH2O
4µl    HY Reaction Buffer (10X)
4µl    Biotin-labelled ribonucleotides
4µl    DTT
4µl    RNase Inhibitor mix
2µl    T7 RNA Polymerase
     28µl  Total

     Add 28µl to each of the cDNAs previously prepared (usually 12µl).

3. Mix by pipetting and spin briefly if necessary.
4. Incubate at 37 0C for 5 hours. Gently mix the reaction every hour by tapping the tube. Spin briefly if necessary.
5. Proceed to ‘Clean-up of cRNA’ or freeze on dry ice and store
at -80 0C.

CLEAN-UP OF cRNA

Important points:

• The cRNA is cleaned using the GeneChip Sample Cleanup Module (Affymetrix) to remove unincorporated dNTP which absorb at 260nm and would interfere with  quantification of the cRNA.
• IVT cRNA Wash Buffer is supplied as a concentrate. Before using for the first time, add 20ml of ethanol (96-100%) to obtain a working solution.
• IVT cRNA Binding Buffer may form a precipitate on storage that can be redissolved by warming in a water bath at 300C then placing at room temperature.
• Perform all steps at room temperature and work without interruption.
• Do not touch the membrane of the spin column with the pipette tip.
• Carry out centrifugation at >10,000 rpm.

METHOD

 1. Add 60µl of RNase-free water to the in vitro transcription reaction and mix by vortexing for 3 secs.
 2.  Add 350µl of IVT cRNA Binding Buffer and mix by vortexing for 3 secs.
 3. Add 250µl ethanol (96-100%) to the lysate and mix by pipetting. Do not spin.
 4. Apply sample (700µl) to the IVT cRNA Cleanup Spin Column sitting in a 2ml collection tube.
 5. Spin for 15 secs at >10,000rpm. Discard flow-through and collection tu

hyb_protocol: Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System. Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: Data was processed using Affymetrix Microarray Suite version 5.0, scaled to a target intensity of 500.

source_name: bone marrow derived macrophages, untreated

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA. Briefly, 10 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA.

growth_protocol: Bone marrow progenitors were harvested from mice and cultured for 7 days on petri dishes in M-CSF supplemented RPMI-1640. Cells were lifted with cold PBS and replated on tissue-culture treated plates.

extract_protocol: Total RNA from BMMΦ was isolated with RNA-bee reagent (Tel-Test) according to the manufacturer's instructions.

treatment_protocol: Macrophages were left untreated (Naïve) or stimulated with 100ng/ml LPS for 24 hours (Tolerant), washed twice with warm PBS and given fresh media (N, T) or 10ng/ml LPS (N+L, T+L) for 4 hours.

tag: bone marrow macrophages from C57BL6 mice, aged 6-8 weeks


title: T+L, rep1

source_name: bone marrow derived macrophages, treated with LPS

tag: bone marrow derived macrophages from C57BL/6 mice aged 6-8 weeks


title: T+L, rep2

source_name: bone marrow derived macrophages, treated with LPS for 24hours, then restimulated

tag: bone marrow macrophages isolated from C57BL/6 mice aged 6-8 weeks


title: Macrophage smi43


title: MyD88_PIC_C-0

status: Public on Jan 30 2007

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

description: MyD88 deficient bone marrow-derived macrophages with and without Zymosan stimulation

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: Bone marrow-derived macrophages, MyD88 -/-, unstimulated, 0 minutes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Macrophages were prepared from bone marrow by growth for 6 days in the presence of recombinant human M-CSF

treatment_protocol: Untreated sample - cells were not activated with any stimuli

tag: Bone marrow-derived macrophages from mice deficient in signaling adaptor molecule MyD88


title: N+L, rep1

tag: bone marrow macrophages from C57BL/6 mice aged 6-8 weeks


title: N+L, rep2

tag: Bone marrow derived macrophages isolated from C57BL/6 mice aged 6-8 weeks


title: MyD88_ZYM_A

source_name: Bone marrow-derived macrophages, MyD88 -/-, Zymosan stimulated, 120 minutes

treatment_protocol: Macrophages were stimulated for 2 hours with 100 ug/ml zymosan


title: macrophages at 48 h post infection with B. melitensis strain 16M, biological rep1

status: Public on Jun 30 2006

first: Yongqun

last: He

address: 018 ARF, 1150 W. Medical Center Dr.

description: Gene expression data from mouse J774.A1 macrophages infected with B. melitensis strain 16M for 48 hours.

