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Sample GSM1295698 Query DataSets for GSM1295698
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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