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| Status |
Public on Jan 01, 2019 |
| Title |
10: NAC NSC |
| Sample type |
SRA |
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| Source name |
Neural progenitor cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Neural progenitor cells
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| Treatment protocol |
48 hrs with PQ or NAC
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| Growth protocol |
N2 media with EGF and bFGF
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL
1) Total RNA treatment a) RNase H Probe (rRNA depletion): Hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. b) Oligo dT Selection (mRNA enrichment): Use oligo dT beads to select mRNA with poly A tail. 2) RNA fragment and reverse transcription Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair and adaptor ligation End repair the dscDNA to blunt end and phosphate at 5’ end, 3’ end forms an “A” cohesive end. And then ligate to the bubble adapter with protruding T of 3’ end. 4) PCR amplification 5) Single strand separation and cyclization Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6)DNA nanoball making7) Sequencing on BGISEQ-500 platform
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Basecalls performed using BaseCall version 1.1.2
Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read) are discarded and then mapped to mm10 whole genome using HISAT2 v2.0.4 with parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000, mapped to gene reference using Bowtie2 v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
Screening DEGs using EBSeq,we defined a gene as a DEG (differentially expressed gene) when foldchange ≥2 and PPEE ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include FPKM values for each Sample.
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| Submission date |
Jul 18, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Jihye Paik |
| E-mail(s) |
Jep2025@med.cornell.edu
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| Organization name |
Weill Cornell Medical College
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| Department |
Pathology
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| Street address |
1300 York Ave.
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| City |
New york |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE117282 |
Gene expression changes in neural stem cells under different redox potential |
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| Relations |
| BioSample |
SAMN09685466 |
| SRA |
SRX4403209 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3290405_10.gene.FPKM.txt.gz |
228.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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