|
| Status |
Public on Sep 17, 2019 |
| Title |
inducible DNp63-expressing LK2 cells with doxycycline_replicate2 [OE_4] |
| Sample type |
SRA |
| |
|
| Source name |
inducible DNp63-expressing LK2 cells with doxycycline
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LK2
cell type: lung squamous cell carcinoma (LUSC) cell lines
genotype/variation: pLIX_403-DNp63
doxycycline treatment: Yes
|
| Treatment protocol |
For inducible DNp63-expressing LK2 cells, cells were treated with or without 2 μg/ml doxycycline for 6 days.
|
| Growth protocol |
LK2 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
LK2_iDNp63_Dox_rep2
|
| Data processing |
Sequencing reads were aligned to the human reference genome hg19/GRCh37 using Tophat (v2.1).
Read counts per RefGene symbol on the USCS database was estimated using the htseq-count function in SAMtools.
The read counts were normalized using DEseq2 normalization algorithm.
Genome_build: hg19/GRCh37 RefGene
Supplementary_files_format_and_content: Text files
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Hideo Watanabe |
| E-mail(s) |
[email protected]
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
|
| Lab |
Hideo Watanabe
|
| Street address |
One Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE137460 |
Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [RNA-seq] |
| GSE137461 |
Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 |
|
| Relations |
| BioSample |
SAMN12757126 |
| SRA |
SRX6852829 |
