 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 28, 2018 |
| Title |
H3122_LR_Pano_1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
H3122 lung cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H3122
treatment: Certinib + Panobinostat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
of
transcript
per
million
fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE81484 |
Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
| GSE81487 |
Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
|
| Relations |
| BioSample |
SAMN05003689 |
| SRA |
SRX1769336 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2154750_H3122_LR_Pano_1_FPKM.txt.gz |
271.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
