|
| Status |
Public on Jul 11, 2015 |
| Title |
SET2 cells persistent to CYT387_replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
SET2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
inhibitor exposure: chronic
cell line: SET-2
|
| Growth protocol |
SET2 cells were cultured in RPMI1640 media + 20% FCS. For persistent cell lines, the respective type I JAK inhibitor was added to the culture media for continuous growth in presence of inhibitor. For acute exposures with inhibitor, DMSO was used as a control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SET2 cells were lysed in Trizol and processed according to instructions with reagent.
poly(A) RNA was isolated using Dynabeads® mRNA DIRECTTM Micro Kit (Life Technologies) from 1 μg of total RNA. mRNA was then fragmentated using RNaseIII and purified. The fragmented samples’ quality and yield were evaluated using Agilent BioAnalyzer. Subsequently, the fragmented material underwent whole transcriptome library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR. Samples were barcoded, template-positive Ion PITM Ion SphereTM Particles (ISPs) were prepared using the ion one touch system II and Ion PITMTemplate OT2 200kit v2 Kit (Life Technologies). Enriched particles were sequenced on a Proton sequencing system using 200 bp version 2 chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
s_SET2_CYT_per2
|
| Data processing |
All sequenced library were mapped to the human genome (hg19) using rnaStar. Unmapped reads were mapped again to the same genome using BWA MEM (version 0.7.5.1)
HTSeq v0.5.3p3 (options -s y -m intersection-strict) is used for feature counting using the Homo_sapiens.GRCh37.69_ENSEMBL gene model also used at the mapping stage
DESeq (v1.10.1) is used for the normalization of count table.
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized count tables from each experiment
|
| |
|
| Submission date |
Jul 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Zhao |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Genomics Core
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE69827 |
Differential expression profiles of type I JAK inhibitor persistent vs. naïve MPN cells |
|
| Relations |
| BioSample |
SAMN03854206 |
| SRA |
SRX1091671 |
