title: ChIPmentation of H3K27me3 for CLL patient 3873, sample 1-5-606

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606


title: ChIPmentation of H3K4me1 for CLL patient 3215, sample 1-5-30597

status: Public on Jun 26 2016

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-30597

library_source: genomic

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair per million; narrowPeak files contain peaks called by MACS2

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient with high leukemic cell count

extract_protocol:
All patients were diagnosed and treated at the Royal Bournemouth Hospital (UK) according to the revised guidelines of the International Workshop Chronic Lymphocytic Leukemia/National Cancer Institute (IWCLL/NCI). Patients were selected to reflect the clinical and biological heterogeneity of the disease. Sequential samples were included for a total of 24 patients. All samples contained more than 80% leukemic cells.
For ATAC-seq, accessible chromatin mapping was performed using the ATAC-seq method as previously described (Buenrostro 2013, doi:10.1038/nmeth.2688), with minor adaptations. In each experiment, 105 cells were washed once in 50 µl PBS, resuspended in 50 µl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and centrifuged for 10 min at 4°C. Upon centrifugation, the pellet was washed briefly in 50 µl MgCl2 buffer (10 mM Tris, pH 8.0, and 5 mM MgCl2) before incubating in the transposase reaction mix (12.5 µl 2x TD buffer, 2 µl transposase (Illumina) and 10.5 µl nuclease-free water) for 30 min at 37°C. After DNA purification with the MinElute kit, 1 µl of the eluted DNA was used in a qPCR reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 basepairs. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro 2013, doi:10.1038/nmeth.2688). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25 basepair paired-end configuration; For RNA-seq, total RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA amount was measured using Qubit 2.0 Fluorometric Quantitation (Life Technologies), and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina). Library amount and quality were determined using Qubit 2.0 Fluorometric Quantitation (Life Technologies) and Experion Automated Electrophoresis System (Bio-Rad). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50 basepair single-read configuration; For ChIPmentation, it was carried out as previously described (Schmidl 2015, doi:10.1038/nmeth.3542), with minor adaptions. Briefly, cells were washed once with PBS and fixed with 1% paraformaldehyde in up to 1 ml PBS for 10 minutes at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 x g for 10 minutes at 4°C (subsequent work was performed on ice and used cool buffers and solutions unless otherwise specified) and washed twice with up to 0.5 ml ice-cold PBS supplemented with 1 μM PMSF. The pellet was lysed in sonication buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 0.25% SDS, 1x protease inhibitors (Sigma), 1 µM PMSF) and sonicated with a Covaris S220 sonicator for 20-30 minutes in a milliTUBE or microTUBE until the size of most fragments was in the range of 200-700 basepairs. Lysates were centrifuged at full speed for 5 minutes at 4°C, and the supernatant containing the sonicated chromatin was transferred to a new tube. The lysate was then brought to RIPA buffer conditions (final concentration: 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 140 mM NaCl, 1% Triton x-100, 0.1% SDS, 0.1% DOC, 1x protease inhibitors (Sigma), 1 µM PMSF) in a volume of 200 µl/immunoprecipitation For each immunoprecipitation, 10 μl magnetic Protein A (Life Technologies) were washed twice and resuspended in PBS supplemented with 0.1% BSA. The antibody was added and bound to the beads by rotating 2 hours at 4°C. Used antibodies were H3K4me1 (0.5 μg/immunoprecipitation, Diagenode pAb-194-050), H3K27ac (1 µg/immunoprecipitation, Diagenode pAB-196-050), H3K27me3 (1 µg/immunoprecipitation, Millipore 07-499). For control libraries an IP with 2.5 µg of a nonspecific IgG rabbit antibody was used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed, and the sonicated lysate was added to the beads followed by incubation for 3-4 hours at 4°C on a rotator. Beads were washed subsequently with RIPA (twice), RIPA-500 (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 500 mM NaCl, 1% Triton x-100, 0.1% SDS, 0.1% DOC,) (twice), and RIPA-LiCl (10 mM Tris- HCl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1% Triton X-100, 0.5% DOC, 0.5% NP40) (twice). Beads were washed once with cold Tris-Cl pH 8.0 to remove detergent, salts, and EDTA. Beads were washed once more with cold Tris-Cl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was transferred to a new tube, and then placed on a magnet to remove supernatant to decrease tagmentation of unspecific chromatin fragments sticking to the tube wall. Beads were then carefully resuspended in 25 μl of the tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10% v/v dimethylformamide) containing 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) and incubated at 37°C for 1-3 minutes in a thermocycler. The beads were washed with RIPA (twice) and once with cold Tris-Cl pH 8. Beads were washed once more with cold Tris-Cl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was again transferred to a new tube, and then placed on a magnet to remove supernatant to remove unspecific tagmented chromatin fragments. Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl pH 8.0) containing 2 μl of Proteinase K (NEB) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Finally, DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2) or Qiagen MinElute columns. 1 μl of each library was amplified in a 10-μl qPCR reaction containing 0.15 μM primers, 1× SYBR Green and 5 μl Kapa HiFi HotStart ReadyMix (Kapa Biosystems) to estimate the optimum number of enrichment cycles with the following program: 72°C for 5 min; 98°C for 30 s; 24 cycles of 98°C for 10 s, 63°C for 30 s; and 72°C for 30 s; and a final elongation at 72°C for 1 min. Kapa HiFi HotStart ReadyMix was incubated at 98°C for 45 s before preparation of all PCR reactions (qPCR and final enrichment PCR) to activate the hot-start enzyme for successful nick translation in the first PCR step. Final enrichment of the libraries was performed in a 50 μl reaction using 0.75 μM primers and 25 μl Kapa HiFi HotStart ReadyMix. Libraries were amplified for N+1 cycles, where N is equal to the rounded-up Cq value determined in the qPCR reaction. Enriched libraries were purified with size selection using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200-400 basepairs. Library preparation was performed using custom Nextera primers as previously described for ATAC-seq (Buenrostro 2013, doi:10.1038/nmeth.2688). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 50 basepair single-read configuration.

value: M

value: mutated

tag: antibody


title: ChIPmentation of H3K27ac for CLL patient 3873, sample 1-5-606

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606

value: F

value: unmutated


title: ChIPmentation of H3K27me3 for CLL patient 3240, sample 1-5-47651

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ChIPmentation of IgG for CLL patient 3873, sample 1-5-606

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606

value: IgG


title: ChIPmentation of IgG for CLL patient 3215, sample 1-5-30597

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-30597


title: ChIPmentation of H3K27me3 for CLL patient 2459, sample 1-5-34053

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-34053


title: ChIPmentation of H3K27ac for CLL patient 3215, sample 1-5-30597

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-30597


title: ChIPmentation of H3K27me3 for CLL patient 3215, sample 1-5-30597

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-30597


title: ChIPmentation of IgG for CLL patient 2459, sample 1-5-34053

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-34053


title: ChIPmentation of H3K27ac for CLL patient 2459, sample 1-5-34053

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-34053


title: ChIPmentation of IgG for CLL patient 2132, sample 1-5-29612

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-29612


title: ChIPmentation of H3K4me1 for CLL patient 2459, sample 1-5-34053

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-34053


title: ChIPmentation of H3K27me3 for CLL patient 2132, sample 1-5-29612

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-29612


title: ChIPmentation of H3K27ac for CLL patient 2132, sample 1-5-29612

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-29612


title: ChIPmentation of H3K27me3 for CLL patient 4784, sample 1-5-52817

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52817


title: ChIPmentation of H3K4me1 for CLL patient 1781, sample 1-5-1614

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: ChIPmentation of H3K27me3 for CLL patient 1781, sample 1-5-1614

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: ChIPmentation of IgG for CLL patient 1781, sample 1-5-1614

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: ChIPmentation of H3K27ac for CLL patient 1781, sample 1-5-1614

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: ChIPmentation of H3K4me1 for CLL patient 2132, sample 1-5-29612

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-29612


title: ATAC-seq for CLL patient 5263, sample 1-5-60462

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462

data_processing:
Library strategy: ATAC-seq
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair per million; narrowPeak files contain peaks called by MACS2


title: ATAC-seq for CLL patient 5277, sample 1-5-57269

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5277, sample 1-5-57269


title: ATAC-seq for CLL patient 5229, sample 1-5-54145

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5229, sample 1-5-54145


title: ATAC-seq for CLL patient 5170, sample 1-5-55531

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5170, sample 1-5-55531


title: ATAC-seq for CLL patient 5199, sample 1-5-50525

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5199, sample 1-5-50525


title: ATAC-seq for CLL patient 5147, sample 1-5-48105

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5147, sample 1-5-48105


title: ATAC-seq for CLL patient 5044, sample 1-5-42061

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5044, sample 1-5-42061


title: ATAC-seq for CLL patient 5204, sample 1-5-58365

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5204, sample 1-5-58365


title: ATAC-seq for CLL patient 4963, sample 1-5-37169

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4963, sample 1-5-37169


title: ATAC-seq for CLL patient 5048, sample 1-5-41821

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5048, sample 1-5-41821


title: ATAC-seq for CLL patient 5019, sample 1-5-39146

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5019, sample 1-5-39146


title: ATAC-seq for CLL patient 4989, sample 1-5-54251

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4989, sample 1-5-54251


title: ATAC-seq for CLL patient 4802, sample 1-5-39590

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4802, sample 1-5-39590


title: ATAC-seq for CLL patient 4747, sample 1-5-64839

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4747, sample 1-5-64839


title: ATAC-seq for CLL patient 4621, sample 1-5-39762

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4621, sample 1-5-39762


title: ATAC-seq for CLL patient 4621, sample 1-5-1674

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4621, sample 1-5-1674


title: ATAC-seq for CLL patient 4668, sample 1-5-2135

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4668, sample 1-5-2135


title: ATAC-seq for CLL patient 4333, sample 1-5-11319

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4333, sample 1-5-11319


title: ATAC-seq for CLL patient 4621, sample 1-5-36904

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4621, sample 1-5-36904


title: ATAC-seq for CLL patient 4251, sample 1-5-19509

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4251, sample 1-5-19509


title: ATAC-seq for CLL patient 4251, sample 1-5-12508

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4251, sample 1-5-12508


title: ATAC-seq for CLL patient 4189, sample 1-5-48773

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: ATAC-seq for CLL patient 4102, sample 1-5-47077

