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Status |
Public on Jan 22, 2013 |
Title |
H2087_NKX2-1_BL4000 |
Sample type |
SRA |
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Source name |
H2087_NKX2-1_BL4000
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Organism |
Homo sapiens |
Characteristics |
cell line: NCI-H2087 antibody: NKX2-1 [Bethyl Laboratories, BL4000]
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Growth protocol |
RPMI1640 +10% FBS
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Extracted molecule |
genomic DNA |
Extraction protocol |
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
IP
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Data processing |
Bowtie alignment (H1819, H2087, H3122_2, H3122_FOXA1_ab23738) or GenePAST alignment (H3122_input and H3122_NKX2-1_BL4000) read counts normalization in 100kb window size Peak calling (MACS 1.4.0) Genome_build: hg18 Supplementary_files_format_and_content: bed
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Submission date |
Aug 08, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Hideo Watanabe |
E-mail(s) |
hideo.watanabe@mssm.edu
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Organization name |
Icahn School of Medicine at Mount Sinai
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Department |
Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
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Lab |
Hideo Watanabe
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Street address |
One Gustave L. Levy Place
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE39998 |
NKX2-1 occupancy in human lung adenocarcinoma cell lines |
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Relations |
SRA |
SRX174817 |
BioSample |
SAMN01109524 |
Supplementary file |
Size |
Download |
File type/resource |
GSM983102_H2087_BL4000_ss50_p6_peaks.bed.gz |
207.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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