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Comparison of gene expression profiles across the normal human body

ABSTRACT: Normal human tissue samples from ten post-mortem donors were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays. Donor information: Donor 1 - 25 year old male; donor 2 - 38 year old male; donor 3 - 39 year old female; donor 4 - 30 year old male; donor 5 - 35 year old male; donor 6 - 52 year old male; donor 7 - 50 year old female; donor 8 - 48 year old female; donor 9 - 53 year old female; donor 10 - 23 year old female Keywords: normal human tissue comparison

ORGANISM(S): Homo sapiens

PROVIDER: GSE3526 | GEO | 2006/03/30

SECONDARY ACCESSION(S): PRJNA93579

REPOSITORIES: GEO

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Transcription profiling by array of human post mortem tissue samples

Project description:Normal human tissue samples from ten post-mortem donors were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays. Donor information: Donor 1 - 25 year old male; donor 2 - 38 year old male; donor 3 - 39 year old female; donor 4 - 30 year old male; donor 5 - 35 year old male; donor 6 - 52 year old male; donor 7 - 50 year old female; donor 8 - 48 year old female; donor 9 - 53 year old female; donor 10 - 23 year old female Experiment Overall Design: Comparison of normal human tissues; 65 tissues represented, including 20 distinct regions of the CNS. This dataset is part of the TransQST collection.

2008-06-14 | E-GEOD-3526 | biostudies-arrayexpress

WGS from transverse colon (ENCSR961ZRM)

Project description:The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO793LXB, a 53 year old female. There are two libraries: PCR-based (9-cycle, ENCLB388OQF) and PCR-free (ENCLB358DLU), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-06-15 | GSE177949 | GEO

DNase-seq from A172 (ENCSR932KWJ)

Project description:DNase-seq on cell line A172 (53 year old male human brain, glioblastoma) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-12-07 | GSE90426 | GEO

Watanabe2018_State Transition Model with Treatment and Costs

Project description:Model with functions depending on Age, Male, BP (Blood Pressure). There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal. The yearly transition probabilities are: Healthy to Dead: Age/1000; Healthy to Sick: According to function F1 depending on Age and Male and BP; Sick to Healthy: 0.1; Sick to Dead: according to function F2 depending on Age and Male. Pre-Transition Rules: Age increased by 1 and BP by Age/10 each simulation cycle. Post-Transition Rules: Treatment = BP>140 , becomes 1 when BP crosses 140 threshold; BP =BP-Treatment*10 , meaning a drop of 10 once treatment is applied; CostThisYear = Age + \Treatment*10 , cost depends on age and if treatment was taken; Cost= Cost + CostThisYear , it accumulates cost over time. Initial conditions: Healthy = (50 Male, 50 Female with Age =1,2,...,50 for each individual), BP =120, Sick = (0,0) and Dead = (0,0). Output: Number of men and women in each disease state for years 1-10 and their ages and costs in each state. A stratified report by male and female and young – up to age 30 and old above age 30 is produced.

2019-01-30 | MODEL1803120006 | BioModels

Transcriptome characterization of CHOPS syndrome, a novel genetic disorder caused by gain-of-function mutations of AFF4

Project description:AFF4 is a component of super elongation complex (SEC), which plays an important role in mobilizing paused RNA polymerase II at gene promoter regions. Using exome sequenging, we have identified a novel genetic disorder caused by missense mutations in AFF4. We propose CHOPS syndrome as a name for this new diagnosis. To evaluate the effect of identified missense mutations of AFF4, utilizing patient derived skin fibroblast cell lines, the gene expression analysis was perfomred. To characterize the transcriptome pattern observed in CHOPS syndrome, the skin fibroblast samples from two CHOPS syndrome probands and three healthy control subjects were used. Samples used for expression array include two CHOPs syndrome samples (CDL160: 6 year-old Caucasian female with 254S mut and CDL444: 12 year-old Caucasian male with 254A mut) and three age gender matched controls (GM01652: 11 year-old Caucasian female, GM02036 11 year-old Caucasian female and GM08398: 8 year-old Caucasian male).

2015-01-27 | E-GEOD-64031 | biostudies-arrayexpress

ECLS Survival in Pediatric HCT Recipient with Presumed Cardiac GVHD

Project description:<p>We report the case of a 15-year-old female with hypodiploid pre-B acute lymphoblastic leukemia status post allogeneic hematopoietic stem cell transplantation (HCT) from a matched unrelated male donor who presented on transplant day +75 with cardiac arrest due to ventricular fibrillation associated with fulminant myocarditis. Using conventional diagnostics, an exhaustive search for microbial pathogens in the heart biopsy as well as nasopharynx, blood, urine, and endotracheal aspirate was performed but did not uncover a candidate pathogen. The family consented to a research study for the use of unbiased next-generation genomic sequencing for pathogen identification in the myocardial biopsy. DNA sequencing was performed on 1.5 x 10<sup>8</sup> sequencing pairs and no microbial pathogens were identified. Interestingly, a significant component of Y-chromosomal human DNA was identified, suggesting infiltration of at least 10 donor leukocytes per host cell. This finding is grossly consistent with the lymphocyte:myocyte ratio in the biopsy according to visual inspection at 40x magnification. This case merits discussion due to (1) her survival after 17 days of veno-arterial extracorporeal life support (ECLS) and (2) the possibility of cardiotropic graft versus host disease (GVHD).</p>

| phs001336 | dbGaP

Clonal cytogenetics changes in progression of multiple myeloma to extramedullary relapse and plasmocellular leukemia – case report

Project description:Extramedullary relapse (EM) of multiple myeloma (MM) is defined as infiltration of plasma cells (PC) outside of the bone marrow. EM is an aggressive form of the disease with a dismal outcome. We present cytogenetic findings of a 52-year-old female patient who was diagnosed with MM in 2008 and progression of MM to EM and plasmocellular leukemia.

2015-10-10 | E-MTAB-3577 | biostudies-arrayexpress

RAMPAGE from A172 (ENCSR208AWA)

Project description:The libraries contained in this experiment come from independent growths of cell line A172, a glioblastoma cell line derived from a 53 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-11-08 | GSE88106 | GEO

Single cell of human retina

Project description:Retinal RNA profiles from macula and periphery of each eye were generated by single-cell sequencing. M11-M14 are macula retina and P11-P14 are peripheral retina from the same 78 year old donor. M21-M24 are macula retina and P21-P24 are peripheral retina from the same 90-year-old donor.

2021-08-11 | GSE155288 | GEO

total RNA-seq from fibroblast of arm (ENCSR797BPP)

Project description:The libraries contained in this experiment come from independent growths of cell line GM23248, a fibroblast primary cell line derived from an arm skin punch of a 53 year old male. They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-03-18 | GSE78670 | GEO

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