|
| Status |
Public on Feb 11, 2013 |
| Title |
MTN_MTG_3D_1 [sandwich] |
| Sample type |
SRA |
| |
|
| Source name |
Sandwich
|
| Organism |
Mus musculus |
| Characteristics |
timepoint: 3day
rnaextractedfrom: Neuron
sandwich type: MTN_MTG
genotype/variation: SOD1_G93A mutant neurons; SOD1_G93A mutant glia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a combination of Trizol (Invitrogen) and RNeasy columns (Qiagen).
Libraries were prepared using either standard protocols from Illumina or the Nextera transposase-mediated method (Gertz J, et al. 2012) and sequenced using the Illumina platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
processed data file: sandwich.txt
|
| Data processing |
bowtie aligned with following parameters: -X 20000 -k 2 -m 2 -q -p 8' & for single ends (Sandwich) are '-k 2 -m 200 --best --strata -q -p 8
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM abundance measurements (RPKM's were normalized as reads per kilobase per million using a method defined by Mortazavi et al. Nat Methods, 5(7):621-628)) values for each Sample
|
| |
|
| Submission date |
Jan 29, 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 |
GPL9250 |
| Series (1) |
| GSE43879 |
An intricate interplay between astrocytes and motor neurons in ALS |
|
| Relations |
| SRA |
SRX220619 |
| BioSample |
SAMN01907264 |