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4102, sample 1-5-47077


title: ATAC-seq for CLL patient 4080, sample 1-5-27302

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302


title: ATAC-seq for CLL patient 4668, sample 1-5-1518

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4668, sample 1-5-1518


title: ATAC-seq for CLL patient 4102, sample 1-5-12088

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4102, sample 1-5-12088


title: ATAC-seq for CLL patient 4102, sample 1-5-41533

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4102, sample 1-5-41533


title: ATAC-seq for CLL patient 5129, sample 1-5-52010

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5129, sample 1-5-52010


title: ATAC-seq for CLL patient 4034, sample 1-5-47284

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4034, sample 1-5-47284


title: ATAC-seq for CLL patient 3980, sample 1-5-49011

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3980, sample 1-5-49011


title: ATAC-seq for CLL patient 4078, sample 1-5-1840

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4078, sample 1-5-1840


title: ATAC-seq for CLL patient 3943, sample 1-5-55787

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3943, sample 1-5-55787


title: ATAC-seq for CLL patient 3811, sample 1-5-39729

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3811, sample 1-5-39729


title: ATAC-seq for CLL patient 3756, sample 1-5-33669

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3756, sample 1-5-33669


title: ATAC-seq for CLL patient 3492, sample 1-5-30784

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3492, sample 1-5-30784


title: ATAC-seq for CLL patient 3823, sample 1-5-12816

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3823, sample 1-5-12816


title: ATAC-seq for CLL patient 4784, sample 1-5-52834

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52834


title: ATAC-seq for CLL patient 3873, sample 1-5-606

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606


title: ATAC-seq for CLL patient 3439, sample 1-5-31907

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3439, sample 1-5-31907


title: ATAC-seq for CLL patient 3439, sample 1-5-6735

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3439, sample 1-5-6735


title: ATAC-seq for CLL patient 3492, sample 1-5-13203

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3492, sample 1-5-13203


title: ATAC-seq for CLL patient 3263, sample 1-5-34818

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3263, sample 1-5-34818


title: ATAC-seq for CLL patient 3386, sample 1-5-37411

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3386, sample 1-5-37411


title: ATAC-seq for CLL patient 3439, sample 1-5-24904

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3439, sample 1-5-24904


title: ATAC-seq for CLL patient 4078, sample 1-5-7213

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4078, sample 1-5-7213


title: ATAC-seq for CLL patient 3240, sample 1-5-47651

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ATAC-seq for CLL patient 3156, sample 1-5-27542

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3156, sample 1-5-27542


title: ATAC-seq for CLL patient 3215, sample 1-5-30597

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-30597


title: ATAC-seq for CLL patient 3215, sample 1-5-6223

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-6223


title: ATAC-seq for CLL patient 3215, sample 1-5-48685

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-48685


title: ATAC-seq for CLL patient 3263, sample 1-5-21872

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3263, sample 1-5-21872


title: ATAC-seq for CLL patient 3215, sample 1-5-34760

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3215, sample 1-5-34760


title: ATAC-seq for CLL patient 3156, sample 1-5-20444

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3156, sample 1-5-20444


title: ATAC-seq for CLL patient 3142, sample 1-5-55865

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3142, sample 1-5-55865


title: ATAC-seq for CLL patient 3823, sample 1-5-51124

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3823, sample 1-5-51124


title: ATAC-seq for CLL patient 3069, sample 1-5-6294

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3069, sample 1-5-6294


title: ATAC-seq for CLL patient 3069, sample 1-5-27496

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3069, sample 1-5-27496


title: ATAC-seq for CLL patient 2977, sample 1-5-7923

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2977, sample 1-5-7923


title: ATAC-seq for CLL patient 2938, sample 1-5-56744

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2938, sample 1-5-56744


title: HTCC1062_Control_Sta_rep4

type: RNA

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

country: USA

institute: Oregon State University

hyb_protocol: 5.5 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package. Analysis includes only Pelagibacter ubique HTCC1062 probes.

label: biotin

molecule: total RNA

organism: Candidatus Pelagibacter ubique HTCC1062

label_protocol: RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.

growth_protocol: Artificial seawater media with 1 µM (Control) or 100 nM (Limited) DMSP, 500 µM pyruvate, 500 µM glycine betaine, 100 µM ammonium, 50 µM phosphate, 10 µM glycine, vitamins, and trace metals. Cells were grown at 16 °C with intermittent light and sparging with air.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: strain

tag: source

value: Carboy 17

tag: dmsp availability

value: Excess

tag: growth phase

value: Stationary

tag: ribosomal protein rna abundance


title: ATAC-seq for CLL patient 2977, sample 1-5-54424

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2977, sample 1-5-54424


title: HTCC1062_Control_Sta_rep2

value: Carboy 16


title: HTCC1062_Control_Tra_rep4

value: Transitioning


title: HTCC1062_Control_Sta_rep1

value: Carboy 15


title: ATAC-seq for CLL patient 2938, sample 1-5-46799

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2938, sample 1-5-46799


title: ATAC-seq for CLL patient 2938, sample 1-5-21490

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2938, sample 1-5-21490


title: ATAC-seq for CLL patient 2938, sample 1-5-20335

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2938, sample 1-5-20335


title: HTCC1062_Limited_Sta_rep6

value: Carboy 10

value: Limited


title: HTCC1062_Limited_Sta_rep4

value: Carboy 13


title: ATAC-seq for CLL patient 2886, sample 1-5-46979

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2886, sample 1-5-46979


title: HTCC1062_Limited_Sta_rep5

value: Carboy 11


title: ATAC-seq for CLL patient 2938, sample 1-5-12095

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2938, sample 1-5-12095


title: HTCC1062_Control_Sta_rep3

value: Carboy 19


title: ATAC-seq for CLL patient 2613, sample 1-5-6916

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2613, sample 1-5-6916


title: HTCC1062_Limited_Sta_rep3

value: Carboy 14


title: HTCC1062_Limited_Sta_rep2

value: Carboy 12


title: ATAC-seq for CLL patient 2483, sample 1-5-39392

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2483, sample 1-5-39392


title: HTCC1062_Control_Exp_rep6

value: Exponential


title: ATAC-seq for CLL patient 2886, sample 1-5-34218

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2886, sample 1-5-34218

value: M

value: mutated


title: HTCC1062_Control_Tra_rep2


title: HTCC1062_Control_Exp_rep5


title: ATAC-seq for CLL patient 2613, sample 1-5-2683

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2613, sample 1-5-2683


title: HTCC1062_Control_Exp_rep4


title: ATAC-seq for CLL patient 2459, sample 1-5-6988

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-6988


title: HTCC1062_Control_Tra_rep1


title: HTCC1062_Limited_Tra_rep6


title: ATAC-seq for CLL patient 2459, sample 1-5-34053

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2459, sample 1-5-34053


title: ATAC-seq for CLL patient 2132, sample 1-5-20842

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-20842

value: F

value: unmutated


title: ATAC-seq for CLL patient 1781, sample 1-5-1614

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: ATAC-seq for CLL patient 2132, sample 1-5-29612

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 2132, sample 1-5-29612


title: HTCC1062_Limited_Sta_rep1


title: ATAC-seq for CLL patient 1303, sample 1-5-35065

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1303, sample 1-5-35065


title: ATAC-seq for CLL patient 1125, sample 1-5-33070

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1125, sample 1-5-33070


title: ATAC-seq for CLL patient 981, sample 1-5-42480

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 981, sample 1-5-42480


title: HTCC1062_Limited_Tra_rep3


title: ATAC-seq for CLL patient 1125, sample 1-5-7260

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 1125, sample 1-5-7260


title: HTCC1062_Control_Tra_rep3

value: Excess


title: HTCC1062_Limited_Tra_rep4


title: HTCC1062_Limited_Tra_rep5


title: ATAC-seq for CLL patient 981, sample 1-5-11335

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 981, sample 1-5-11335


title: ATAC-seq for CLL patient 680, sample 1-5-10787

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 680, sample 1-5-10787


title: ATAC-seq for CLL patient 680, sample 1-5-33943

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 680, sample 1-5-33943


title: HTCC1062_Limited_Tra_rep2


title: HTCC1062_Limited_Tra_rep1


title: HTCC1062_Limited_Exp_rep3


title: HTCC1062_Control_Exp_rep3


title: HTCC1062_Control_Exp_rep2


title: ATAC-seq for CLL patient 653, sample 1-5-45881

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 653, sample 1-5-45881


title: HTCC1062_Limited_Exp_rep1


title: ATAC-seq for CLL patient 552, sample 1-5-20486

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 552, sample 1-5-20486


title: ATAC-seq for CLL patient 552, sample 1-5-12302

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 552, sample 1-5-12302


title: HTCC1062_Control_Exp_rep1


title: ATAC-seq for CLL patient 244, sample 1-5-16241

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 244, sample 1-5-16241


title: ATAC-seq for CLL patient 244, sample 1-5-33025

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 244, sample 1-5-33025


title: ATAC-seq for CLL patient 50, sample 1-5-35290

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 50, sample 1-5-35290


title: ATAC-seq for CLL patient 653, sample 1-5-6768

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from CLL patient 653, sample 1-5-6768


title: D53

city: Los Angeles

first: Ritchie

last: Ho

state: California

address: AHSP 8405 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

description: Sample obtained from Birth Defects Research Laboratory at the University of Washington

hyb_protocol: Hybridizations were performed by UCLA Clinical Microarray Core following standard Affymetrix GeneChip Expression Analysis protocol.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 7G. The acquisition of array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC).

