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| Status |
Public on May 17, 2019 |
| Title |
Hand2 cKO 3 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: aDPW+OFT
developmental stage: E9.5
genotype/variation: Hand2flox/flox; Mef2c-AHF-Cre
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| Extracted molecule |
total RNA |
| Extraction protocol |
aDPW and OFTs were dissected from embryos and pooled. RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) .
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Base CaIllumina bcl2fastq version 2.18 were used to the basecalling
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the mm8 reference using STAR (v2.5.1b) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
FPKM values were log2-transformed with an offset value of 1.0.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample
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| Submission date |
May 16, 2019 |
| Last update date |
May 17, 2019 |
| Contact name |
Meng Xia |
| E-mail(s) |
[email protected]
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| Organization name |
Nanjing unversity
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| Department |
Model Animal Research Center
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| Lab |
Zhongzhou Yang
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| Street address |
XueFu Road 12
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| City |
Nanjing |
| State/province |
JiangSu |
| ZIP/Postal code |
210061 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE131362 |
Transcritptome analysis of anterior dorsal pericardial wall (aDPW) and cardiac outflow tract (OFT) from control and Hand2flox/flox; Mef2c-AHF-Cre embryos at E9.5 |
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| Relations |
| BioSample |
SAMN11663550 |
| SRA |
SRX5849950 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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