|
| Status |
Public on Jun 09, 2013 |
| Title |
Neuron_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Differentiated and FACS from NSCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: differentiated neuronal progeny
differentiation day: 11
redstar+: Positive
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 4
|
| 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 |
|
| Relations |
| BioSample |
SAMN02141702 |
| SRA |
SRX276675 |