data_processing: The raw data from these CEL files, in conjunction with previously published CEL files described in Ho et al. 201X was processed using the RMA algorithm and was implemented using R (Bioconductor).

label: Biotin

source_name: Fetal spinal cord

label_protocol: Biotinylated aRNA was generated using Ambion MessageAmp™ Premier RNA Amplification Kit on 120 ng of starting RNA.

growth_protocol: not applicable

extract_protocol: Trizol extraction of total RNA was performed, run through a Qiagen Rneasy kit with on column Dnase digestion.

treatment_protocol: No special treatments were applied to samples.

tag: time in culture

value: not applicable

tag: age of tissue donor

value: 53 days post conception (estimated)

tag: gender

value: not determined


title: D97

value: 97 days post conception (estimated)

value: female


title: HTCC1062_Limited_Exp_rep2

value: Carboy 10

value: Limited


title: SHH_POS

description: HB9-GFP reporter HUES3 cells differentiated towards motor neurons and flow sorted

source_name: HB9-GFP positive motor neuron

extract_protocol: As described in Amoroso et al. J Neurosci, 2013, and additionally run through a Qiagen Rneasy kit with on column Dnase digestion.

value: 31 days differentiation

value: male


title: X14_MN

description: iPSCs differentiated towards motor neurons

source_name: iPSC-derived motor neuron

extract_protocol: As described in Sareen et al. Sci Transl Med, 2013, and additionally run through a Qiagen Rneasy kit with on column Dnase digestion.

value: 7 weeks differentiation

value: 35 years


title: X14_iPSC

description: iPSCs derived from healthy control fibroblasts obtained from Coriell Institute for Medical Research

source_name: Induced pluripotent stem cell

growth_protocol: Cell lines were cultured in hESC cell media mTESR on Matrigel.

extract_protocol: Zymogen Quick-RNA extraction of total RNA was performed, run through a Qiagen Rneasy kit with on column Dnase digestion.


title: HFD_liver_1

status: Public on Jun 25 2016

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026655 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: liver, HFD for 20 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen).

treatment_protocol: Male C57/BJ mice aged 6 weeks were randomly assigned to a high-fat diet (D12331; ResearchDiets, NJ, USA) or control chow diet (Provimi Kliba). All mice were sacrificed under anesthesia 20 weeks after food treatment and the livers were harvested.

tag: strain/background

tag: tissue

value: liver

tag: age

value: 26 wks

tag: treatment

value: high-fat diet (HFD)


title: chow_liver_1

source_name: liver, chow diet for 20 weeks

value: control chow diet


title: chow_liver_4


title: chow_liver_2


title: HFD_liver_2


title: D52

value: 52 days post conception (estimated)


title: SHH_NEG

source_name: HB9-GFP negative cell

growth_protocol: As described in Amoroso et al. J Neurosci, 2013


title: X83_iPSC

value: 21 years


title: X00_iPSC

value: 6 years


title: X83_MN

extract_protocol: As described in Sareen et al. Sci Transl Med, 2013, , and additionally run through a Qiagen Rneasy kit with on column Dnase digestion.


title: X00_MN

growth_protocol: As described in Sareen et al. Sci Transl Med, 2013


title: chow_liver_3


title: HFD_liver_3


title: CM_stretch_Rep6

city: Louisville

first: Bradley

middle: B.

last: Keller

state: United States

address: 302 E Muhammad Ali Blvd

department: Cardiovascular Innovation Institute

institute: University of Louisville

description: Gene expression after cultured 7 days with 48 hours mechanical stretch in rat engineered cardiac tissure

hyb_protocol: 1.65ug labeled with Cy3 for each sample was fragmented, denatured and then hybridized to Agilent 4x44 rat whole genome micrarray slides for 17 hours at 65C. Slides were then washed according to the protocol.

scan_protocol: Microarrays were scanned with Agilent Technologies Scanner (G2505C US45102880) at 5um resolution at 100% PTM. The images were then imported into Agilent Feature Extraction Software.

data_processing: The raw data files extraced from Agilent Feature extraction software are processed and analyzed by GeneSpring GX11 software.

organism: Rattus norvegicus

source_name: engineered cardiac tissure, cultured 7day, with 48 hours of mechanical stretch

label_protocol: Following Agilent One-Color Microarray-Based Gene Expression protocol of the Low RNA Input Fluoresent Linear Amplification Kit Plus (Agilent, Santa Clara, CA), 200ng RNA with the addtion of One-Color Spike Mix was denatured and incubate with T7 Promoter perimer. Synthesis of cDNA followed with the addtion of First-Strand buffer, DTT, dNTP mix, MMLV-RT and RNAse Out and incubation at 40C for 2 hours. Transcription of the product incorporated the Cyanine 3-CTP in the master Mix with incubation at 40C for 2 hours.

growth_protocol: Approximately 200 µL of cell/matrix mixture, containing approximately 1x106 cells, was poured into the trough and incubated for 150 min in a standard CO2 incubator (37°C, 5% CO2) to form a cylindrical construct. Both ends of the construct were held by anchors attached to the Tissue Train culture plate. When the tissue was formed, the culture plate was filled with a growth medium containing 10% fetal bovine serum (Invitrogen), 1% antibiotic–antimycotic solution (Atlanta Biologicals), and 1% chicken embryo extract. Constructed engineered tissues were cultured for 7 days and the culture medium was changed every other day

extract_protocol: Fresh ECT samples were homogenized by an Omnitip Tissue homogenizer (Cat. No.:  6615-7273, USA Scientific, Ocala, FL, USA). Total RNAs were isolated using Invitrogen Trizol and purified by RNeasy® Mini Kit (Qiagen, Cat. No.: 74104). Then the RNA quality and quantity were measured using the NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA) and the Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: To determine the effect of cyclic mechanical stretch and/or p38MAPK inhibition on ECT gene changes, we exposed culture day-5 ECT to uniaxial cyclic mechanical stretch (0.5 Hz and 5% elongation); to p38MAPK inhibition by BIRB796 (Catalog No. S1574, Selleck Chemicals, 10µM), or both stretch and BIRB796.

value: embryo venticle

value: Sprague Dawley rats

tag: gestational day


title: CM_stretch_BIRB796_Rep4

description: Gene expression after cultured 7 days with 48 hours mechanical stretch and BIRB treatment in rat engineered cardiac tissure

source_name: engineered cardiac tissure, cultured 7day, with 48 hours of mechanical stretch and inhibitor culture


title: CM_stretch_BIRB796_Rep3

value: cultured 7 days with 48 hours mechanical stretch and BIRB treatment in rat engineered cardiac tissure


title: CM_non-stretch_BIRB796_Rep3

description: Gene expression after cultured 7 days with 48 hours BIRB treatment in rat engineered cardiac tissure

source_name: engineered cardiac tissure, cultured 7day, with 48 hours of inhibitor culture


title: CM_non-stretch_BIRB796_Rep4

value: cultured 7 days with 48 hours BIRB treatment in rat engineered cardiac tissure


title: CM_stretch_Rep1

value: cultured 7 days with 48 hours mechanical stretch in rat engineered cardiac tissure


title: CM_stretch_Rep5


title: CM_non-stretch_BIRB796_Rep1


title: CM_stretch_Rep2


title: CM_stretch_BIRB796_Rep2


title: CM_stretch_Rep4


title: CM_stretch_Rep7


title: CM_non-stretch_Rep5

description: Gene expression after cultured 7 days without mechanical stretch in rat engineered cardiac tissure

source_name: engineered cardiac tissure, cultured 7day, without mechanical stretch


title: TI_1_DM1

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

description: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: DM mice treated with mcIRBP

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

treatment_protocol: Mice were treated with 2.5 nmol mcIRBP.

tag: disease state

value: diabetic

value: treated with 2.5 nmol mcIRBP

value: BALB/c

value: Male

value: Muscle


title: CM_non-stretch_BIRB796_Rep2


title: TI_2_DM1

extract_protocol: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).


title: CM_stretch_BIRB796_Rep1


title: CM_non-stretch_Rep4

value: cultured 7 days without mechanical stretch in rat engineered cardiac tissure


title: CM_stretch_Rep3


title: TI_3_normal

source_name: Normal mice treated with mcIRBP

value: normal

value: Female


title: TI_2_normal


title: CM_non-stretch_Rep3


title: CM_non-stretch_Rep2


title: TI_3_DM1


title: CM_non-stretch_Rep1


title: Mock_1_DM1

source_name: DM mice

value: untreated


title: Mock_3_DM1


title: CM_non-stretch_Rep6


title: CM_non-stretch_Rep7


title: intestine_adult mice_I/R1

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

country: China

institute: The Second Hospital of Dalian Medical University

description: Experimental animals were male and commercially-available C57BL/6 mice (Laboratory Animal Center, Dalian, China).

