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Sample GSM1346236

Query DataSets for GSM1346236

Status

Public on Sep 03, 2014

Title

HeLa_H3K36me3_Input

Sample type

SRA

Source name

HeLa cells

Organism

Homo sapiens

Characteristics

cell line: HeLa
cell type: HeLa
chip antibody: None

Treatment protocol

FLAG-H3.3 stably expressing HeLa cells was established using a retroviral expressing system.

Growth protocol

Cells were maintained in Dulbecco’s modified Eagle’s medium (Hyclone) containing 10% FBS (Hyclone).

Extracted molecule

genomic DNA

Extraction protocol

Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina Genome Analyzer IIx

Data processing

base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs2 with the following setting:--qvalue=0.05 --broad -g hs
Genome_build: hg19
Supplementary_files_format_and_content: peak list

Submission date

Mar 11, 2014

Last update date

May 15, 2019

Contact name

Yang Shi

E-mail(s)

yshi@hms.harvard.edu

Organization name

Fudan university

Street address

NO. 138, Yi-Xue-Yuan Road