|
| Status |
Public on Dec 31, 2017 |
| Title |
mouse upf1 depletion replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
myoblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: C2C12
|
| Treatment protocol |
Where specified, cells were transiently transfected with siRNA using Lipofectamine RNAiMAX (Invitrogen) and/or plasmids using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions.
|
| Growth protocol |
Adult human skeletal-muscle (hSkMc) myoblasts (Cell Applications) were propagated in SkMc cell-growth medium (PromoCell), mouse skeletal-muscle C2C12 myoblasts were propagated in DMEM (GIBCO-BRL) containing 15% fetal bovine serum (FBS), and HeLa cells (ATCC) were propagated in DMEM (GIBCO-BRL) containing 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from total cell-lysates using TRIzol (Invitrogen)
All samples polyA selected and libraries prepared according to Jacobs et al. Nature 516:242-245, except polyA selected rather than rRNA depleted RNA was used: StrandSpecific, Rd1 is antisense to coding strand (Rd2 is sense)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNAseq 1a: the 100x100bp pairedEnd reads for 6 of the samples were trimmed at the 3' ends to 95x58
RNAseq 1b: the 100x58bp pairedEnd reads for the remaining samples were trimmed at the 3' ends to 95x58
RNAseq 2: reads mapping (by bowtie2) to repeatMasker elements in mouse (mouse samples) or human (human samples) were discarded.
RNAseq 3: reads were mapped by tophat2 to mm9 (mouse samples) or hg19 (human samples) assisted by gtf files of UCSC Known Genes for the appropriate assembly.
RNAseq 4: The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
RNAseq 5: The coverage summed over all exonic positions of a gene was divided by 153 (95+58) to determine the read per gene for a sample. This was done for all mm9/hg19 UCSC KnownGenes.
RNAseq 6: For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: Excel Workbook with DESEQ output, refined through multiple tables to identify genes with significantly increased expression level upon depletion of Staufen or Upf1 in mouse and human myoblasts
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Manuel Ares |
| E-mail(s) |
ARES@UCSC.EDU
|
| Phone |
831 459-4628
|
| Organization name |
UC Santa Cruz
|
| Department |
MCDB
|
| Lab |
Ares
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE89588 |
Convergent exaptation of Alu and B/ID SINEs for Staufen-mediated mRNA decay |
|
| Relations |
| BioSample |
SAMN05990772 |
| SRA |
SRX2332358 |
