|
| Status |
Public on Jan 01, 2018 |
| Title |
WT_RES_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: shTRIM24
genotype/variation: wild type rescue
cell line: MCF7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to Illumina's instructions
Libraries were constructed using Illumina's standard protocoles.
RNA-Seq with poly-A selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
RNA-Seq data was generated at the Institute of Applied Cancer Science of the UT MD Anderson cancer center. The data were processed with CASAVA pipeline. The sequences in the FASTQ files were aligned to the Hg19/GRCh37 assembly of Human genome using Bowtie aligner.
Bioconductor package easyRNASeq was used to quantitate the expression using the genes.gtf annotations provided by ENSEMBL.
The data were filtered, normalized and differential expression was obtained with edgeR Bioconductor package.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: Tabl delimited text file for raw count data (raw_data_matrix_6samples.txt) and filtered, normalized data with annotations (filtered_normalized_counts_6samples.txt).
|
| |
|
| Submission date |
Jan 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
srikanth appikonda |
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE77140 |
Gene expression profiles of rescue with wild type or SUMO double mutant TRIM24 |
|
| Relations |
| BioSample |
SAMN04435503 |
| SRA |
SRX1542011 |
