|
| Status |
Public on Feb 08, 2022 |
| Title |
SREBP2-1 |
| Sample type |
SRA |
| |
|
| Source name |
G1E-ER4 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: untreated
transduction: transduced with active SREBP2
cell type: Embryonic stem cells
|
| Treatment protocol |
treated with Vehicle or β-estradiol (500nM) for 6 h
|
| Growth protocol |
G1E-ER4 cells were transduced with retrovirus to express active SREBP2 (1-468aa) or empty vector for 24 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Text Document include Raw and Normalized read counts for each Sample
|
| |
|
| Submission date |
Sep 13, 2021 |
| Last update date |
Feb 08, 2022 |
| Contact name |
Zhiyuan Lu |
| E-mail(s) |
[email protected]
|
| Phone |
+8613220588767
|
| Organization name |
Shandong First Medical University & Shandong Academy of Medical Sciences
|
| Department |
School of Pharmaceutical Sciences & Institute of Materia Medica
|
| Street address |
6699 Qingdao road
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250117 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE184002 |
The mechanistic studies of GATA1 regulation of SREBP2 in G1-ER4 cells |
|
| Relations |
| BioSample |
SAMN21401162 |
| SRA |
SRX12153041 |
