|
| Status |
Public on Jul 04, 2024 |
| Title |
OPC_Dor |
| Sample type |
SRA |
| |
|
| Source name |
Oligodendrocyte procurcer cell (OPC)
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Oligodendrocyte procurcer cell (OPC)
chip antibody: Dor (rabbit, InvitrogenPA538729)
|
| Treatment protocol |
Isolated rat OPCs were grown in Sato growth medium supplemented with PDGF-AA (10 ng/ml) and bFGF (20 ng/ml) and differentiated in Sato medium supplemented with T3 (15 nM) and CNTF (10 ng/ml).
|
| Growth protocol |
Primary rat OPCs were isolated as described(Chen et al., 2007). Briefly, mixed glial cells were initially cultured in DMEM-F12 medium plus 15% fetal bovine serum and then changed to B104 conditioned medium for 2 d before isolating OPCs by mechanical detachment in an orbital shaker.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Tag libraries preparing and sequencing. To prepare sequencing libraries of Cut&Tag, fresh specimens from rat were processed following the protocol of Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina® (Yeasen Biotech Co., Ltd.).
Library concentration was measured using Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and library fragment analysis was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Qualified libraries were sequenced on Novaseq 6000 sequencer (Illumina) with 150 bp paired-end reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads processing. Raw reads of were firstly processed through in-house perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing too many N (>= 10%) and reads with low-quality (>= 50% of bases with Q <= 5).
Clean reads were mapped to reference genome of rat (UCSC, rn5) using bowtie2 (v2.4.4), and low-quality mapped reads were removed and uniquely mapped reads were kept through sambamba (v0.8.1).
To facilitate visualization, BIGWIG files were generated from BAM files via deepTools (v3.5.1).
Peak-calling and data analysis. Primary peaks were identified by using MACS2 (v2.2.7.1) with ‘-p 1e-5 -f BAMPE’, followed by peaks filtering with P-value < 1e-9.
Assembly: rn5
Supplementary files format and content: bigWig, narrowPeak files contain signals density and peaks of CUT&Tag, respectively.
Library strategy: CUT&Tag
|
| |
|
| Submission date |
May 26, 2023 |
| Last update date |
Jul 04, 2024 |
| Contact name |
XueLian He |
| Organization name |
Sichuan University
|
| Lab |
State Key Laboratory of Biotherapy
|
| Street address |
Renmin Road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE233591 |
Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline [CUT&Tag] |
| GSE233593 |
Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline |
|
| Relations |
| BioSample |
SAMN35439814 |
| SRA |
SRX20525337 |
