|
Status |
Public on Nov 28, 2023 |
Title |
2_2DG_IP |
Sample type |
SRA |
|
|
Source name |
Mouse immature neurons
|
Organism |
Mus musculus |
Characteristics |
cell type: immature neurons chip antibody: ATF4 antibody (Sigma-Millipore: catalog number ABE387) condition: IP treatment: 2-DG
|
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 2-DG
|
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 |
SAMN31608691 |
SRA |
SRX18171659 |