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Sample GSM359207 Query DataSets for GSM359207
Status Public on Jan 26, 2009
Title HepG2_tot_up
Sample type SRA
 
Source name HepG2
Organism Homo sapiens
Characteristics liver carcinoma cell line
Treatment protocol none
Growth protocol HeLa cells were grown in suspension culture, HepG2 cells on plates in DMEM containing 10% FBS, 1% Penn/Strep and harvested at subconfluent concentration.
Extracted molecule total RNA
Extraction protocol RNA was extraceted with phenol, other column purified, TAP treated, adapters were addad by C-tailing, 5' ligation and RT using primer with a polyG stretch. PCR amplificaiton was used for enrichment and followed by gel purification of expected size range.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Description HepG2_tot_up
variable: whole cell RNA size range 50-200 nt
Data processing Reads were aligned to the reference genome (hg18 assembly version), and the fragment count at any given position (25-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).
 
Submission date Jan 09, 2009
Last update date May 15, 2019
Contact name Katalin Fejes Toth
E-mail(s) fejes@cshl.edu
Organization name Cold Spring Harbor Labs
Lab Hannon
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL9115
Series (1)
GSE14362 Genome-wide annotation of small RNAs expressed in HeLa and HepG2 cells
Relations
SRA SRX002648
BioSample SAMN02195569

Data table header descriptions
SEQUENCE
COUNT COUNT

Data table
SEQUENCE COUNT
AAAAAAAAACAAAAAA 0
AAAAAAAAACAAAAAAAA 0
AAAAAAAAACAAAAAAAAACAAAAAACA 0
AAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAA 0
AAAAAAAAACAAAAAAAAAGAAAAAA 0
AAAAAAAAACAAAAAAAACA 0
AAAAAAAAACAAAAAAAACAAAAAGA 0
AAAAAAAAACAAAAAAAACAAAACCA 0
AAAAAAAAACAAAAAAAACAAGAAAA 0
AAAAAAAAACAAAAAAAACACAAGCA 0
AAAAAAAAACAAAAAAAACCAAAAAAAA 0
AAAAAAAAACAAAAAAAAGAAAAAAA 0
AAAAAAAAACAAAAAAACAAAAAAAA 0
AAAAAAAAACAAAAAAACAAAAAAAAACAAAAAAAA 0
AAAAAAAAACAAAAAAACAAAAACAA 0
AAAAAAAAACAAAAAAACAAAACAAC 0
AAAAAAAAACAAAAAAACAAAACAAT 0
AAAAAAAAACAAAAAAACACAAACAA 0
AAAAAAAAACAAAAAAACACAACAAC 0
AAAAAAAAACAAAAAAATAAAAAAAA 0

Total number of rows: 282827

Table truncated, full table size 7843 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Processed data included within Sample table
Processed data are available on Series record
Raw data are available in SRA

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