|
| Status |
Public on Jul 05, 2011 |
| Title |
DNase_G1E_seq |
| Sample type |
SRA |
| |
|
| Source name |
G1E cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129
genotype/variation: Gata1-null
developmental stage/cell type: Erythroid committed, immature progenitor murine cell line
|
| Treatment protocol |
G1E-ER4 cells were induced in the presence of 10^(-8) mol/L (beta)-estradiol for 24 hours.
|
| Growth protocol |
G1E and G1E-ER4 cells were grown in IMDM media with 15% fetal calf serum 2U/ml erythropoietin (Amgenâs EpoGen) and 50ng/ml stem cell factor. Erythroid cells were obtained by enriching fresh E14.5 fetal liver preps for Ter119-positive cells using an anti-Ter119 antibody coupled to magnetic beads (StemCell EasySep Kit #18554).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, ChIP DNA or input DNA was amplified by Illumina ChIP-Seq library preparation kit. To prepare the sequencing libraries, the ChIP DNA fragments were repaired to generate blunt ends, with a single A nucleotide adding to each end. Double-stranded Illumina adaptors were ligated to both ends of the fragments. Ligation products were amplified by 18 cycles of PCR, and the PCR products between 200 and 400 bp were gel purified. The quality of the library was evaluated by qPCR and bio-analyzer to make sure it meets the requirements by Illumina.
For DNase-seq, nuclei isolated from G1E and G1E-ER4+E2 cells were lightly digested with DNaseI to expose regions hypersensitive to the enzyme. Digested ends of the DNA were ligated to a biotinylated and phosphorylated linker and enriched on streptavidin-coated DynaI beads. This was followed by MmeI restriction enzyme digestion, which cuts 20 bases downstream of the recognition site contained within the biotinylated linker. A second linker was ligated to the MmeI cut sites and ligation-mediated polymerase chain reaction performed prior to being sequenced.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
DNase-seq for DNase hypersensitive sites
|
| Data processing |
Alignment: Sequencing reads were mapped to the mouse genome (mm8 assembly) using the program Efficient Local Alignment of Nucleotide Data (ELAND) or Bowtie.
|
| |
|
| Submission date |
Jun 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ross Hardison |
| E-mail(s) |
[email protected]
|
| Organization name |
Pennsylvania State University
|
| Street address |
303 Wartik Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE30142 |
Genome-wide maps of epigenetic features in G1E model and in mouse primary erythroblasts. |
|
| Relations |
| SRA |
SRX079859 |
| BioSample |
SAMN00630459 |
