|
| Status |
Public on Feb 29, 2016 |
| Title |
cKO_1 |
| Sample type |
SRA |
| |
|
| Source name |
Chd7 cKO_spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed
age: Postnatal day 8
geneotype/variation: Chd7f/f; Olig1-cre
tissue: spinal cord
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking)
|
| |
|
| Submission date |
Sep 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
CBDI
|
| Lab |
Lu Lab,T6.525
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE72726 |
Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [RNA-seq] |
| GSE72727 |
Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination. |
|
| Relations |
| BioSample |
SAMN04032819 |
| SRA |
SRX1184186 |
