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Sample GSM5320080 Query DataSets for GSM5320080
Status Public on May 18, 2021
Title Neuron - Basal, BRG1 IP
Sample type SRA
 
Source name neuron
Organism Mus musculus
Characteristics genotype: wild type
cell type: Primary cultured cortical neurons
treatment: Basal level of KCl
chip antibody: J1 anti-BRG1/BRM
Treatment protocol For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.
Growth protocol Primary cortical neurons were culture from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and BAF-DNA complexes were isolated with antibody.
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 Illumina HiSeq following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing BWA was used to map raw reads to mouse reference genome mm10 with default parameter setting.
Brg1 binding sites were detected by SICER 1.0 with default parameter setting.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig; the columns in the peak files are chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold
 
Submission date May 17, 2021
Last update date May 18, 2021
Contact name Zhenyu Xuan
E-mail(s) zhenyu.xuan@utdallas.edu
Phone 972-883-2518
Organization name UT Dallas
Street address 800 West Campbell
City Richardson
State/province TX
ZIP/Postal code 75080
Country USA
 
Platform ID GPL13112
Series (2)
GSE174581 Genome-wide maps of BRG1 binding sites in cortical neuron under basal and depolarized conditions [ChIP-seq]
GSE174585 BRG1 role in neuronal activity
Relations
BioSample SAMN19235146
SRA SRX10913845

Supplementary file Size Download File type/resource
GSM5320080_ChIP_Brg1_Ctrl_mm10.bw 195.7 Mb (ftp)(http) BW
GSM5320080_ChIP_Brg1_Ctrl_mm10_rmdp-W200-G600-islands-summary-FDR0.01.txt.gz 21.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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