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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 31, 2019 |
| Title |
Mouse E10.5 S3 |
| Sample type |
SRA |
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| Source name |
E10.5_periocular neural crest
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: E10.5
tissue: periocular neural crest
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| Extracted molecule |
total RNA |
| Extraction protocol |
pNC (E10.5) or Cornea (E14.5, E16.5) were dissected from embryonic tissue and immersed in Trizol. RNA extraction performed by BGI.US®. In brief, mRNA is purified by Dnase I and oligodt magnetic beads, followed by the addition of sequencing adaptors and PCR amplification. Quality and Quantity of library fragments are assessed by Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-time PCR system.
Libraries were prepared by BGI.US® with Standard Illumina Protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
M10_3A
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| Data processing |
Raw reads produced by Illumina HS2000 are subjected to quality control (QC) to remove reads with adaptors, with more than 10% unknowns, and low quality reads. Resulting clean reads are stored in FASTQ format.
Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. An average mapping ratio of 77.71% to the reference gene and 91.47% to the genome were generated from Genome Reference Consortium Build 38 (GRCm38)
Reads are quantified using RSEM and normalized to FPKM values to determine transcript expression.
Differentially expressed genes (DEGs) were screened for using NOISeq method with parameter of abs(log2) ≥1 and probability ≥0.8.
Data was further annotated for functional classification using GO and pathway enrichment using KEGG.
Supplementary_files_format_and_content: FPKM values for each sample
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| Submission date |
Oct 09, 2018 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Peter Y Lwigale |
| E-mail(s) |
lwigale@rice.edu
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| Phone |
7133486785
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| Organization name |
Rice University
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| Department |
BioSciences
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| Street address |
6100 Main street
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE121044 |
RNA seq analysis of the mouse pNC and Cornea transcriptome |
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| Relations |
| BioSample |
SAMN10225141 |
| SRA |
SRX4821673 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3425010_M10_3A.gene.FPKM.txt.gz |
253.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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