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip mouse 430 2.0 arrays according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: murine macrophage J774.A1 cell line, from ATCC (#TIB-67)

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

growth_protocol: J774.A1 macrophage cells were plated in 12 75-cm^2 flasks in c-DMEM without antibiotics 1 day prior to infection at a concentration of 8 x 10^6 cells per flask. Following 4h incubation at 37°C in an atmosphere containing 5% CO2, the cells were washed three times with PBS and treated with 50 ug/ml gentamicin to kill extracellular Brucella. The cells were collected for RNA isolation at 48 h post infection.

extract_protocol: Trizol extraction of total RNA was performed, followed by Qiagen RNeasy Mini Kit cleanup according to the manufacturers' instructions.

treatment_protocol: J774.A1 macrophages were infected with B. melitensis strain 16M

tag: infected with Brucella melitensis strain 16M for 48 hours


title: macrophages at 4 h post infection with B. melitensis strain 16M, biological rep3

description: Gene expression data from mouse J774.A1 macrophages infected with B. melitensis strain 16M for 4 hours.

growth_protocol: J774.A1 macrophage cells were plated in 12 75-cm^2 flasks in c-DMEM without antibiotics 1 day prior to infection at a concentration of 8 x 10^6 cells per flask. Following 4h incubation at 37°C in an atmosphere containing 5% CO2, the cells were washed three times with PBS, and treated with TRIzol and Qiagen kit for RNA preparation.

tag: infected with Brucella melitensis strain 16M for 4 hours


title: macrophages at 48 h post infection with B. melitensis strain 16M, biological rep2


title: MyD88_LPS_M2-0


title: macrophages at 24 h post infection with B. melitensis strain 16M, biological rep2

description: Gene expression data from mouse J774.A1 macrophages infected with B. melitensis strain 16M for 24 hours.

growth_protocol: J774.A1 macrophage cells were plated in 12 75-cm^2 flasks in c-DMEM without antibiotics 1 day prior to infection at a concentration of 8 x 10^6 cells per flask. Following 4h incubation at 37°C in an atmosphere containing 5% CO2, the cells were washed three times with PBS and treated with 50 ug/ml gentamicin to kill extracellular Brucella. The cells were collected for RNA isolation at 24 h post infection.

tag: infected with Brucella melitensis strain 16M for 24 hours


title: Naive-rep2

treatment_protocol: Macrophages were left untreated (Naïve) or stimulated with 100ng/ml LPS for 24 hours (Tolerant), washed twice with warm PBS and given fresh media (N, T) or 10ng/ml LPS (N+L, T+L).

tag: Strain

tag: Age

value: 6-8 weeks

tag: Tissue


title: macrophages at 24h post infection with B. melitensis strain 16M, biological rep1


title: macrophages at 4 h post infection with B. melitensis strain 16M, biological rep2


title: MyD88_ZYM_B

status: Public on Jan 29 2007


title: macrophages at 48 h post infection with B. melitensis strain 16M, biological rep3


title: macrophages at 24 h post infection with B. melitensis strain 16M, biological rep3


title: macrophages at 0h post infection with B. melitensis strain 16M, biological rep1

description: Gene expression data from uninfected mouse J774.A1 macrophages.

growth_protocol: J774.A1 macrophage cells were plated in 12 75-cm^2 flasks in c-DMEM without antibiotics 1 day prior to infection at a concentration of 8 x 10^6 cells per flask.

treatment_protocol: J774.A1 macrophages were treated with DMEM complete medium.

tag: uninfected control


title: macrophages at 4 h post infection with B. melitensis strain 16M, biological rep1


title: macrophages at 0h post infection with B. melitensis strain 16M, biological rep2


title: macrophages at 0h post infection with B. melitensis strain 16M, biological rep3