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Series GSE179076 Query DataSets for GSE179076
Status Public on Apr 05, 2022
Title Longitudinal blood transcriptome analysis of two patients with cyclic thrombocytopenia
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cyclic thrombocytopenia (CTP) is a rare disease of characterized by periodic platelet count oscillations of uncertain etiology. As part of a study that applied systems biology approaches to investigate two patients with CTP, we performed whole blood transcriptome analyses on semi-weekly collected sequential samples covering two platelet cycles. This blood transcriptome analysis revealed cyclical gene expression changes of platelet-specific genes that are in parallel with, and leading platelet count oscillations in both patients. In addition, erythrocyte-specific genes and neutrophil-specific genes also exhibited cyclic patterns which preceded platelet-specific genes. These findings revealed cyclical trilineage hematopoiesis, most pronounced in megakaryopoiesis in both patients with CTP.
 
Overall design This study was approved by the Stanford University Institutional Review Board. Two patients with CTP were consented and enrolled in the study. 24 consecutive blood samples from patient 1 (CT1), and 15 samples from patient 2 (CT2) were collected in EDTA blood tubes every 3-4 days covering two platelet cycles. Total RNAs were extracted after red blood cell lysis. 3SEQ (3’-end sequencing for expression quantification) analyses were performed on blood RNA samples. HiSeq 2000 system and NextSeq 500 (Illumina) were used to generate sequencing data for CT1 and CT2, respectively. 3SEQ data were filtered and mapped to human transcriptome hg19, and read counts for each gene were generated. Quantitative analysis of the Significance Analysis of Microarrays-Seq (SAMseq) algorithm was used to obtain genes that are quantitatively associated with platelet count.
 
Contributor(s) Zhang H, Hou Y, Han P, Chien M, Guo X, Gotlib JR, Zehnder JL
Citation(s) 35381066
Submission date Jun 28, 2021
Last update date Jul 05, 2022
Contact name Haiyu Zhang
Organization name Stanford University
Street address 300 Pasteur Dr.
City Palo Alto
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (38)
GSM5406058 CT1_1
GSM5406059 CT1_2
GSM5406060 CT1_3
Relations
BioProject PRJNA742067
SRA SRP325899

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MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE179076_CT1_exp_all_samples.xlsx 2.8 Mb (ftp)(http) XLSX
GSE179076_CT2_exp_all_samples.xlsx 2.0 Mb (ftp)(http) XLSX
GSE179076_RAW.tar 4.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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