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Sample GSM3569361 Query DataSets for GSM3569361
Status Public on Jul 01, 2020
Title FACS-ed feto-placental endothelial cells Sample 5 Mutant
Sample type SRA
 
Source name FACS-ed feto-placental endothelial cells
Organism Mus musculus
Characteristics tissue: feto-placental endothelial
strain: C57BL/6J
developmental stage: E16
Sex: Male
genotype: Mutant
Growth protocol Feto-placental endothelial cells (FPEC - defined as CD31+/CD41- cells) were isolated by FACS from E16 labyrinthine zone placentae, using an Aria-Fusion cell sorter (BD Bioscience), with exclusion of cell duplets and dying cells (7AAD+).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sorted FPEC using RNeasy Plus Micro Kits (Qiagen – 74034). Quantity and quality were verified using the RNA 6000 Pico Kit (Agilent – 5067-1513) and an Agilent 2100 Bioanalyzer. Only RNA samples with RNA integrity numbers (RIN) >9.0 were used.
Total RNA (2 ng) was whole-transcriptome amplified using the Ovation RNA–Seq System V2 (NuGEN). To prepare the RNA–seq libraries the amplified cDNA (2μg per sample) was fragmented to 200bp using a Bioruptor Sonicator (Diagenode), end repaired and barcoded using the Ovation Rapid DR Library System (NuGEN).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description FACS-ed feto-placental endothelial cells Sample 5 Mutant
sample name in processed data file:
Sample 5
Data processing The reads were aligned onto the mouse GRCm38 genome using TopHat 2.0.11
Gene abundance and differential expression were determined with Cufflinks 2.2.1 and expressed in fragments per kilobase per million mapped reads (FPKM). The cut off for expression was set at ≥1 FPKM.
Genes with a linear fold expression change greater than 1.5 and a Benjamini–Hochberg false discovery rate (FDR) <5% were considered differentially expressed.
FPKM values are included in this submission
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM values are included in this submission as tab-delimited text
 
Submission date Jan 18, 2019
Last update date Jul 01, 2020
Contact name Brian Yee Hong Lam
E-mail(s) yhbl2@cam.ac.uk
Organization name University of Cambridge
Department Metabolic Research Laboratories
Street address Box 289 Addenbookes Hospital, Hills Road
City Cambridge
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE125351 Fetus-derived IGF2 matches placental development to fetal demand [RNA-seq]
GSE125434 Fetus-derived IGF2 matches placental development to fetal demand
Relations
BioSample SAMN10774576
SRA SRX5263032

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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