|
| Status |
Public on Sep 30, 2017 |
| Title |
Rep1_7Days_AplusN |
| Sample type |
SRA |
| |
|
| Source name |
Dissected P0 cortical astrocytes in culture for 2 weeks
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Astrocye
treatment: P0-dissected hippocampal neurons
days grown: 7
|
| Treatment protocol |
Cells were incubated in TrypLE for 10mins and centrifuged to collect cells, then resuspended in PBS and subjected to FACS sorting by TdTomato fluorescence.
|
| Growth protocol |
Astrocytes were dissected and grown in culture in DMEM with 10% FBS and 2mM glutamate with pen/strep and expanded at 80% confluency with TrypLE. When confluent, astrocytes were treated by plating 1x10^6 dissected hippocampal neurons from TdTomato+ P0 mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen) followed by Ribogone treatment for mammalian cells (Clontech)
cDNA synthesis and indexed Illumina libraries were made using the SMARTer Universal Low Input RNA kit for Sequencing and the SMARTer Low Input Library Prep Kit. Six libraries were mixed at equal concentration and sequenced by an Illumina HiSeq 2000 sequencer at the OSU Center for Genome Research and Biocomputing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
4-30-14-7D-AplusN
|
| Data processing |
Sequenced reads were trimmed of first 11 nucleotides which were of low read quality, then mapped to the mouse mm9 genome using Subread (default settings)
Raw gene level counts were calculated using FeatureCounts (default settings)
Genome_build: mm9
Supplementary_files_format_and_content: raw read counts for each gene in comma-separated values (.csv) format
|
| |
|
| Submission date |
Jun 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Christopher McGann |
| E-mail(s) |
mcgann@ohsu.edu
|
| Phone |
503-720-6748
|
| Organization name |
Oregon Health and Science University
|
| Department |
Vollum Institute
|
| Lab |
Mandel
|
| Street address |
3181 SW Sam Jackson Park Road
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE69731 |
Determination of astrocyte transcripts regulated by neuronal contact |
|
| Relations |
| BioSample |
SAMN03768364 |
| SRA |
SRX1054902 |