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: intestine

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then the superior mesenteric artery was identified through a midline laparotomy and occluded gently by an atraumatic microvascular clamp for 45 minutes. The occlusion was confirmed when the mesenteric pulsations ceased and the intestines became pale. A 4 hour reperfusion was then performed. All animals were killed at the end of the reperfusion, and tissues samples were obtained for analysis.

value: 8 weeks old


title: Mock_2_DM1


title: intestine_adult mice_sham3


title: intestine_adult mice_sham2


title: intestine_adult mice_sham1


title: late-lactation

city: Xi'an

first: Zhi

last: Chen

state: Select a State or Province

address: 22 Xinong Road, Yangling

department: Shaanxi Key Laboratory of Molecular Biology for Agriculture

institute: College of Animal Science and Technology, Northwest A&F University,  China

description:
SAMPLE 3
SAMPLE 4
150 days after parturition
S-Poly(T) assay

data_processing:
All real-time reactions, including controls with no templates, were carried out on a Bio-Rad CFX96 real-time PCR detection system (Bio-Rad, USA) in triplicate. Relative expression was calculated using the 2-△△Ct method.
We profiled the differential miRNAs expression between peak-lactation and late-lactation in goat mammary gland with S-Poly (T) real-time RT-PCR method, including 267 Capra hircus primary miRNAs and 793 Bos taurusprimary miRNAs from miRBase and the new discovered miRNAs by Solexa sequencing.

label: FAM

organism: Capra hircus

source_name: 150 days after parturition, monocytes

label_protocol: The mature miRNA expression level was determined using the S-Poly(T) assay (Kang et al., 2012).The primer was used as specific reverse primer, respectively. Briefly, reverse transcription was performed as follows: a 10 µl reaction including 0.2 µg total RNA, 2.5 µl of 4×reaction buffer, 1 µl of polyA/RT enzyme mix, 1µl of 0.5 µM RT primer. The reaction was performed at 37 ℃ for 30 min, followed by 42 ℃ for 30 min, then 75 ℃ for 5 min. The RT products were amplified and detected using a universal Taqman○R probe, a 20 µl PCR reaction containing 0.3 µl of RT products, 4 µl of 5×qPCR probe Mix , 0.5 unit of Go Taq○R Hot Start Polymerase(Promega, USA), 0.2 mM universal Taqman probe, and 0.5µM forward primer and universal reverse primer, respectively. The PCR reaction was performed at 95 ℃ for 3min, followed by 40 cycles of 95 ℃ for 10 s and 60 ℃ for 30 s. The 18S rRNA was used as internal control.

extract_protocol: Three biological samples per tissue were pooled and snap-frozen immediately in liquid nitrogen. The quantity and quality of RNA was determined using a NanoDrop ND-1000 spectrophotometer (Nanodrop, USA) and the RNA were stored at -80℃ before use.

tag: breed

value: Xinong Sanen dairy goat

tag: lactation stage

value: late-lactation

value: mammary gland

tag: cell type

value: monocyte


title: peak-lactation

description:
SAMPLE 1
SAMPLE 2
60 days after parturition
S-Poly(T) assay

source_name: 60 days after parturition, monocytes

value: peak-lactation


title: intestine_adult mice_I/R2


title: Mock_2_normal

source_name: Normal mice

tag: strain


title: intestine_adult mice_I/R3


title: Mock_1_normal


title: Nkx3.1 +/+ Seminal Vesicle, 5253sv

status: Public on Jun 24 2016

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

hyb_protocol: Hybridized to Affymetrix GeneChips (Mu74AV2).

scan_protocol: Arrays were scanned.

data_processing: Data were loaded using library affy and the resulting matrix was RMA normalized in R-studio Version 0.99.484.

source_name: Seminal vesicle, Nkx3.1 +/+, 15 months

label_protocol: cDNA was labeled using a BioArray High-Yield RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) and purified using an RNeasy kit (Qiagen, Chatsworth, CA).

treatment_protocol: Seminal vesicle from 15-month-old Nkx3.1+/+ mice was harvested, and snap frozen for subsequent molecular analysis.

tag: genotype/variation

value: 15 months

value: Seminal vesicle


title: cerebral malaria Malawi2_D10_815_586508

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

description: circulating P. falciparum, directly analyzed from whole blood

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

organism: Plasmodium falciparum

source_name: whole blood

label_protocol: biotin

growth_protocol: 3mL of whole blood from venipunture of Malawian children with cerebral malaria was directly added to Tri-regeant BD(Molecular Research Center)

extract_protocol: the RNA sample was thawed at room temperature and RNA was extracted following manufacturers instructions

treatment_protocol: the samples were immediately frozen at minus 80, and shipped in liquid nitrogen

value: whole blood

tag: malaria retinopathy

tag: temperature

tag: respirations per minute

tag: parasitemia

tag: hematocrit

tag: outcome

value: death


title: Nkx3.1 +/+ Seminal Vesicle, 3578sv

tag: strain/background


title: cerebral malaria Malawi2_D07_807_586446

tag: tissue

value: Yes

tag: age (months)

tag: gender

value: female


title: Nkx3.1 +/+ Seminal Vesicle, 3577sv

tag: age


title: Nkx3.1 +/+ Seminal Vesicle, 5656sv


title: cerebral malaria Malawi2_B07_761_586532


title: Mock_3_normal

tag: disease state

tag: treatment

value: BALB/c

value: Muscle


title: TI_1_normal

value: normal

value: treated with 2.5 nmol mcIRBP


title: cerebral malaria Malawi2_B03_752_586428


title: cerebral malaria Malawi2_C06_785_586500

value: male


title: 013 AAR

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

source_name: cardiac biopsy

label_protocol: standard Agilent protocol

extract_protocol: none provided by submitter

value: Female

value: 12 months

value: Sham

tag: biopsy type

value: Area at risk


title: 008 AAR

value: IPC


title: 008 RM

value: Remote myocardium


title: cerebral malaria Malawi2_A09_733_586600

value: No


title: cerebral malaria Malawi1_A08_807_563040


title: cerebral malaria Malawi2_D03_798_586488


title: 012 AAR


title: cerebral malaria Malawi2_A08_728_586440


title: cerebral malaria Malawi2_C04_783_586436


title: 004 RM


title: cerebral malaria Malawi2_B09_763_586460


title: cerebral malaria Malawi1_A04_729_563012

value: sequela


title: cerebral malaria Malawi2_C11_791_586598

value: whole blood


title: cerebral malaria Malawi2_D05_801_586534


title: cerebral malaria Malawi2_C05_784_586430


title: cerebral malaria Malawi2_D11_816_586476

value: full recovery


title: cerebral malaria Malawi2_C01_777_586602

value: Yes


title: cerebral malaria Malawi2_D09_813_586530

value: female


title: 004 AAR


title: cerebral malaria Malawi2_D01_794_586490

value: Male


title: cerebral malaria Malawi2_C07_786_586586


title: cerebral malaria Malawi1_A02_722_563078

value: death


title: cerebral malaria Malawi2_D04_800_586560


title: cerebral malaria Malawi2_B08_762_586584


title: cerebral malaria Malawi1_A01_712_563118


title: cerebral malaria Malawi2_C02_781_586492


title: cerebral malaria Malawi2_E03_826_586612


title: cerebral malaria Malawi2_B06_760_586480


title: cerebral malaria Malawi2_A11_743_586424


title: cerebral malaria Malawi2_A04_717_586452


title: cerebral malaria Malawi2_A03_713_586578


title: cerebral malaria Malawi2_A01_707_586486


title: cerebral malaria Malawi2_E01_825_586432


title: cerebral malaria Malawi2_C12_793_586552


title: cerebral malaria Malawi1_A07_797_563072


title: cerebral malaria Malawi2_D02_795_586604


title: cerebral malaria Malawi2_C08_788_586550


title: cerebral malaria Malawi2_D08_809_586558


title: cerebral malaria Malawi2_D12_820_586576


title: cerebral malaria Malawi2_C09_789_586464


title: cerebral malaria Malawi2_B05_755_586568


title: cerebral malaria Malawi2_B10_764_586458


title: cerebral malaria Malawi2_B01_747_586596


title: cerebral malaria Malawi2_A02_708_586538


title: cerebral malaria Malawi1_A11_826_563070


title: cerebral malaria Malawi2_B02_749_586462


title: cerebral malaria Malawi2_B04_754_586528


title: cerebral malaria Malawi2_A12_745_586426


title: cerebral malaria Malawi2_A10_741_586484


title: cerebral malaria Malawi2_C10_790_586536


title: cerebral malaria Malawi2_A07_724_586594


title: cerebral malaria Malawi1_A05_753_563100


title: cerebral malaria Malawi2_A06_720_586544


title: cerebral malaria Malawi1_A09_821_563020


title: cerebral malaria Malawi1_A10_824_563114


title: cerebral malaria Malawi1_A12_831_563074


title: cerebral malaria Malawi1_A06_759_563132


title: Liver, GD8 Cylindrospermopsin, 12 hr post dose sample, 6189799002D

city: RTP

first: Neil

last: Chernoff

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description:
Maternal liver sampled after 1 dose on GD 8
6189799002D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalized expression of probe level data was calculated in R using Bioconductor's Illumina package

