|
| Status |
Public on May 05, 2016 |
| Title |
703R1 - pLK01 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 xenograft tumors_pLKO
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HCT116 xenograft tumors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeAsy Mini Kit (Qiagen, cat # 217004)
Libraries were prepared according to the NEBNext RNA Seq protocol and sequenced on an Illumina 2500 HiSeq using v3 chemistry according to the Illumina Sequencing User’s Guide. 50M 100bp paired-end reads were generated per library (100M total reads per sample). Base calling and fastq was done using Illumina’s HiSeq Control Software version 1.5.15.1 (RTA v1.13.18 and bclfastq v1.8.3).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cuffdiff_out_pLKO1_vs_shLPA2.tar.gz, cuffdiff_out_pLKO1_vs_shNHERF2.tar.gz
SL58669
|
| Data processing |
Sequenced reads were mapped to the human reference genome UCSC version hg19 with TopHat version 1.3.3, and differentially expressed genes were assessed using Cuffdiff, a part of the Cufflinks version 1.3.0 package.
Please note that standard cufflinks/cuffdiff output files are provided in the compressed tar files as processed data and Cufflinks/Cuffdiff output file content/formats are described at:
https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-output-files
https://cole-trapnell-lab.github.io/cufflinks/file_formats/
(also included in the 'readme.txt' file)
Genome_build: hg19
Supplementary_files_format_and_content: compressed tar files containing output of cufflinks/cuffdiff.
|
| |
|
| Submission date |
Apr 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Viren Patel |
| Organization name |
Emory University School of Medicine
|
| Department |
EICC
|
| Street address |
101 Woodruff Circle
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE67931 |
Disruption of Na+/H+ exchanger regulatory factor 2 scaffold suppresses colon cancer proliferation |
|
| Relations |
| BioSample |
SAMN03486523 |
| SRA |
SRX996392 |
