|
| Status |
Public on Jul 23, 2023 |
| Title |
hapa1-6 cell Raf_knockdown by HieffNGS kit repeat2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell line: hepa1-6
cell type: live cancel
genotype: Raf_knockdown
treatment: hapa1-6 cell Raf_knockdown by HieffNGS kit
|
| Treatment protocol |
No special treatment
|
| Growth protocol |
HEK293T cells and Hepa1-6 cells were maintained in DMEM medium (Gibco, Cat #11965092) + 10% FBS (Gibco, Cat#16000044) and 1% penicillin/streptomycin (Gibco, Cat#15140122) at 37°C with 5%CO2, Mycobacterium smegmatis was maintained in Middlebrook 7H9 broth base medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mouse tissue with TRIzol, Total RNA from Cell line or bacterium was extracted by MolPure® Cell/Tissue Total RNA Kit
RNA libraries for RNA-seq were prepared using DADCSeq, HieffNGS kit and SHERRY following manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MM_HWTvsHRaf_matrix.txt
|
| Data processing |
Raw reads from sequencing were firstly subjected to Trimmomatic (v0.39) for quality control and adaptor trimming
reads were mapped to genome using STAR (v2.7.10a)
gene counts was statisticed with featurecount
Genes with FPKM >0.5 were considered to be expressed
Assembly: Homo_sapiens.GRCh38, Mus_musculus.GRCm39, Mycobacterium_smegmatis.NZ_CP054795.1
Supplementary files format and content: tab-delimited text file includes raw counts for each
Supplementary files format and content: Sampletab-delimited text files include FPKM values for each Sample mRNA Fragmentation and cDNA synthesis.
|
| |
|
| Submission date |
Jul 13, 2023 |
| Last update date |
Jul 23, 2023 |
| Contact name |
zaiqiao sun |
| E-mail(s) |
2019102040019@whu.edu.cn
|
| Phone |
+8616620125505
|
| Organization name |
wuhan university
|
| Street address |
No.299
|
| City |
wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE237259 |
high efficiency and multiplexable Strand specificity RNA sequencing by Double Adapter Directional Capture |
|
| Relations |
| BioSample |
SAMN36437130 |
| SRA |
SRX21006004 |
