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Sample GSM2399016 Query DataSets for GSM2399016
Status Public on Dec 19, 2016
Title tph2+/- AGM-1
Sample type SRA
 
Source name mouse
Organism Mus musculus
Characteristics cell type: AGM cells
genotype/variation: tph2+/-
age: E11.5
tissue: embryos
strain: C57BL/6
Extracted molecule total RNA
Extraction protocol The total RNA was extracted using TRNzol (Tiangen, Beijing) using the AGMs from two littermate pairs of tph2+/+, tph2+/- or tph2-/- at E11.5
Approximately 1 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 150 bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description AGM of tph2+/- rep1
164-3
Data processing Reads were aligned to the GRCm38 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Identifieded differentially expressed genes with R package DEGseq
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression for each gene of all samples
 
Submission date Nov 22, 2016
Last update date May 15, 2019
Contact name Lv Junhua
E-mail(s) huashuo001@126.com
Organization name INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES
Street address 1 Beichen West Road, Chaoyang District
City beijing
State/province beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL21493
Series (1)
GSE90130 5-hydroxytryptamine synthesized in the Aorta-Gonad-Mesonephros regulates hematopoietic stem and progenitor cell survival
Relations
BioSample SAMN06046985
SRA SRX2366731

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

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