|
| Status |
Public on Jul 15, 2013 |
| Title |
NonTG_Day130_B |
| Sample type |
SRA |
| |
|
| Source name |
Spinal cord purified microglia
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: B6/SJL
genotype: wild type
age/disease timepoint: Day 130
sample type: End-stage control
disease state: End-stage control amyotrophic lateral sclerosis
cell type: microglia
|
| Treatment protocol |
B6SJL SOD1G93A, SOD1WT, Non-transgenic mice were collected at day 65 (pre-symptomatic), day 100 (symptomatic), and end-stage (or day 130). B6SOD1G93A at end-stage, B6 non-transgenic or B6 mice injected intraperitoneally with LPS (48 hours prior) were used for spinal cord dissection and microglia collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were transcardially perfused with PBS to remove blood, spinal cords dissected, run over a 37%/70% percoll gradient to isolate immune cells. CD11b magnetic beads were used to purify microglia from these leukocytes, RNA was harvested using Trizol reagent and RNeasy columns. Bioanalyzer chips were used to assay quality of RNA prior to amplifcation using the Ovation RNAseq system. Paired-end libraries were generated by standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GCCAAT
Paired end RNA-Seq on the Illumina platform
|
| Data processing |
Reads were aligned to the mouse genome (mm9) using Bowtie.
Gene levels were calculated by counting genomic and splice alignments for each RefSeq transcript (as defined in the known Isoforms table, http://genome.ucsc.edu) using TopHat and Cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) was used as a normalized expression value for each sample, and are displayed for each gene across all samples in the processed data file
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including all sample RPKM values for each RefSeq transcript id, with gene aliases
|
| |
|
| Submission date |
Jan 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sean O'Keeffe |
| E-mail(s) |
so2346@columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
701 West 168th Street
|
| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE43366 |
Defining the microglia transcriptome during disease progression in ALS transgenic mice |
|
| Relations |
| SRA |
SRX215721 |
| BioSample |
SAMN01884199 |
