|
| Status |
Public on Jul 01, 2020 |
| Title |
FACS-ed feto-placental endothelial cells Sample 1 Control |
| 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: Control
|
| 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 1 Control
sample name in processed data file:
Sample 1
|
| 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 |
SAMN10774582 |
| SRA |
SRX5263028 |
