|
| Status |
Public on Mar 05, 2015 |
| Title |
Patski_FirreKD_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Patski cells
|
| Organism |
Mus musculus x Mus spretus |
| Characteristics |
strain: BL6/spretus
genotype/variation: stable Firre knockdown
cell type: Fibroblasts derived from hybrid embryonic kidney
|
| Treatment protocol |
Two biological replicates from control or stable Firre knockdown (si&shRNA) Patski cells were used for RNA-seq.
|
| Growth protocol |
Standard cell culturing protocol using 10% FBS in DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from Patski cells by the Qiagen RNeasy kit with on-column DNaseI digestion.
RNA-seq indexed libraries were prepared using Illumina TruSeq RNA sample preparation kit with standard Illumina protocols. Index adators 6 and 12 were used for Patski_control rep1 and 2 resepecitvely, as well as for Patski_Firre KD rep1 and 2 resepecitvely.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6. Two individual RNA samples prepared from Patski cells with the Firre knockdown were used for indexed library preparation. Index adators 6 and 12 were used for Patski_Firre KD rep1 and 2 respectively.
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were first sorted by their index sequencing for each replicate. A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat with default parameters, except that the “min-isoform-fraction” flag was set to zero, "--no-novel-juncs" was specified to constrain the search to annotated exon:exon boundaries, and the RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks with default parameters and “min-isoform-fraction” set to zero.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read count, spretus-exon-SNP-read count.
|
| |
|
| Submission date |
Feb 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
dengx2@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Laboratory Medicine and Pathology
|
| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16617 |
| Series (2) |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
| GSE66172 |
Effects of Firre knockdown on mouse gene expression |
|
| Relations |
| BioSample |
SAMN03360958 |
| SRA |
SRX885295 |
