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| Status |
Public on Jan 24, 2019 |
| Title |
Wild type cortex rep1 |
| Sample type |
SRA |
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| Source name |
E16.5 cortex
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| Organism |
Mus musculus |
| Characteristics |
strain/background: mixed genetic background (C57BL/6J, 129S6, CD1)
genotype/variation: wild type
tissue: brain cortex
developmental stage: Embryonic day 16.5
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| Treatment protocol |
Cortex from E16.5 WT mice and Pax6 sey/sey mutant mice were dissected in ice-cold HBSS. These tissues were flash frozen in the nitrogen and then stored into -80 oC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
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 HiSeq 2500 |
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| Description |
Wild type littermate
processed data file: Pax6_Mutants_E16_Neocortex.txt
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| Data processing |
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:GRCm38.p4) using TopHat (version:2.0.9).
Cufflinks (version:2.2.1) was used to count the read numbers mapped to each gene, and standardized the counts using TMM (Trimmed mean of M values).
edgeR was used to find the differential expression genes.
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pax6_Mutants_E16_Neocortex.txt: Tab-delimited text file includes FPKM values for each sample.
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| Submission date |
Oct 14, 2018 |
| Last update date |
Jan 24, 2019 |
| Contact name |
Guoping Liu |
| E-mail(s) |
gpliu@fudan.edu.cn
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| Phone |
18521006300
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| Organization name |
Fudan University
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| Street address |
138 Yi Xue Yuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE121213 |
Transcription Factors Dlx1/2 Are Required for Making All Interneurons in the Olfactory Bulb [Pax6] |
| GSE121215 |
Dlx1/2 Are Central and Essential Components in the Transcriptional Code for Generating Olfactory Bulb Interneurons |
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| Relations |
| BioSample |
SAMN10238852 |
| SRA |
SRX4882755 |
| 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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