GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM359183

Query DataSets for GSM359183

Status

Public on Jan 26, 2009

Title

hepg2_cip_tap_pasr

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_cip_tap_pasr
variable: CIP treatment prior to TAP

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)

[email protected]

Organization name

Cold Spring Harbor Labs

Lab

Hannon

Street address

1 Bungtown Rd

City

Cold Spring Harbor

State/province

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

SRX002622

BioSample

SAMN02195551

Data table header descriptions
SEQUENCE
COUNT	COUNT

Data table
SEQUENCE	COUNT
AAAAAAAAACAAAAAA	0
AAAAAAAAACAAAAAAAA	0
AAAAAAAAACAAAAAAAAACAAAAAACA	0
AAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAA	0
AAAAAAAAACAAAAAAAAAGAAAAAA	0
AAAAAAAAACAAAAAAAACA	0
AAAAAAAAACAAAAAAAACAAAAAGA	1
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 Selector

Processed data included within Sample table

Processed data are available on Series record

Raw data are available in SRA