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Sample GSM1701710 Query DataSets for GSM1701710
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
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
BioSample SAMN03755643
SRA SRX1046455

Supplementary file Size Download File type/resource
GSM1701710_RPL_human_yeast_ligase_rep2.pairs.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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