|
| Status |
Public on Feb 07, 2024 |
| Title |
brain cortex, IgG CTL |
| Sample type |
SRA |
| |
|
| Source name |
brain cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain cortex
cell type: homogenous mix
age: E17-18
genotype: WT
treatment: none
chip antibody: Cell Signaling, #3900S
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
developing cortex of mouse embryos at embryonic day 17 to 18 was extracted for ChIP-seq
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 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 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 IIx |
| |
|
| Description |
Phf6_vs_IgG_peaks.bed
Phf6_vs_IgG_summits.bed
|
| Data processing |
Raw reads were aligned to the mouse genome assembly version mm10 withbowtie2(version 2.3.4.1) using the“--very-sensitive-local” mode.
Duplicate reads were removed usingsamtools(version 1.9).
ChIP-seq peaks were identified usingMACS(version 1.4) with a permissive p-value threshold of 0.001, using “--nomodel” option. Fragment size was specified using “--shiftsize” argument, with the fragment length obtained by cross-correlation analysis usingphantompeakqualtools.
Bigwig files were created from BAM files using bamCoverage (version 3.5.1, --binSize 10).
Assembly: mm10
Supplementary files format and content: bed
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Arezu Jahani-Asl |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Ottawa
|
| Department |
Department of Cellular and Molecular Medicine
|
| Street address |
451 Smyth Road
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H 8M5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE247836 |
Transcriptional reprogramming of neural stem cells by a PHF6/EphR signalling pathway [ChIP-Seq] |
| GSE247838 |
Transcriptional reprogramming of neural stem cells by a PHF6/EphR signalling pathway |
|
| Relations |
| BioSample |
SAMN38266980 |
| SRA |
SRX22536522 |
