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| Status |
Public on Sep 25, 2017 |
| Title |
18_Neonates_micro |
| Sample type |
SRA |
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| Source name |
Pure microglia
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
microglia population: Neonatal mouse CD11C negative
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ex vivo microglia isolation using CD11C and CD11B and CD45
Illumina TruSeq RNA-preparation kit standard protocol
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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 |
Star Aligner 2.3.11 allowing for 2 mismatches to map reads to genome
SAM tools 0.1.19 to sort aligned reads
HT-seq 0.5.4 for quantification, mode=union, stranded=no, Ensembl version 71
EdgeR 3.12.0 for data exploration and differential expression
WGCNA 1.49 for co-expression network analysis and detection of modules
Genome_build: GRCm38
Supplementary_files_format_and_content: HT-seq count .txt files
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| Submission date |
Mar 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Inge Holtman |
| E-mail(s) |
irholtman@gmail.com
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| Organization name |
UCSD
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| Department |
CMM
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| Lab |
Glass
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| Street address |
9500 Gilman Drive
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| City |
La Jolla, |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE78809 |
Novel neuroprotective and neurogenic phenotype of microglia |
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| Relations |
| BioSample |
SAMN04526781 |
| SRA |
SRX1608963 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2078143_18_Neonates_micro.htseq.txt.gz |
143.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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