source_name: Liver GD8 Cylindrospermopsin, 12 hr post dose sample

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

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

tag: Sex

tag: age at dosing

value: Gestation Day 8

tag: chemical

value: Cylindrospermopsin

tag: vehicle

value: Distilled water

tag: dose

value: 50 ug/kg

tag: route

value: IP injection

tag: sample time

value: Liver


title: Liver, GD8 vehicle control, 12 hr post dose sample, 6189799011C

description:
Maternal liver sampled after 1 dose on GD 8
6189799011C

source_name: Liver GD8 vehicle control, 12 hr post dose sample

tag: strain

value: Female

value: 0 ug/kg


title: Liver, GD8 vehicle control, 12 hr post dose sample, 6189799011E

description:
Maternal liver sampled after 1 dose on GD 8
6189799011E


title: Liver, GD8 vehicle control, 6 hr post dose sample, 6189799012F

description:
Maternal liver sampled after 1 dose on GD 8
6189799012F

source_name: Liver GD8 vehicle control, 6 hr post dose sample


title: Liver, GD8 vehicle control, 6 hr post dose sample, 6152689036B

description:
Maternal liver sampled after 1 dose on GD 8
6152689036B


title: Liver, GD8 Cylindrospermopsin, 24 hr post dose sample, 6189799001F

description:
Maternal liver sampled after 1 dose on GD 8
6189799001F

source_name: Liver GD8 Cylindrospermopsin, 24 hr post dose sample


title: Liver, GD8 vehicle control, 24 hr post dose sample, 6189799011H

description:
Maternal liver sampled after 1 dose on GD 8
6189799011H

source_name: Liver GD8 vehicle control, 24 hr post dose sample


title: Liver, GD8 Cylindrospermopsin, 6 hr post dose sample, 6189799012G

description:
Maternal liver sampled after 1 dose on GD 8
6189799012G

source_name: Liver GD8 Cylindrospermopsin, 6 hr post dose sample


title: Liver, GD8 Cylindrospermopsin, 24 hr post dose sample, 6152689036E

description:
Maternal liver sampled after 1 dose on GD 8
6152689036E


title: Liver, GD8 Cylindrospermopsin, 6 hr post dose sample, 6189799012A

description:
Maternal liver sampled after 1 dose on GD 8
6189799012A


title: Liver, GD8 Cylindrospermopsin, 12 hr post dose sample, 6152689045F

description:
Maternal liver sampled after 1 dose on GD 8
6152689045F


title: Liver, GD8 Cylindrospermopsin, 12 hr post dose sample, 6189799011F

description:
Maternal liver sampled after 1 dose on GD 8
6189799011F


title: Liver, GD8 vehicle control, 6 hr post dose sample, 6189799009A

description:
Maternal liver sampled after 1 dose on GD 8
6189799009A


title: Liver, GD8 vehicle control, 24 hr post dose sample, 6189799002H

description:
Maternal liver sampled after 1 dose on GD 8
6189799002H


title: Liver, GD8 vehicle control, 6 hr post dose sample, 6152689063G

description:
Maternal liver sampled after 1 dose on GD 8
6152689063G


title: Liver, GD8 vehicle control, 24 hr post dose sample, 6152689043A

description:
Maternal liver sampled after 1 dose on GD 8
6152689043A


title: Liver, GD8 vehicle control, 24 hr post dose sample, 6189799008E

description:
Maternal liver sampled after 1 dose on GD 8
6189799008E


title: Liver, GD8 vehicle control, 12 hr post dose sample, 6189799001D

description:
Maternal liver sampled after 1 dose on GD 8
6189799001D


title: Liver, GD8 Cylindrospermopsin, 24 hr post dose sample, 6152689063A

description:
Maternal liver sampled after 1 dose on GD 8
6152689063A


title: Liver, GD8 vehicle control, 12 hr post dose sample, 6152689063E

description:
Maternal liver sampled after 1 dose on GD 8
6152689063E


title: Cell_10%_50ppm_rec_replicate 2

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

institute: Southeast University

description:
Rec_008
Gene expression of ZnO-impacted cells after recovery incubation.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-066407 N. europaea ATCC 19718 Microarrays (8x15K, Agilent Technologies) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37 °C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 11.0.1.1, Agilent). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). Differentially expressed genes with statistical significance were identified through Volcano Plot filtering (P≤0.05, Fold-change ≥ 2.0).

organism: Nitrosomonas europaea ATCC 19718

source_name: Cells, 10% ARA decline, 50ppm ZnO NPs, recovered

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, USA) on the Agilent Array platform. Fluorescent cRNA was produced and labeled with Cy3-UTP using Quick Amp Labeling Kit, One-Color (Agilent Technologies, Inc., Palo Alto, CA, USA). The labeled cRNAs were then purified with RNeasy Mini Kit. The concentrations of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) before hybridization onto the N. europaea ATCC 19718 Microarray (8x15K, Agilent Technologies).

growth_protocol: The studied N. europaea (ATCC 19718) was cultured in a constantly stirred (100~150 rpm) chemostat bioreactor (3L working volume, 2.2 d hydraulic residence time (HRT)) in the dark at 25℃~28℃ with the dissolved oxygen (DO) concentration in the reactor maintained at 2.0±0.10 mg/L by air aeration. The chemical composition of the cultivation medium was the same as we reported before (Yu and Chandran, 2010), and the medium pH in the reactor was controlled at 7.45±0.05 with a 40% NaHCO3 solution as buffer automatically titrated with a pH controller (Meller, Taiwang, China).

extract_protocol: The cells were collected by centrifuging 40 mL sample at 9300 rpmm for 10 min. The pellet was immediately re-suspended in 1 mL Trizol solution (Invitrogen, Carlsbad, CA, USA) and stored at -80 °C. The total RNA was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality control was assessed by electrophoresis on a denaturing agarose gel before microarray hybridization.

treatment_protocol: The sterile feeding medium containing 50 ppm ZnO NPs was introduced into the bioreactor when the bioreactor were added with ZnO NPs to the same concentration as in the feeding medium. The cultures were sampled for microarray analysis when the ARA declined by 10% in the chemostat bioreactor. The sampled ZnO NPs impaired cells after removing NPs were further re-suspended in the fresh sterile medium for recovery incubation at 25°C for 12 h in the dark; after that, cells were also sampled for whole-genome microarray analysis.

value: exposure to 50ppm ZnO NPs, followed by 12hr recovery


title: Cell_10%_50ppm_rec_replicate 1

description:
Rec_007
Gene expression of ZnO-impacted cells after recovery incubation.


title: Liver, GD8 Cylindrospermopsin, 12 hr post dose sample, 6085341028C

description:
Maternal liver sampled after 1 dose on GD 8
6085341028C


title: Liver, GD8 Cylindrospermopsin, 6 hr post dose sample, 6189799011B

description:
Maternal liver sampled after 1 dose on GD 8
6189799011B


title: Cell_10%_50ppm_rec_replicate 3

description:
Rec_009
Gene expression of ZnO-impacted cells after recovery incubation.


title: Liver, GD8 Cylindrospermopsin, 6 hr post dose sample, 6189799002E

description:
Maternal liver sampled after 1 dose on GD 8
6189799002E


title: Cell_10%_50ppm_exp_replicate 3

description:
Exp_006
Gene expression after exposure to 50ppm ZnO NPs.

source_name: Cells, 10% ARA decline, 50ppm ZnO NPs, exposed

value: exposure to 50ppm ZnO NPs


title: Cell_10%_50ppm_exp_replicate 2

description:
Exp_005
Gene expression after exposure to 50ppm ZnO NPs.


title: Liver, GD8 Cylindrospermopsin, 6 hr post dose sample, 6085341028E

description:
Maternal liver sampled after 1 dose on GD 8
6085341028E


title: Liver, GD8 vehicle control, 3 hr post dose sample, 6189799012B

description:
Maternal liver sampled after 1 dose on GD 8
6189799012B

source_name: Liver GD8 vehicle control, 3 hr post dose sample


title: Cell_10%_0ppm_con_replicate 3

description:
Con_003
Gene expression of normal cells.

source_name: Cells, 10% ARA decline, 0ppm ZnO NPs, control


title: Cell_10%_50ppm_exp_replicate 1

description:
Exp_004
Gene expression after exposure to 50ppm ZnO NPs.


title: Cell_10%_0ppm_con_replicate 2

description:
Con_002
Gene expression of normal cells.


title: Cell_10%_0ppm_con_replicate 1

description:
Con_001
Gene expression of normal cells.


