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| Status |
Public on Apr 26, 2017 |
| Title |
SAM24327524 ngf.dmso |
| Sample type |
SRA |
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| Source name |
RNA from primary DRG neurons grown for 4 days in vitro
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| Organism |
Mus musculus |
| Characteristics |
tissue: dorsal root ganglion neurons
sample_id: SAM24327524
treatment: ngf.dmso
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from primary DRGs (ca 400,000 cells/well) treated with NGF, anti-NGF, and 4 individual wells for ISRIB/anti-NGF and DLKi/anti-NGF using RNeasy Plus Mini Kit (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
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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 |
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
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| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| E-mail(s) |
[email protected]
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| Organization name |
Genentech
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| Department |
Bioinformatics
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| Street address |
1 DNA Way
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| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE95672 |
Response in the NGF withdrawal model |
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| Relations |
| BioSample |
SAMN06473775 |
| SRA |
SRX2611401 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2520954_sample11.tsv.gz |
314.1 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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