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Status |
Public on Dec 19, 2016 |
Title |
tph2-/- AGM-1 |
Sample type |
SRA |
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Source name |
mouse
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Organism |
Mus musculus |
Characteristics |
cell type: AGM cells genotype/variation: tph2-/- age: E11.5 tissue: embryos strain: C57BL/6
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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Description |
AGM of tph2-/- rep1 164-2
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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
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Submission date |
Nov 22, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Lv Junhua |
E-mail(s) |
huashuo001@126.com
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Organization name |
INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES
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Street address |
1 Beichen West Road, Chaoyang District
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City |
beijing |
State/province |
beijing |
ZIP/Postal code |
100101 |
Country |
China |
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Platform ID |
GPL21493 |
Series (1) |
GSE90130 |
5-hydroxytryptamine synthesized in the Aorta-Gonad-Mesonephros regulates hematopoietic stem and progenitor cell survival |
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Relations |
BioSample |
SAMN06046983 |
SRA |
SRX2366733 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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