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Sample GSM1138456 Query DataSets for GSM1138456
Status Public on Jun 09, 2013
Title NSC_H3K4me3
Sample type SRA
Source name Derived from mESCs
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: neural stem cellsderived from mouse embryonic stem cells
differentiation day: 0
redstar+: Negative
passages: 25-30
chip antibody: H3K4me3
chip antibody vendor: Active Motif
chip antibody cat. #: 39159
Treatment protocol NSCs were differentiated into neurons in Euromed-N supplemented with 1/2x N2, 5ng/ml FGF2 and 1/2x B27. After four days, immature neurons were replated into N2B27 and matured for seven days, before FACS purification based on RedStar fluorescence.
Growth protocol NSCs were routinely cultured in Euromed-N (Euroclone) supplemented with 1x N2, 10ng/ml FGF2 and 10ng/ml EGF (Peprotech)
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% HCHO and lysed in 1% SDS lysis buffer. Chromatin was sheared to 300bp and immunoprecipitated with antibodyies against H3K4me3, H3K27me3, total histone H3 and IgG. Total H3 was from Abcam (ab1791) and rabbit IgG from Santa Cruz (SC-2027) were used to precipitate all samples, in addition to the IPs done with H3K4me3 and H3K27me3. Only the K4/K27 were sequenced.
Libraries were prepared according to standard Illumina Solexa protocols
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Sample 1
Data processing Reads were QC checked using FastQC
Reads were aligned using Bowtie, using 'best' alignment, with a seed sequence length of 15bp and Solexa quality v1.3 quality scores.
Duplicates were removed and reads were sorted and indexed using SamTools
Peaks were called using SICER, with a window size of 200bp and a gap size of 1 for H3K4me3 and 3 for H3K27me3, a threshold of 1 and a genome fraction of 0.75
Peaks were annotated to the nearest gene using the Iranges library and BiomaRt in R
Genome_build: mm9
Supplementary_files_format_and_content: Files contain raw output from SICER peak calling, with genomic coordinates (*bed files). Second processed file contains peak annotation to nearest Ensembl gene (*csv files)
Submission date May 09, 2013
Last update date May 15, 2019
Contact name Matt Burney
Organization name King's College London
Street address 125 Coldharbour Lane
City London
ZIP/Postal code SE5 9NU
Country United Kingdom
Platform ID GPL9185
Series (2)
GSE46792 An epigenetic signature of developmental potential in neural stem cells and early neurons [ChIP-seq]
GSE46793 An epigenetic signature of developmental potential in neural stem cells and early neurons
BioSample SAMN02141699
SRA SRX276672

Supplementary file Size Download File type/resource
GSM1138456_NSC_H3K4me3_SICER_peaks.bed.gz 859.9 Kb (ftp)(http) BED
GSM1138456_nearest_peak_to_gene_NSC_H3K4me3.csv.gz 1.4 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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