|
| Status |
Public on Feb 25, 2021 |
| Title |
11_Input DNA_Day0_mES_s_4_sequence |
| Sample type |
SRA |
| |
|
| Source name |
Mouse ES
|
| Organism |
Mus musculus |
| Characteristics |
strain: AINV15
cell type: Esrrb_Rescue Clone
time point: Day0
fraction: Input DNA
|
| Treatment protocol |
Esrrb_R rescue clone was grown in +Dox (1ug/ml) media_Day0; Dox withdrawal was performed for 5 days performing H3K4me3 and H3K27me3 ChIP-Seq at the respective days: Day0 ( Esrrb expressed) and days 1,3 and 5 ( Esrrb non expressed)
|
| Growth protocol |
Esrrb_R rescue clone was grown under under typical ES conditions; D-MEMâHigh Glucose (Dulbeccoâs modified Eagleâs medium-1X-High Glucose) (Gibco®, Invitrogen), 15% FBS (Fetal bovine serum) (Hyclone, Thermo Scientific), 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, Penicillin/Streptomycin (Gibco, Invitrogen) and 103 U ml-1 LIF (Chemicon, Millipore) on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes or Esrrb (TF)-complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Input DNA
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the Mouse July, 2007 (NCBI37/mm9) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Aug 24, 2011 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Ana Sevilla |
| E-mail(s) |
anasevilla@ub.edu
|
| Phone |
+34 675348398
|
| Organization name |
Universidad de Barcelona
|
| Department |
Departamento de Biologia Celular, Fisiologia e Inmunologia
|
| Lab |
4 Floor.
|
| Street address |
Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE31640 |
An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feedback Interactions [ChIP-seq] |
| GSE31842 |
An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. |
|
| Relations |
| SRA |
SRX093176 |
| BioSample |
SAMN00714104 |
