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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 08, 2019 |
| Title |
cNSC-FF_Cre_Rep1 |
| Sample type |
SRA |
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| Source name |
cultured cortical NSCs
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cultured cortical neural stem cells (NSCs)
treatment: Ad:Cre
developmental stage: Derived from embryonic day 12.5
genotype/variation: Pnky(fl/fl) +Ad:Cre
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| Growth protocol |
Acutely dissected cortical NSCs cultured with media containing EGF/FGF.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by Trizol (Life Technologies), purified using Direct-zol (Zymo) kit with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (Illumina, #20020594).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Pnky(fl/fl) +Ad:Cre Rep1
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| Data processing |
For NSC culture RNA-seq, reads were psuedoaligned to Genocde GRCm38.p5 mouse transriptome with kallisto v0.43.0 using 100 bootstrap replications. DESeq2 was used to perform differential expression analysis.
Genome_build: mouse mm10, Gencode GRCm38.p5 mouse transriptome
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| Submission date |
Mar 07, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Tomasz Nowakowski |
| E-mail(s) |
[email protected]
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| Organization name |
UCSF
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| Street address |
1550 4th St
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| City |
San Francisco |
| State/province |
Ca |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE127987 |
The long noncoding RNA Pnky is a trans-acting regulator of cortical development in vivo |
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| Relations |
| BioSample |
SAMN11082138 |
| SRA |
SRX5491731 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3659651_cNSC-FF_Cre_Rep1_abundance.h5 |
60.8 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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