|
| Status |
Public on Oct 14, 2011 |
| Title |
Duke_DnaseSeq_MCF-7_Hypoxia_LacAcid |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: DnaseSeq
datatype description: DNaseI HS Sequencing
cell description: mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
treatment description: 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford)
labversion: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.05
replicate: 1,2
cell description: mammary gland, adenocarcinoma. (PMID: 4357757)
cell karyotype: cancer
cell lineage: ectoderm
cell sex: F
treatment: Hypoxia_LacAcid
treatment description: Hypoxia and Lactic acidosis: 1% p02 and 10 mM Lactate, pH of 6.7 for 24 hours (Crawford)
labversion: align_on_cluster_bwa.pl v 1
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
Hypoxia_LacAcid
|
| Growth protocol |
MCF-7_Crawford_protocol.pdf
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase
|
| |
|
| Submission date |
Oct 13, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE32970 |
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) |
|
| Relations |
| Reanalyzed by |
GSE53962 |
| Reanalyzed by |
GSE54296 |
| Reanalyzed by |
GSE59016 |
| SRA |
SRX100917 |
| BioSample |
SAMN00739128 |
| Named Annotation |
GSM816670_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacBaseOverlapSignal.bigWig |
| Named Annotation |
GSM816670_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacSig.bigWig |
