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| Status |
Public on Jan 22, 2013 |
| Title |
H3122_input |
| Sample type |
SRA |
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| Source name |
H3122_input
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NCI-H3122
antibody: none
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| Growth protocol |
RPMI1640 +10% FBS
|
| 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 Genome Analyzer IIx |
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| Description |
Input
|
| 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
|
| 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 |
GPL10999 |
| Series (1) |
| GSE39998 |
NKX2-1 occupancy in human lung adenocarcinoma cell lines |
|
| Relations |
| SRA |
SRX174812 |
| BioSample |
SAMN01109519 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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