|
| Status |
Public on Aug 01, 2015 |
| Title |
RPL_human_yeast_mix_ligase_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878 lymphoblastoid cell line and S. cerevisiae strain FY
|
| Organisms |
Saccharomyces cerevisiae; Homo sapiens |
| Characteristics |
cell type: mixture of human B-lymphocyte and yeast (FY) cells
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Treatment protocol |
Cells were treated in situ using the RPL protocol as described in the associated manuscript
|
| Growth protocol |
GM12878 were grown at 37 in RPMI-1640 containing 15% FBS, 1X Anti-Anti, and 1X Plasmocin; FY were struck out on YPD plates and grown at 30
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZol and Zymo DirectZOL columns
Illumina TruSeq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter trimming and read fusion of mate-pairs by SeqPrep
Alignment via STAR/2.4.0 (following parameters:
Processing of STAR intron calls using custom bash/python scripts provided with manuscript
Genome_build: hg19 / SacCer3
Supplementary_files_format_and_content: "Pairs" files that document coordinates of ligation junctions between/within molecular species
|
| |
|
| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Vijay Ramani |
| Organization name |
UCSF
|
| Department |
Biochemistry & Biophysics
|
| Lab |
Ramani Lab
|
| Street address |
600 16th St, GH-S312B
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL20276 |
| Series (1) |
| GSE69472 |
RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ |
|
| Relations |
| BioSample |
SAMN03755643 |
| SRA |
SRX1046455 |
