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Status
Public on Jan 17, 2009
Title
WholeCerebellum_1month_Ptc+-_Ink4c--_rep2
Sample type
SRA
Source name
cerebellum
Organism
Mus musculus
Characteristics
Ptch1+/-, Ink4c (p18) -/-, age 1 month genotype: Ptch1+/-, Ink4c (p18) -/-; Tissue: cerebellum; Age: 1 month
Growth protocol
Standard mouse facility
Extracted molecule
total RNA
Extraction protocol
Total RNA extraction by Trizol
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
Illumina Genome Analyzer
Description
Barcode used in pool: 5MLJ Raw data file: CSHL_FC12772_5_Medullo_4.fastq
Data processing
The reads were deconvoluted by barcode, collapsed to unique sequences, aligned to the genome and annotated. Read-counts for miRNA sequences were cubic-spline normalized then log-transformed. The R-project software (http://www.R-project.org ), including Bioconductor were used for data analysis.
Submission date
Jan 16, 2009
Last update date
Mar 04, 2023
Contact name
Fedor Karginov
E-mail(s)
karginov@ucr.edu
Organization name
UC Riverside
Department
MCSB
Street address
900 University Ave
City
Riverside
State/province
California
ZIP/Postal code
92521
Country
USA
Platform ID
GPL9185
Series (1)
GSE14470
MicroRNA profiling in mouse medulloblastomas and normal cerebellar tissues
Relations
BioSample
SAMN02195492
Data table header descriptions
SEQUENCE
COUNT
Read-counts for miRNA sequences were cubic-spline normalized then log-transformed
Data table
SEQUENCE
COUNT
mmu-let-7a (main)
2.885973143
mmu-let-7a (other)
0.040908942
mmu-let-7b (main)
3.188780186
mmu-let-7b (other)
0.040908942
mmu-let-7c (main)
3.836174818
mmu-let-7c (other)
0.040908942
mmu-let-7c$mmu-let-7a (main)
0.040908942
mmu-let-7c$mmu-let-7a (other)
0.040908942
mmu-let-7c$mmu-let-7a$mmu-let-7c$mmu-let-7a (main)
1.283291272
mmu-let-7d (main)
2.742158476
mmu-let-7d (other)
0.723981549
mmu-let-7e (main)
2.419863209
mmu-let-7e (other)
0.040908942
mmu-let-7f (main)
3.168113496
mmu-let-7f (other)
0.040908942
mmu-let-7g (main)
3.005068336
mmu-let-7g (other)
0.283390889
mmu-let-7i (main)
2.709778741
mmu-let-7i (other)
0.040908942
mmu-mir-1 (main)
0.190057735
Total number of rows: 528 Table truncated, full table size 16 Kbytes .Supplementary data files not provided
Processed data included within Sample table