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Sample GSM6710447 Query DataSets for GSM6710447
Status Public on Nov 28, 2023
Title 9_Control_IP
Sample type SRA
 
Source name Mouse immature neurons
Organism Mus musculus
Characteristics cell type: immature neurons
chip antibody: None
condition: IP
treatment: Control
Treatment protocol These primary immature neurons were either untreated (Control), or treated with 10mM 2-DG for 6h.
Growth protocol Primary immature neurons were cultured from E14 mouse embryos and plated on poly-D-Lysine coated plates in the EMEM plus GlutMAX medium added with 10% fetalk bovine serum, 5% horse serum, and 1% Penicillin/Streptomycin. These neurons (two days in vitro) were treated with 2-Deoxyglucose (2-DG).
Extracted molecule genomic DNA
Extraction protocol Purified RNA was extracted from these samples using Nucleospin RNA kit (Macherey-Nagel) and follwing its protocol. RNA concentration determined by Nanodrop 1000 (Thermofisher scientific).
Libraries were prepared according to Illumina's instructions
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description IP Control
Data processing BWA was used for alignment
Picard was used for removing duplicates
MACS2 was used for peak calling
DiffBind for differential peak calling
Assembly: mm10
Supplementary files format and content: peaks
 
Submission date Nov 04, 2022
Last update date Nov 28, 2023
Contact name Riki Kawaguchi
Organization name University of California, Los Angeles
Department Department of Psychiatry and Neurology Department of Psychiatry
Lab AMRF Functional Genomics Common Research Resource
Street address 760 Westwood Plaza, Room 37-420
City Los Angeles
State/province CA
ZIP/Postal code 90095-1759
Country USA
 
Platform ID GPL24247
Series (2)
GSE217282 The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models [ChIP-seq]
GSE217284 The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models
Relations
BioSample SAMN31608684
SRA SRX18171666

Supplementary file Size Download File type/resource
GSM6710447_9_Control_IP.macs2_peaks.narrowPeak.bed.gz 129.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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