|
| Status |
Public on Nov 23, 2022 |
| Title |
H446 cells, NEUROD1 gRNA #297, clone 15, JQ1, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
H446
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H446
cell type: small cell lung cancer SCLC-N subtype
genotype: NEUROD1 knockout
treatment: JQ1
time: 24 hours
|
| Treatment protocol |
Cells were treated with JQ1 (1µM) or DMSO for 24 hours.
|
| Growth protocol |
H446 NEUROD1-knockout derivatives and control cell clones were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ⁰C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Library Prep following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
H446_ND1_KO_cl_15_JQ1_3
Biological replicate 3
mRNA
|
| Data processing |
CCBR Pipeliner. Details can be found at https://ccbr.github.io/pipeliner-docs/RNA-seq/Gene-and-isoform-expression-overview/
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt.
Trimmed sequence reads were mapped to hg19 using STAR for two passes.
Read count extraction and normalization were performed using RSEM.
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files include normalized counts or FPKM values for all samples.
|
| |
|
| Submission date |
Jul 29, 2022 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Haobin Chen |
| E-mail(s) |
[email protected]
|
| Phone |
(845) 300-2498
|
| Organization name |
National Institutes of Health
|
| Department |
Thoracic Surgery Branch
|
| Street address |
10 Center Drive, Room 3-5888
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE210101 |
BET inhibitors target the SCLC-N subtype of small-cell lung cancer by blocking NEUROD1 transactivation |
| GSE210114 |
BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation |
|
| Relations |
| BioSample |
SAMN30056433 |
| SRA |
SRX16736509 |
