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| Status |
Public on Jan 26, 2016 |
| Title |
sample 7 - microglia - lps |
| Sample type |
SRA |
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| Source name |
RNA from sorted brain cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell type: microglia
treatment: lps
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.
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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 NCBIM37 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 include Entrez Gene IDs, adjusted RPKM and counts.
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| Submission date |
Nov 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brad A Friedman |
| E-mail(s) |
friedmab@gene.com
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| Organization name |
Genentech, Inc.
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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 |
CA |
| ZIP/Postal code |
94133 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
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| Relations |
| BioSample |
SAMN04283962 |
| SRA |
SRX1441591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1947169_sample7.txt.gz |
237.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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