|
| Status |
Public on Mar 31, 2024 |
| Title |
KO_Day6_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
dentate gyrus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: dentate gyrus
cell type: Neural progenitor cells (NPCs)
genotype: KO
time: Day 6
treatment: BMP4/FGF2; Lenti-Cre-GFP
|
| Treatment protocol |
To induce quiescence, cells were plated into the proliferation medium at a density of 35,000-65,000 cells/cm2, and, after 16 h, fresh quiescence medium was added without EGF and with 20 ng/ml BMP4 and 20 ng/ml FGF2. Quiescent NPC cultures were infected with lentivirus expressing GFP (WT) or Cre-GFP (Setd1a KO). WT and Setd1a KO cultures were treated with DMSO (control) or ORY-1001.
|
| Growth protocol |
Adult NSCs were derived from the dentate gyrus of 7~8-week-old Hopx-CreERT2::Setd1afl/fl::H2B-GFP mice and cultured in the proliferation medium containing Neurobasal medium, 20 ng/ml FGF2, 20 ng/ml EGF, 2% B27, Glutamax, and Penicillin/Streptomycin, on culture dishes precoated with poly-D-lysine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZOL (Invitrogen) and the kit of Zymo RNA Clean & Concentrator™-5. 300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared based on SMART-seq2 method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software
Trimmed sequence reads were mapped to mouse reference genome GRCm38 using STAR v2.5.2a
Only uniquely mapped reads were quantified at the gene level and summarized to gene counts using STAR-quantMode (GeneCounts), with multimapping and chimeric alignments discarded.
Assembly: GRCm38
Supplementary files format and content: excel file including raw count of all genes for all the samples
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Mar 31, 2024 |
| Contact name |
Ting Zhao |
| E-mail(s) |
ting820217@gmail.com
|
| Organization name |
University of Pennsylvannia
|
| Street address |
415 curie blvd
|
| City |
philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE250276 |
Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a [RNA-Seq] |
| GSE250278 |
Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a |
|
| Relations |
| BioSample |
SAMN38855151 |
| SRA |
SRX22898571 |
