|
| Status |
Public on Jun 22, 2020 |
| Title |
KP-N3 |
| Sample type |
SRA |
| |
|
| Source name |
KP cells with Npm1 WT
|
| Organism |
Mus musculus |
| Characteristics |
treatment: no Doxycline
cell type: KP
|
| Treatment protocol |
Control group includes KP-N3, KP-N4 and KP-N5 stable cell lines (Npm1 is normally expressed); Knockdown group includes KP-N3, KP-N4 and KP-N5 stall cell lines treated with Doxycycline ( Npm1 is Knockdown).
|
| Growth protocol |
Mouse KP cells were transfected with pLKO.1-Tet on-shNpm1-3(N3), pLKO.1-Tet on-shNpm1-4(N4) or pLKO.1-Tet on-shNpm1-5 (N5) and then selected by using 2ug/ml puromycin, to get the 3 stable cell lines. These 3 stable cell lines (N3, N4 or N5) were treated with or without 100ng/ml Doxycline .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extract total RNA by using Rneasy Plus Mini Kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (counts per gene)
|
| |
|
| Submission date |
Jun 30, 2019 |
| Last update date |
Jun 24, 2020 |
| Contact name |
Alireza Khodadadi-Jamayran |
| Organization name |
New York University, NYU Langone Medical Center
|
| Department |
Division of Advanced Research Technologies (DART)
|
| Lab |
Applied Bioinformatics Laboratories (ABL)
|
| Street address |
550 1st Ave, MSB 304
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE133555 |
RNA seq to compare gene expression profiles between Npm1 WT and Npm1 knockdown cells |
|
| Relations |
| BioSample |
SAMN12167560 |
| SRA |
SRX6384793 |
