|
| Status |
Public on Jul 20, 2016 |
| Title |
Human ES S6 DALT Dnase 131220 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
strain: HuES6
tissue: embryonic stem cell
|
| Growth protocol |
Mouse embryonic stem cell culture was performed according to previously published protocols(Sherwood et al., 2014 PMID 24441470). Undifferentiated 129P2/OlaHsd mouse ES cells were maintained on gelatin-coated plates feeder-free in mES media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (Life Technologies), Glutamax (Life Technologies), 0.55mM 2-mercaptoethanol (Sigma), 1X ESGRO LIF (Millipore), 5 nM GSK-3 inhibitor XV and 50 nM UO126.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed according to the “Mammalian ChIP-on-chip” protocol (Agilent) using a polyclonal antibody against Nrf1 antibody (ab34682, Abcam) and Protein G Dynabeads (Life Technologies). 10-100 million cells were used for each experiment. qPCR using positive and negative control primers was performed to ensure ChIP enrichment. Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter. DNase-seq was performed as described previously (Sherwood et al., 2014 PMID 24441470). 10-100 million cells were digested with 60-100 units of DNase I (Promega) per 107 nuclei. 50-125 bp hypersensitive DNA was collected using E-Gel SizeSelect Agarose 2% gels (Life Technologies). Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Dnase-seq on human ES cells
|
| Data processing |
Alignments done via bcbio-nextgen with BWA with default settings
Peak calling for NRF performed via GEM with default settings
SLOT sequence merging and reconstruction via FLASH -m 50 -M 150 -x 0.3
Dnase-seq data was used to train the synergistic sequence model, and parameters were dumped as a binary file that is then zipped into an archive.
Genome_build: mm10/hg19
Supplementary_files_format_and_content: NRF binding sites in the .csv file, .zip file contains fitted model parameters and input data. Input directory contains genome and read files in compressed binary format necessary to reproduce the run. Output contains model parameters in binary format with VARIABLENAME_loopid.bin where loopid determines the regularization value (stored in ETA_loopid.bin). All bin files are binary vectors of floats that can be parsed 8-bytes at a time. Summary contains parsed outputs including summary plots (pdf format) and binary prediction vectors over the genome used in the paper.
|
| |
|
| Submission date |
Apr 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
David Gifford |
| Organization name |
MIT
|
| Street address |
32 Vassar St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE80105 |
Synergistic model of chromatin predicts Dnase-I accessibility |
|
| Relations |
| BioSample |
SAMN04632459 |
| SRA |
SRX1690197 |
