NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1297496 Query DataSets for GSM1297496
Status Public on Dec 25, 2013
Title k562vitro
Sample type SRA
 
Source name Human bone marrow, chronic myelogenous leukemia
Organism Homo sapiens
Characteristics cell line: K562
cell type: Human erythromyeloblastoid leukemia cells
Treatment protocol 300ul or 400 ul of DMS was added to 15mls of cells
Growth protocol cells were grown to 1million/ml
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Triazol
RNA was randomply fragmented using Ambion fragmentation reagents. Fragments of 60-70mers were ligated to linker-1(IDTdna). Premature reverse transciptase producs were isolated by size selection. The cDNA was circularized with CircLigase(epicentre), and subjected to PCR for 8-10 cycles with primers for standard illumina sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing stripped files were aligned to transcript model representing the longest splicing isoform, downloaded from RefSeq
only uniquely aligned reads with less than two mismatches were taken.
Total counts per position per transcript were written to .txt files
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are .txt files and represents alignments to the transcriptome downloaded from RefSeq. For genes with multiple splicing isoforms, the longest isoform was used. Reads were filtered for 2 or less mismatches and unique alignments only. The txt file has three colums, 1= ref seq ID, 2=position , 3= number of aligned reads that passed filters
 
Submission date Dec 24, 2013
Last update date May 15, 2019
Contact name Silvi Rouskin
E-mail(s) srouskin@wi.mit.edu
Organization name Whitehead Institute
Street address 455 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02141
Country USA
 
Platform ID GPL11154
Series (1)
GSE45803 Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
Relations
BioSample SAMN02485666
SRA SRX398504

Supplementary file Size Download File type/resource
GSM1297496_K562vitro.txt.gz 55.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap