|
| Status |
Public on Sep 07, 2013 |
| Title |
SPGCBKO_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
spleen_GCB_9V/null
|
| Organism |
Mus musculus |
| Characteristics |
age: 28 wks at the time of RNA isolation
background strain: C57BL/129Sv/FVB
genotype: 9V/null
treatment: GCB (velaglucerase)
tissue: spleen
|
| Treatment protocol |
9V/null mice were injected weeklyvia tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice weere injected with same volume of saline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
9V/null mice were sacrificed one wk after the last injection along with WT mice, lung, liver and spleen were collected for RNA analysis.
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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
run0110_lane6_index10=T324_T471_T468SP~mouse_align
vela treated Spleen of 9V/null
|
| Data processing |
mRNA-Seq reads were aligned to the mm9 version of the mouse genome reference using the TopHat/Cufflinks pipeline. First, sequences were aligned to the genome with TopHat , which efficiently aligned reads spanning known or novel splice junctions. Each sample was then independently processed with Cufflinks in order to generate an initial transcriptome. Finally, the Cuffmerge tool was used to merge the known and any novel isoforms into a single BAM file, and simultaneously extended partial transcripts.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq and edgeR were used to evaluate the DEGs from the mRNA-Seq data. DESeq via R script was performed on the filtered reads by Avadis NGS software using three functions (estimate size factors, estimate dispersions and negative binomial test).
For DESeq normalization, the sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values for each Sample
|
| |
|
| Submission date |
Feb 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
nupur dasgupta |
| Phone |
513-803-1768
|
| Organization name |
Cincinnati Children's Hopital Medical Center
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE44674 |
Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase [RNA-Seq] |
| GSE44675 |
Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase |
|
| Relations |
| Reanalysis of |
GSM1088300 |
| SRA |
SRX245789 |
| BioSample |
SAMN01925553 |
