|
| Status |
Public on Feb 20, 2016 |
| Title |
B39-d1 rep#2 DNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
hFOB
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hFOB
cell type: Fetal bone immortalized using ts SV40 pUCSVtsA58 vector
treatment: untreated, grow at 39oC in BM
concentration: Basal Media
time: 24h
replicate: replicate 2
growth proptocol: BM, basal madia: DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin
|
| Treatment protocol |
Cells were plated for experiments at the same time and shifted to respective temperature after 24 hours. Cells were harvested after 1 or 2 days.
|
| Growth protocol |
see additional columns of the SAMPLES section
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed, resuspended in Trypsin and nuclei prepared in hypotonic buffer as per protocol
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hs_RC_B39_24_RC_GH682xGH1031x2_FDR0.csv
|
| Data processing |
RTA 1.12.42 was used for Basecalling and Casava 1.8.2 ws used for demultiplexing.
Alignment was performed by Bowtie2 software with the hg19 reference genome.
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited (CSV) text files include genomic locations (Chromosome, start, end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.
|
| |
|
| Submission date |
Nov 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
|
| Department |
CCR
|
| Lab |
LRBGE
|
| Street address |
41 Library Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE75231 |
Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (Dnase-Seq) |
| GSE75232 |
Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation |
|
| Relations |
| BioSample |
SAMN04281814 |
| SRA |
SRX1440141 |
