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| Status |
Public on Feb 19, 2020 |
| Title |
SmoM2 rep 1 |
| Sample type |
SRA |
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| Source name |
P0Cor1smo
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| Organism |
Mus musculus |
| Characteristics |
strain: a mixed genetic background of C57BL/6J, 129S6 and CD1
tissue: Cortex
developmental stage: Postnatal day 0
genotype: hGFAP-Cre, SmoM2f mice brain
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| Treatment protocol |
Cortex from P0 WT mice, ShhN IUE mice and hGFAP-Cre,SmoM2f/+ 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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| 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 Hisat2（version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized 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
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
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| Submission date |
Oct 15, 2019 |
| Last update date |
Feb 19, 2020 |
| 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) |
| GSE138878 |
Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [bulk RNA-seq] |
| GSE140817 |
Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog |
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| Relations |
| BioSample |
SAMN13031893 |
| SRA |
SRX6993231 |
| 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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