title: Liver, GD8 vehicle control, 3 hr post dose sample, 6189799009C

description:
Maternal liver sampled after 1 dose on GD 8
6189799009C


title: Liver, GD8 vehicle control, 1 hr post dose sample, 6152689063B

description:
Maternal liver sampled after 1 dose on GD 8
6152689063B

source_name: Liver GD8 vehicle control, 1 hr post dose sample


title: Liver, GD8 Cylindrospermopsin, 1 hr post dose sample, 6152689036D

description:
Maternal liver sampled after 1 dose on GD 8
6152689036D

source_name: Liver GD8 Cylindrospermopsin, 1 hr post dose sample


title: Liver, GD8 Cylindrospermopsin, 1 hr post dose sample, 6152689043G

description:
Maternal liver sampled after 1 dose on GD 8
6152689043G


title: Liver, GD8 vehicle control, 1 hr post dose sample, 6189799001E

description:
Maternal liver sampled after 1 dose on GD 8
6189799001E


title: Liver, GD8 Cylindrospermopsin, 3 hr post dose sample, 6189799008G

description:
Maternal liver sampled after 1 dose on GD 8
6189799008G

source_name: Liver GD8 Cylindrospermopsin, 3 hr post dose sample


title: Liver, GD8 Cylindrospermopsin, 3 hr post dose sample, 6152689045D

description:
Maternal liver sampled after 1 dose on GD 8
6152689045D


title: Liver, GD8 vehicle control, 1 hr post dose sample, 6152689045H

description:
Maternal liver sampled after 1 dose on GD 8
6152689045H


title: Liver, GD8 vehicle control, 1 hr post dose sample, 6189799008F

description:
Maternal liver sampled after 1 dose on GD 8
6189799008F


title: Liver, GD8 Cylindrospermopsin, 1 hr post dose sample, 6189799011D

description:
Maternal liver sampled after 1 dose on GD 8
6189799011D


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6189799009D

description:
Maternal liver sampled after 1 dose on GD 13
6189799009D

source_name: Liver GD13 vehicle control, 24 hr post dose sample

value: Gestation Day 13


title: Liver, GD8 vehicle control, 1 hr post dose sample, 6152689036G

description:
Maternal liver sampled after 1 dose on GD 8
6152689036G


title: Liver, GD8 Cylindrospermopsin, 3 hr post dose sample, 6152689045G

description:
Maternal liver sampled after 1 dose on GD 8
6152689045G


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6152689063C

description:
Maternal liver sampled after 1 dose on GD 13
6152689063C


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6152689045C

description:
Maternal liver sampled after 1 dose on GD 13
6152689045C


title: Liver, GD8 Cylindrospermopsin, 1 hr post dose sample, 6189799001C

description:
Maternal liver sampled after 1 dose on GD 8
6189799001C


title: Liver, GD8 Cylindrospermopsin, 3 hr post dose sample, 6152689045B

description:
Maternal liver sampled after 1 dose on GD 8
6152689045B


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6189799012H

description:
Maternal liver sampled after 1 dose on GD 13
6189799012H


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6189799002F

description:
Maternal liver sampled after 1 dose on GD 13
6189799002F


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6085341028F

description:
Maternal liver sampled after 1 dose on GD 13
6085341028F

source_name: Liver GD13 Cylindrospermopsin, 24 hr post dose sample


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6189799012E

description:
Maternal liver sampled after 1 dose on GD 13
6189799012E


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6189799012D

description:
Maternal liver sampled after 1 dose on GD 13
6189799012D


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6189799001A

description:
Maternal liver sampled after 1 dose on GD 13
6189799001A


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6189799009F

description:
Maternal liver sampled after 1 dose on GD 13
6189799009F


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6152689043H

description:
Maternal liver sampled after 1 dose on GD 13
6152689043H


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6152689063F

description:
Maternal liver sampled after 1 dose on GD 13
6152689063F


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6189799001G

description:
Maternal liver sampled after 1 dose on GD 13
6189799001G


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6152689043C

description:
Maternal liver sampled after 1 dose on GD 13
6152689043C


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6085341028D

description:
Maternal liver sampled after 1 dose on GD 13
6085341028D


title: Liver, GD13 vehicle control, 12 hr post dose sample, 6152689036C

description:
Maternal liver sampled after 1 dose on GD 13
6152689036C

source_name: Liver GD13 vehicle control, 12 hr post dose sample


title: Liver, GD13 Cylindrospermopsin, 24 hr post dose sample, 6152689043E

description:
Maternal liver sampled after 1 dose on GD 13
6152689043E


title: Liver, GD13 vehicle control, 12 hr post dose sample, 6189799009H

description:
Maternal liver sampled after 1 dose on GD 13
6189799009H


title: cerebral malaria Malawi2_C03_782_586556

description: circulating P. falciparum, directly analyzed from whole blood

source_name: whole blood

value: whole blood

tag: malaria retinopathy

value: No

tag: temperature

tag: respirations per minute

tag: parasitemia

tag: hematocrit

tag: outcome


title: Liver, GD13 Cylindrospermopsin, 12 hr post dose sample, 6189799008A

description:
Maternal liver sampled after 1 dose on GD 13
6189799008A

source_name: Liver GD13 Cylindrospermopsin, 12 hr post dose sample

tag: tissue


title: Liver, GD13 vehicle control, 12 hr post dose sample, 6085341028H

description:
Maternal liver sampled after 1 dose on GD 13
6085341028H


title: Liver, GD13 Cylindrospermopsin, 12 hr post dose sample, 6085341028G

description:
Maternal liver sampled after 1 dose on GD 13
6085341028G


title: Liver, GD13 Cylindrospermopsin, 12 hr post dose sample, 6189799008C

description:
Maternal liver sampled after 1 dose on GD 13
6189799008C


title: Liver, GD13 vehicle control, 12 hr post dose sample, 6152689063D

description:
Maternal liver sampled after 1 dose on GD 13
6152689063D


title: 20 SP6-embryonic skin-rep2

city: Richmond

first: Amanda

middle: J

last: Dickinson

state: Virginia

address: 1000 W Cary street

department: Biology

institute: Virginia Commonwealth University

hyb_protocol: following the manufacturer instructions with GeneChip 3'IVT PLUS Reagent Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 +7G

data_processing: All microarray data preprocessing and analysis was done using R. Affy CEL files were imported using the affy package. Expression intensities were summarized, normalized, and transformed using Robust Multiarray Average algorithm. Please note that all the genes that did not map to an Entrez ID were excluded, resulting in 16,755 data rows.

organism: Xenopus laevis

source_name: 20 SP6-embryonic skin

growth_protocol: embryos are grown in 0,1x MBS at 15 °C

extract_protocol: Trizol extraction of Total RNA was performed according the manufacturer's instructions

treatment_protocol: 100mM SP600125 (Jnk inhibitor) treatment from stage 14 to stage 24

tag: developmental stage

value: embryonic stage 24

tag: treated with

value: 100mM SP600125 (from stage 14 to stage 24)

value: whole embryonic skin


title: Liver, GD13 vehicle control, 6 hr post dose sample, 6189799011A

description:
Maternal liver sampled after 1 dose on GD 13
6189799011A

source_name: Liver GD13 vehicle control, 6 hr post dose sample

tag: Sex


title: 20 SP6-embryonic skin-rep1


title: Liver, GD13 vehicle control, 6 hr post dose sample, 6189799008H

description:
Maternal liver sampled after 1 dose on GD 13
6189799008H

tag: age at dosing


title: Liver, GD13 Cylindrospermopsin, 12 hr post dose sample, 6189799009G

description:
Maternal liver sampled after 1 dose on GD 13
6189799009G

tag: chemical


title: Liver, GD13 Cylindrospermopsin, 6 hr post dose sample, 6152689063H

description:
Maternal liver sampled after 1 dose on GD 13
6152689063H

source_name: Liver GD13 Cylindrospermopsin, 6 hr post dose sample

tag: vehicle


title: 20 ctl-embryonic skin-rep2

source_name: 20 ctl-embryonic skin

value: none (control)


title: 20 ctl-embryonic skin-rep1


title: Liver, GD13 Cylindrospermopsin, 6 hr post dose sample, 6189799012C

description:
Maternal liver sampled after 1 dose on GD 13
6189799012C

tag: dose


title: cerebral malaria Malawi2_B12_775_586448

value: Yes

tag: age (months)

tag: gender

value: female

value: full recovery


title: Liver, GD13 vehicle control, 24 hr post dose sample, 6085341028A

description:
Maternal liver sampled after 1 dose on GD 13
6085341028A

tag: strain

value: Distilled water

tag: route

tag: sample time


title: Liver, GD13 Cylindrospermopsin, 6 hr post dose sample, 6085341028B

description:
Maternal liver sampled after 1 dose on GD 13
6085341028B

value: Cylindrospermopsin

value: 50 ug/kg

value: IP injection


title: Liver, GD8 vehicle control, 3 hr post dose sample, 6189799002C

description:
Maternal liver sampled after 1 dose on GD 8
6189799002C

value: Female

value: Gestation Day 8

value: 0 ug/kg

value: Liver


title: Liver, GD13 vehicle control, 3 hr post dose sample, 6152689043F

description:
Maternal liver sampled after 1 dose on GD 13
6152689043F

source_name: Liver GD13 vehicle control, 3 hr post dose sample

value: Gestation Day 13


title: Liver, GD13 Cylindrospermopsin, 12 hr post dose sample, 6189799002B

description:
Maternal liver sampled after 1 dose on GD 13
6189799002B


title: Liver, GD13 vehicle control, 3 hr post dose sample, 6189799002A

description:
Maternal liver sampled after 1 dose on GD 13
6189799002A

source_name: Liver GD13 vehicle control, 3 hr post dose sample,


title: Liver, GD13 Cylindrospermopsin, 6 hr post dose sample, 6152689036F

description:
Maternal liver sampled after 1 dose on GD 13
6152689036F


title: Liver, GD13 Cylindrospermopsin, 3 hr post dose sample, 6189799008D

description:
Maternal liver sampled after 1 dose on GD 13
6189799008D

source_name: Liver GD13 Cylindrospermopsin, 3 hr post dose sample


title: Liver, GD13 Cylindrospermopsin, 6 hr post dose sample, 6152689043D

description:
Maternal liver sampled after 1 dose on GD 13
6152689043D


title: Liver, GD13 Cylindrospermopsin, 3 hr post dose sample, 6189799002G

description:
Maternal liver sampled after 1 dose on GD 13
6189799002G


title: Liver, GD13 vehicle control, 6 hr post dose sample, 6189799001H

description:
Maternal liver sampled after 1 dose on GD 13
6189799001H


title: Liver, GD13 Cylindrospermopsin, 3 hr post dose sample, 6152689036H

description:
Maternal liver sampled after 1 dose on GD 13
6152689036H


title: Liver, GD13 vehicle control, 1 hr post dose sample, 6189799011G

description:
Maternal liver sampled after 1 dose on GD 13
6189799011G

source_name: Liver GD13 vehicle control, 1 hr post dose sample


title: Liver, GD13 vehicle control, 1 hr post dose sample, 6189799009B

description:
Maternal liver sampled after 1 dose on GD 13
6189799009B


title: Liver, GD13 Cylindrospermopsin, 1 hr post dose sample, 6189799008B

description:
Maternal liver sampled after 1 dose on GD 13
6189799008B

source_name: Liver GD13 Cylindrospermopsin, 1 hr post dose sample


title: Liver, GD13 vehicle control, 1 hr post dose sample, 6152689045A

description:
Maternal liver sampled after 1 dose on GD 13
6152689045A


title: Liver, GD13 Cylindrospermopsin, 3 hr post dose sample, 6189799009E

description:
Maternal liver sampled after 1 dose on GD 13
6189799009E


title: Liver, GD 13 pooled Cylindrospermopsin, 24 hr post dose sample

description: Maternal liver sampled after 1 dose on GD 13

hyb_protocol: Microarray hybridization was performed at the EDGE2 Program, University of Wisconsin

scan_protocol: Scanning was performed at the EDGE2 Program, University of Wisconsin

