|
| Status |
Public on Oct 22, 2014 |
| Title |
compound C1 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
SMA type I fibroblasts_compound C1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM03813
cell type: SMA type I fibroblasts
treated with: 100nM SMN-C1 for 24hrs
|
| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM03813
|
| Treatment protocol |
Fibroblast cells derived from type 1 SMA patients were treated with SMN-C3 at 500 nM for 24 hours (cell line PNN 1-46 ), or SMN-C1 at 100nM for 24 hours (cell line GM03813).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with the RNeasy Mini Kit (Qiagen)
Template DNA molecules suitable for cluster generation were prepared from 1 ug of total RNA samples using the TruSeq RNA Sample Preparation Kit v2. Libraries were quantified using the KAPA Library Quantification Kit (KK4824, Kapa Biosystems, Boston, MA). The libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the HiSeq 2500 (Illumina Inc., San Diego, CA) for both clustering and sequencing. The libraries were extended and bridge-amplified to create single sequence clusters using the TruSeq Rapid PE Cluster Kit - HS (Illumina Inc., San Diego, CA). Amplified clusters in the flow cell were then sequenced with 50-bp paired-end reads using the TruSeq Rapid SBS Kit - HS (Illumina Inc., San Diego, CA) in rapid run mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SMN-C1_100nM_Run1
|
| Data processing |
Real time image analysis and base calling were performed on the the HiSeq 2500 instrument using the HiSeq Sequencing Control Software (HCS).
CASAVA software version 1.8 was used for de-multiplexing and production of FASTQ sequence files
Sequenced reads were mapped to humanRefSeq transcripts and hg19 whole genome using bowtie2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample (first column=entrezgene id, second column=rpkm value)
|
| |
|
| Submission date |
Oct 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Friedrich Metzger |
| Organization name |
F. Hoffmann-La Roche
|
| Street address |
Grenzacherstr.
|
| City |
Basel |
| ZIP/Postal code |
CH-4070 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE62540 |
SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy |
|
| Relations |
| BioSample |
SAMN03121616 |
| SRA |
SRX736918 |
