|
| Status |
Public on Jun 13, 2016 |
| Title |
Zeb2 cKO_pooled sciatic nerves 1 |
| Sample type |
SRA |
| |
|
| Source name |
Zeb2 cKO_pooled sciatic nerves
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed
age: postnatal day 7
genotype/variation: Zeb2 cKO
tissue: sciatic nerves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sciatic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
processed data files:
P7Zeb2cKO1~mouse_cufflinks.txt, gene_exp_control2vsZeb2cKO2diff.xlsx
|
| 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); Differential gene expression analysis Cuffdiff output file
|
| |
|
| Submission date |
Oct 27, 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 (1) |
| GSE74381 |
Gene expression profiling of sciatic nerves from Zeb2cKO and control mice |
|
| Relations |
| BioSample |
SAMN04217050 |
| SRA |
SRX1386838 |
