|
| Status |
Public on Dec 21, 2013 |
| Title |
NPCRingIB_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Neural Progenitor cell (NPC)
|
| Organism |
Mus musculus |
| Characteristics |
antibody: Ring1B Ab generated in Di Croce´s lab
cell type: Neural Progenitor cell (NPC)
cell line: E14TG2a
|
| Growth protocol |
NPCs were derived by ESC (E14TG2a strain) according to this protocols (Colombo et al, Stem Cells, 2006). ESC-derived NPC were grown in N2 medium supplemented with EGF and FGF2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NPC were crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 0.125 M glycine for 5 min. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 12 min in a Bioruptor. ChIP-Seq experiments were performed as previously described (Morey et al, Cell Stem Cell. 2012, 10: 47-62)
It was performed using the NEBNext DNA Sample Prep Reagents Set 1
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against Ring1B
|
| Data processing |
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: text files containing peak coordinates
|
| |
|
| Submission date |
Dec 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Luciano Di Croce |
| E-mail(s) |
luciano.dicroce@crg.eu
|
| Phone |
+34933160132
|
| Organization name |
Centre for Genomic Regulation
|
| Street address |
Dr. Aiguader, 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE53540 |
Zrf1 is required to establish and maintain neural progenitor identity (ChIP-Seq) |
| GSE53542 |
Zrf1 is required to establish and maintain neural progenitor identity |
|
| Relations |
| BioSample |
SAMN02483580 |
| SRA |
SRX397010 |
