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Status |
Public on May 18, 2021 |
Title |
Neuron - Basal, BRG1 IP |
Sample type |
SRA |
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Source name |
neuron
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Organism |
Mus musculus |
Characteristics |
genotype: wild type cell type: Primary cultured cortical neurons treatment: Basal level of KCl chip antibody: J1 anti-BRG1/BRM
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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.
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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).
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
May 17, 2021 |
Last update date |
May 18, 2021 |
Contact name |
Zhenyu Xuan |
E-mail(s) |
zhenyu.xuan@utdallas.edu
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Phone |
972-883-2518
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Organization name |
UT Dallas
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Street address |
800 West Campbell
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City |
Richardson |
State/province |
TX |
ZIP/Postal code |
75080 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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