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package.

source_name: Liver, GD 13 Cylindrospermopsin, sampled 24 hours post dose

label_protocol: RNA labeling was performed at the EDGE2 Program, University of Wisconsin

extract_protocol: Liver samples were homogenized in TRI reagent (Sigma-Aldrich, St. Louis, MO) and processed through alcohol precipitation on the same day; RNA pellets were then stored at −80oC

tag: age at initial dose

value: 24 hours

tag: number of sample in pool


title: Liver, GD13 Cylindrospermopsin, 1 hr post dose sample, 6152689045E

description:
Maternal liver sampled after 1 dose on GD 13
6152689045E


title: Liver, GD 13 pooled Cylindrospermopsin, 6 hr post dose sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 6 hours post dose

value: 6 hours


title: Liver, GD13 vehicle control, 3 hr post dose sample, 6152689043B

description:
Maternal liver sampled after 1 dose on GD 13
6152689043B


title: Liver, GD 13 pooled Cylindrospermopsin, 12 hr post dose sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 12 hours post dose

value: 12 hours


title: Liver, GD13 Cylindrospermopsin, 1 hr post dose sample, 6152689036A

description:
Maternal liver sampled after 1 dose on GD 13
6152689036A


title: Liver, GD13 Cylindrospermopsin, 1 hr post dose sample, 6189799001B

description:
Maternal liver sampled after 1 dose on GD 13
6189799001B


title: Liver, GD 13 pooled vehicle control, 3 hr post dose sample

source_name: Liver, GD 13 vehicle control, sampled 3 hours post dose

value: 3 hours


title: Liver, GD 13 pooled vehicle control, 1 hr post dose sample

source_name: Liver, GD 13 vehicle control, sampled 1 hour post dose

value: 1 hour


title: Liver, GD 13 pooled vehicle control, 24 hr post dose sample

source_name: Liver, GD 13 vehicle control, sampled 24 hours post dose


title: Liver, GD 13 pooled Cylindrospermopsin, 1 hr post dose sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 1 hour post dose


title: Liver, GD 13 pooled Cylindrospermopsin, 3 hr post dose sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 3 hours post dose


title: Liver, GD 13 pooled vehicle control, 6 hr post dose sample

source_name: Liver, GD 13 vehicle control, sampled 6 hours post dose


title: Liver, GD 8 pooled Cylindrospermopsin, 24 hr post dose sample

description: Maternal liver sampled after 1 dose on GD 8

source_name: Liver, GD 8 Cylindrospermopsin, sampled 24 hours post dose


title: Doxorubicin6 vs Control6, 7 week post treatment, reverse labelling

city: Didcot

first: Emma

middle: Louise

last: Marczylo

state: Oxfordshire

address: Harwell Campus, Chilton

department: Toxicology

country: United Kingdom

institute: Public Health England

description: Biological replicate 6 of 6, reverse labelling, 7 week

hyb_protocol: Control and doxorubicin samples were randomly paired and pooled and treated according to the labelling kit's manufacturer's instructions. Samples were denatured for 3-10 min at 65oC and incubated for 30 min at 37oC prior to hybridisation overnight at 37oC using a Genetix hybridisation chamber. Arrays were washed on a rocking platform set at 50 oscillations per min for 5 min each at RT, firstly in 2X SSC containing 0.05% (w/v) SDS, secondly in 1X SSC and finally in 0.5X SSC, and dried by centrifugation.

scan_protocol: Slides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Result files were normalised using the LOESS within array followed by the quantile between array commands in the Bioconductor limma library package of R version 2.15.2. Normalised log2[Cy5/Cy3] for forward labelling arrays and log2[Cy3/Cy5] for reverse labelling arrays were compiled into a single matrix file. All array control and empty values were removed and excluded from normalisation in R.

source_name: Testis RNA, Doxorubicin6, 7 week post treatment

label_protocol: 500 ng of total RNA was labelled with either Flashtag RNA labelling kit (Genisphere) or Label IT miRNA labelling kit (Mirus) according to the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice, 8-10 weeks old. 12 hour light/dark cycle. Food and water provided ad libitum, 24 hours a day.

extract_protocol: 1 whole testis was lysed in 1ml of Tri reagent (Sigma). RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Mice were randomly assigned to groups. Dosing was performed via intraperitoneal injection. Treated mice received 3 x 3mg/kg of doxorubicin (in 0.85% (v/v) saline) per week (9mg/kg in total), controls received vehicle only; in a dose volume of 10ml/kg. 1, 4 or 7 wk after the final administration mice were sacrificed under isoflurane anaesthesia and exsanguinated. Testes were taken for analysis.

value: Male

value: Testis

source_name: Testis RNA, Vehicle only6, 7 week post treatment


title: Liver, GD 8 pooled Cylindrospermopsin, 1 hr post dose sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 1 hour post dose


title: Liver, GD 8 pooled vehicle control, 1 hr post dose sample

source_name: Liver, GD 8 vehicle control, sampled 1 hour post dose


title: Liver, GD 13 pooled vehicle control, 5 day sample

description: Maternal liver samples taken 5 days after the initiation of a 5 consecutive days dosing regime

source_name: Liver, GD 13 vehicle control, sampled 5 day post initial dose

extract_protocol: Liver samples were immediately homogenized in TRI reagent (Sigma-Aldrich, St. Louis, MO) and processed through alcohol precipitation on the same day; RNA pellets were then stored at −80oC

value: 5 days post initial dose

tag: number of samples in pool


title: Doxorubicin5 vs Control5, 7 week post treatment, reverse labelling

description: Biological replicate 5 of 6, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin5, 7 week post treatment

source_name: Testis RNA, Vehicle only5, 7 week post treatment


title: Liver, GD 13 pooled Cylindrospermopsin, 2 day sample

description: Maternal liver samples taken 2 days after the initiation of a 5 consecutive days dosing regime

source_name: Liver, GD 13 Cylindrospermopsin, sampled 2 day post initial dose

value: Distilled water

value: 2 days post initial dose


title: Liver, GD 13 pooled Cylindrospermopsin, 4 day sample

description: Maternal liver samples taken 4 days after the initiation of a 5 consecutive days dosing regime

source_name: Liver, GD 13 Cylindrospermopsin, sampled 4 day post initial dose

value: Cylindrospermopsin

value: 50 ug/kg

value: 4 days post initial dose


title: Liver, GD 13 pooled Cylindrospermopsin, 5 day sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 5 day post initial dose

value: Female

value: IP injection


title: Liver, GD 8 pooled Cylindrospermopsin, 3 hr post dose sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 3 hours post dose

value: Gestation Day 8

value: Liver


title: Liver, GD 8 pooled vehicle control, 6 hr post dose sample

source_name: Liver, GD 8 vehicle control, sampled 6 hours post dose

value: 0 ug/kg


title: Liver, GD 13 pooled vehicle control, 12 hr post dose sample

source_name: Liver, GD 13 vehicle control, sampled 12 hours post dose

value: Gestation Day 13


title: Liver, GD 8 pooled vehicle control, 4 day sample

source_name: Liver, GD 8 vehicle control, sampled 4 day post initial dose


title: Liver, GD 8 pooled Cylindrospermopsin, 4 day sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 4 day post initial dose


title: Liver, GD 8 pooled vehicle control, 3 hr post dose sample

source_name: Liver, GD 8 vehicle control, sampled 3 hours post dose


title: Liver, GD 13 pooled vehicle control, 2 day sample

source_name: Liver, GD 13 vehicle control, sampled 2 day post initial dose


title: Liver, GD 13 pooled vehicle control, 1 day sample

description: Maternal liver samples taken 1 day after the initiation of a 5 consecutive day dosing regime

source_name: Liver, GD 13 vehicle control, sampled 1 day post initial dose

value: 1 day post initial dose


title: Liver, GD 8 pooled Cylindrospermopsin, 6 hr post dose sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 6 hours post dose

value: 6 hours


title: Liver, GD 13 pooled vehicle control, 4 day sample

source_name: Liver, GD 13 vehicle control, sampled 4 day post initial dose


title: Liver, GD 8 pooled Cylindrospermopsin, 12 hr post dose sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 12 hours post dose

value: 12 hours


title: Liver, GD 8 pooled vehicle control, 12 hr post dose sample

source_name: Liver, GD 8 vehicle control, sampled 12 hours post dose


title: Liver, GD 13 pooled Cylindrospermopsin, 1 day sample

source_name: Liver, GD 13 Cylindrospermopsin, sampled 1 day post initial dose


title: Liver, GD 8 pooled Cylindrospermopsin, 5 day sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 5 day post initial dose


title: Liver, GD 8 pooled vehicle control, 24 hr post dose sample

source_name: Liver, GD 8 vehicle control, sampled 24 hours post dose

value: 24 hours


title: Liver, GD 8 pooled vehicle control, 2 day sample

source_name: Liver, GD 8 vehicle control, sampled 2 day post initial dose


title: Doxorubicin4 vs Control4, 7 week post treatment, reverse labelling

description: Biological replicate 4 of 6, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin4, 7 week post treatment

