|
| Status |
Public on Jul 29, 2024 |
| Title |
10T-PATZ1-OE1 |
| Sample type |
SRA |
| |
|
| Source name |
10T1/2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 10T1/2
treatment: D8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol Reagent (Invitrogen). The aqueous phase containing the RNA was loaded onto a gDNA Eliminator Spin Column (Qiagen, USA) for elimination of genomic DNA, and RNA was isolated using the RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. Total RNA (500 to 1000 ug) was reverse transcribed into cDNA using the M-MLV reverse transcriptase (Invitrogen),
Strand-specific libraries were generated from 500 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
cDNA libraries were single-end sequenced (50bp) on an Illumina HiSeq 2000 or 4000. Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed one alignment with up to two mismatches per read. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline. All FPKMs represent an average from three biological replicates for in-vitro studies for library construction. A gene was included in the analysis if it met all of the following criteria: The maximum FPKM reached 10 at any time point, the gene length was > 200bp as determined by the DESeq2 package in R Bioconductor. P values were adjusted using the Benjamini-Hochberg procedure of multiple hypothesis testing
Assembly: mm10 (GRCm38)
Supplementary files format and content: Gene count
|
| |
|
| Submission date |
Jul 29, 2024 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Prashant Rajbhandari |
| E-mail(s) |
prashant.rajbhandari@gmail.com
|
| Phone |
5172316099
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1468 Madison Ave, Annenberg 18-10
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE273317 |
Transcription factor PATZ1 promotes adipogenesis by controlling promoter regulatory loci of adipogenic factors [RNA-seq] |
|
| Relations |
| BioSample |
SAMN42892597 |
| SRA |
SRX25500967 |
