Dataset Information

High burden of Clonal Hematopoiesis in First Responders Exposed to the World Trade Center Disaster

ABSTRACT: High burden of Clonal Hematopoiesis in First Responders Exposed to the World Trade Center Disaster

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo Sapiens

SUBMITTER: AECOM

PROVIDER: PRJEB49193 | EVA | 2021-12-05

REPOSITORIES: EVA

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Dataset's files

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			Action	DRS
	HGV_analysis_affected_merged.vcf.gz	Vcf
	HGV_analysis_affected_merged.vcf.gz.csi	Vcf
	HGV_analysis_affected_merged.vcf.gz.tbi	Vcf
	HGV_analysis_control_merged.vcf.gz	Vcf
	HGV_analysis_control_merged.vcf.gz.csi	Vcf

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Project description:Human placenta bulk mRNA-sequencing from n=124 first trimester (59 female, 65 male) and n=43 third trimester (18 female, 25 male) tissue samples. A subset of 23 pregnancies has matched placenta tissue collected at both first and third trimester. Tissue was collected at Cedars-Sinai Medical Center in Los Angeles, California, USA. First trimester placenta was collected at gestational ages of 70-100 days from leftover tissue from chorionic villus sampling for prenatal genetic diagnosis, after cleaning to remove maternal decidua. Third trimester placenta was collected after delivery at gestational ages 254-290 days from the fetal side near the umbilical cord insertion site beneath the amnion. Tissue was stored in RNAlater RNA Stabilization Solution (Invitrogen) at -80C until further processing. All pregnancies were conceived without fertility treatments, were normal karyotype, and resulted in live singleton births. Mothers with pre-existing diabetes or hypertension were excluded from the study, but not excluded if complications developed during pregnancy, though most pregnancies were uncomplicated. The average parental age was advanced (over 35 years old) but principal components analysis did not show clustering by either maternal or paternal age. RNA extraction was performed with physical homogenization of tissue followed by the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN), then 1 ug of the total RNA elution was used for library construction using the Illumina TruSeq Stranded mRNA library preparation kit (Illumina), with polyA mRNA selection then cDNA synthesis using SuperScript II reverse transcriptase (Invitrogen) and random primers. The cDNA was converted into double stranded DNA and PCR-amplified, then purified with Agencourt AMPure XP beads (Beckman Coulter). Sample libraries were multiplexed and sequenced on a NovaSeq 6000 platform (Illumina) using 75bp single-end mRNA-sequencing, with average 30 million reads per sample. Differential expression analysis was performed with DEseq2 to compare first versus third trimester placenta, adjusted for fetal sex [PubMed ID: 38271627]. Subanalyses were also performed to identify sex differences.

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High burden of Clonal Hematopoiesis in First Responders Exposed to the World Trade Center Disaster

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