value: Male

value: Testis

source_name: Testis RNA, Vehicle only4, 7 week post treatment


title: Liver, GD 8 pooled vehicle control, 5 day sample

source_name: Liver, GD 8 vehicle control, sampled 5 day post initial dose

value: Distilled water

value: 5 days post initial dose


title: Doxorubicin3 vs Control3, 7 week post treatment, reverse labelling

description: Biological replicate 3 of 6, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin3, 7 week post treatment

source_name: Testis RNA, Vehicle only3, 7 week post treatment


title: Liver, GD 8 pooled vehicle control, 1 day sample

source_name: Liver, GD 8 vehicle control, sampled 1 day post initial dose

value: 1 day post intial dose


title: Doxorubicin2 vs Control2, 7 week post treatment, reverse labelling

description: Biological replicate 2 of 6, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin2, 7 week post treatment

source_name: Testis RNA, Vehicle only2, 7 week post treatment


title: Control4 vs Doxorubicin4, 7 week post treatment, forward labelling

description: Biological replicate 4 of 6, forward labelling, 7 week


title: Control3 vs Doxorubicin3, 7 week post treatment, forward labelling

description: Biological replicate 3 of 6, forward labelling, 7 week


title: Doxorubicin3 vs Control3, 4 week post treatment, reverse labelling

description: Biological replicate 3 of 6, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin3, 4 week post treatment

source_name: Testis RNA, Vehicle only3, 4 week post treatment


title: Doxorubicin2 vs Control2, 4 week post treatment, reverse labelling

description: Biological replicate 2 of 6, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin2, 4 week post treatment

source_name: Testis RNA, Vehicle only2, 4 week post treatment


title: Doxorubicin1 vs Control1, 4 week post treatment, reverse labelling

description: Biological replicate 1 of 6, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin1, 4 week post treatment

source_name: Testis RNA, Vehicle only1, 4 week post treatment


title: Control2 vs Doxorubicin2, 7 week post treatment, forward labelling

description: Biological replicate 2 of 6, forward labelling, 7 week


title: Control6 vs Doxorubicin6, 4 week post treatment, forward labelling

description: Biological replicate 6 of 6, forward labelling, 4 week

source_name: Testis RNA, Vehicle only6, 4 week post treatment

source_name: Testis RNA, Doxorubicin6, 4 week post treatment


title: Control1 vs Doxorubicin1, 7 week post treatment, forward labelling

description: Biological replicate 1 of 6, forward labelling, 7 week

source_name: Testis RNA, Vehicle only1, 7 week post treatment

source_name: Testis RNA, Doxorubicin1, 7 week post treatment


title: Control5 vs Doxorubicin5, 4 week post treatment, forward labelling

description: Biological replicate 5 of 6, forward labelling, 4 week

source_name: Testis RNA, Vehicle only5, 4 week post treatment

source_name: Testis RNA, Doxorubicin5, 4 week post treatment


title: Liver, GD 8 pooled Cylindrospermopsin, 1 day sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 1 day post initial dose

value: Cylindrospermopsin

value: 50 ug/kg


title: Control6 vs Doxorubicin6, 7 week post treatment, forward labelling

description: Biological replicate 6 of 6, forward labelling, 7 week

source_name: Testis RNA, Vehicle only6, 7 week post treatment

source_name: Testis RNA, Doxorubicin6, 7 week post treatment


title: Liver, GD 8 pooled Cylindrospermopsin, 2 day sample

source_name: Liver, GD 8 Cylindrospermopsin, sampled 2 day post initial dose

value: Female

value: 2 days post initial dose


title: Doxorubicin1 vs Control1, 7 week post treatment, reverse labelling

description: Biological replicate 1 of 6, reverse labelling, 7 week


title: Control5 vs Doxorubicin5, 7 week post treatment, forward labelling

description: Biological replicate 5 of 6, forward labelling, 7 week

source_name: Testis RNA, Vehicle only5, 7 week post treatment

source_name: Testis RNA, Doxorubicin5, 7 week post treatment


title: Control3 vs Doxorubicin3, 4 week post treatment, forward labelling

description: Biological replicate 3 of 6, forward labelling, 4 week

source_name: Testis RNA, Vehicle only3, 4 week post treatment

source_name: Testis RNA, Doxorubicin3, 4 week post treatment


title: Doxorubicin6 vs Control6, 4 week post treatment, reverse labelling

description: Biological replicate 6 of 6, reverse labelling, 4 week


title: Doxorubicin5 vs Control5, 4 week post treatment, reverse labelling

description: Biological replicate 5 of 6, reverse labelling, 4 week


title: Doxorubicin4 vs Control4, 4 week post treatment, reverse labelling

description: Biological replicate 4 of 6, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin4, 4 week post treatment

source_name: Testis RNA, Vehicle only4, 4 week post treatment


title: Control4 vs Doxorubicin4, 4 week post treatment, forward labelling

description: Biological replicate 4 of 6, forward labelling, 4 week


title: Control1 vs Doxorubicin1, 4 week post treatment, forward labelling

description: Biological replicate 1 of 6, forward labelling, 4 week

source_name: Testis RNA, Vehicle only1, 4 week post treatment

source_name: Testis RNA, Doxorubicin1, 4 week post treatment


title: WT1

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description: 18; Gene expression data from wild type

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mogene Array.

scan_protocol: GeneChips were scanned using the Affemetrix scanner 7G.

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.0.187

source_name: Normal Thymic T cells from wild type littermate 1 of Lck-Dlx5 Transgenic mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were husbandried under normal condition

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

tag: genotype/variation

value: WT

value: thymic T cell


title: Lck-akt2 72/3153 +

description: 13; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line72 cell3153

tag: tissue

value: thymic T cell lymphoma


title: WT3

description: 21; Gene expression data from wild type

source_name: Normal Thymic T cells from wild type littermate 3 of Lck-Dlx5 Transgenic mouse


title: WT2

description: 20; Gene expression data from wild type

source_name: Normal Thymic T cells from wild type littermate 2 of Lck-Dlx5 Transgenic mouse


title: Lck-akt2 420/1672

description: A; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line420 cell1672


title: Lck-akt2 72/3148 +

description: 11; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line72 cell3148


title: Lck-akt2 420/1623

description: 29; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line420 cell1623


title: Control2 vs Doxorubicin2, 4 week post treatment, forward labelling

description: Biological replicate 2 of 6, forward labelling, 4 week

source_name: Testis RNA, Vehicle only2, 4 week post treatment

source_name: Testis RNA, Doxorubicin2, 4 week post treatment


title: Doxorubicin5 vs Control5, 1 week post treatment, reverse labelling

description: Biological replicate 5 of 6, reverse labelling, 1 week

source_name: Testis RNA, Doxorubicin5, 1 week post treatment

source_name: Testis RNA, Vehicle only5, 1 week post treatment


title: Doxorubicin4 vs Control4, 1 week post treatment, reverse labelling

description: Biological replicate 4 of 6, reverse labelling, 1 week

source_name: Testis RNA, Doxorubicin4, 1 week post treatment

source_name: Testis RNA, Vehicle only4, 1 week post treatment


title: Doxorubicin1 vs Control1, 1 week post treatment, reverse labelling

description: Biological replicate 1 of 6, reverse labelling, 1 week

source_name: Testis RNA, Doxorubicin1, 1 week post treatment

source_name: Testis RNA, Vehicle only1, 1 week post treatment


title: Control5 vs Doxorubicin5, 1 week post treatment, forward labelling

description: Biological replicate 5 of 6, forward labelling, 1 week


title: Lck-akt2 420/1404

description: 5; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line420 cell1404


title: Control6 vs Doxorubicin6, 1 week post treatment, forward labelling

description: Biological replicate 6 of 6, forward labelling, 1 week

source_name: Testis RNA, Vehicle only6, 1 week post treatment

source_name: Testis RNA, Doxorubicin6, 1 week post treatment


title: Doxorubicin2 vs Control2, 1 week post treatment, reverse labelling

description: Biological replicate 2 of 6, reverse labelling, 1 week

source_name: Testis RNA, Doxorubicin2, 1 week post treatment

source_name: Testis RNA, Vehicle only2, 1 week post treatment


title: Lckakt2 420 * dlx5 256+/+ F47

description: D; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-Dlx5 (founder line47);MyrAkt2 Transgenic mouse


title: lck dlx5 801 F86

description: 4; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-Dlx5 Transgenic mouse founder line86


title: Lck dlx5(F86) * Lck akt2 242+/+

description: 28; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-Dlx5 (founder line86);MyrAkt2 Transgenic mouse


title: Lck dlx5(F86) * Lck akt2 241+/+

description: 27; Gene expression data from lymphoma


title: Control4 vs Doxorubicin4, 1 week post treatment, forward labelling

description: Biological replicate 4 of 6, forward labelling, 1 week


title: lck dlx5 f47-918

description: 22; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-Dlx5 Transgenic mouse founder line47


title: Lck-dlx5 F63

description: 1; Gene expression data from lymphoma

source_name: Thymic tumor from Lck-Dlx5 Transgenic mouse founder line63


title: Lckakt2 420 * dlx5 265+/+ F47

description: G; Gene expression data from lymphoma


title: Control1 vs Doxorubicin1, 1 week post treatment, forward labelling

description: Biological replicate 1 of 6, forward labelling, 1 week


title: Control2 vs Doxorubicin2, 1 week post treatment, forward labelling

description: Biological replicate 2 of 6, forward labelling, 1 week