|
Status |
Public on Aug 01, 2015 |
Title |
RPL_human_noligase |
Sample type |
SRA |
|
|
Source name |
GM12878 lymphoblastoid cell line
|
Organism |
Homo sapiens |
Characteristics |
cell type: B-lymphocyte
|
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 |
GPL18573 |
Series (1) |
GSE69472 |
RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ |
|
Relations |
BioSample |
SAMN03755639 |
SRA |
SRX1046451 |