|
| Status |
Public on Dec 19, 2013 |
| Title |
GM12878 native deproteinized replicate 1, S1 |
| Sample type |
SRA |
| |
|
| Source name |
rRNA depleted RNA S1 nuclease at 37°C
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: rRNA depleted
cell line: GM12878
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Treatment protocol |
RNA is isolated from the cells using 1) Trizol and poly(A)+ selected or 2)lysed with 0.1% SDS, 0.25% Na deoxycholate, phenol extracted, before structure probing at 37˚C
|
| Growth protocol |
GM12878, GM12891 and GM12892 cells were grown at 37˚C to ~0.6million cells/ml in RPMI media supplemented with 15% FBS, 2mM L-glutamine and 1% PenStep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cleavage sites are captured and cloned using Ambion RNA sequencing kit compatible with the Illumina platform (Ambion)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Single strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12878
|
| Data processing |
Raw reads were trimmed to 50bp (trimmed 51bp from the 3'end)
Trimmed reads were mapped to hg19 transcriptome using bowtie2, where the hg19 transcriptome was aggragated from UCSC RefSeq and Gencode v12 databases
The number of single and double strand reads were calculated by passing through the SAM file accordingly, and numbers were then normalized by sequencing depth
Genome_build: Hg19 Transcriptome, aggragated from UCSC RefSeq and Gencode v12 databases
Supplementary_files_format_and_content: The processed .tab file contains two tab-seprated columns, the first column is the transcript ID, and the second column is a list of semi-colon seprated numbers indicating the S1/V1 counts for each base of that transcript
Supplementary_files_format_and_content: On the Series record, a table of transcript-level normalized counts.
|
| |
|
| Submission date |
Sep 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE50676 |
Landscape and variation of RNA secondary structure across the human transcriptome |
|
| Relations |
| BioSample |
SAMN02350647 |
| SRA |
SRX346863 |
