 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 28, 2017 |
| Title |
EP400 shRNA rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MKL-1 line with Dox inducible EP400 shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MKL-1
cell type: Merkel cell carcinoma
merkel cell polyomavirus: positive
dox treatment: +
ep400 shrna expression: +
|
| Treatment protocol |
Cells were treated with or without doxycycline to induce expression of EP400 shRNA.
|
| Growth protocol |
MKL-1 cells grow as suspension clumps in RPMI medium supplemented with 10% FBS, Penicillin-Streptomycin, and glutamax
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified from MKL-1 cells using RNeasy plus mini kit (Qiagen). mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England Biolabs). 50 cycles single-end sequencing was performed on HiSeq2000 system at CCCB.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The reads were mapped to hg19 with tophat-2.0.4
"FPKM_tracking" files were produced by Cufflinks
the reads were sorted using samtools (samtools-0.1.19)
Using HTSeq-0.6.1_python-2.7.3, Transcript parts per million (TPM) counts were calculated and assigned to genes A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008.
Differentially expressed genes were called using DEseq2 with the Benjamini-Hochberg (BH) adjusted p-value of 0.1
Genome_build: hg19
Supplementary_files_format_and_content: "FPKM tracking" files include FPKM values for each sample, count.txt files include TPM counts for each sample, results.csv and diffexp.text files summarize all 6 samples.
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingwei Cheng |
| E-mail(s) |
jingweic@gmail.com
|
| Phone |
617-632-4797
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
James A. DeCaprio
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE69876 |
EP400 is required for Max and MCPyV mediated gene activation |
| GSE69878 |
MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex |
|
| Relations |
| BioSample |
SAMN03775162 |
| SRA |
SRX1058423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1711853_JC15_MKL1_p400shDox_02_10_15RNASeq_cufflinks_out_genes.fpkm_tracking.gz |
801.2 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1711853_shp400_2.count.txt.gz |
96.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
