|
| Status |
Public on Oct 31, 2023 |
| Title |
RNA_HS19_to_20_del_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cortex
cell line: cortex-neuron
cell type: neuron
genotype: HS19_to_20_del -/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.
|
| |
|
| Submission date |
Feb 13, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Xiao Ge |
| Organization name |
Shanghai JiaoTong University
|
| Street address |
No. 800 Dongchuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE210817 |
Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation |
| GSE225162 |
Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [RNA-seq] |
|
| Relations |
| BioSample |
SAMN33269860 |
| SRA |
SRX19351872 |
