|
| Status |
Public on Jun 08, 2017 |
| Title |
2_3__A |
| Sample type |
SRA |
| |
|
| Source name |
CWR22Pc
|
| Organism |
Homo sapiens |
| Characteristics |
lentivirus: shNT
dht: -
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell RNA extraction via RNAeasy Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner
The 2 pass mapping method47 was used in which the reads were mapped twice
The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanonical flag is used)
post-processed the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which sorts the file and converts it to the compressed BAM format.
computed the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq48 (www-huber.embl.de/users/anders/DESeq), which was used to both normalize the full dataset
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include DESeq values for each Sample
|
| |
|
| Submission date |
Jun 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rohit Bose |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
1275 York Ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE83649 |
Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [22PC RNA-seq] |
| GSE83653 |
Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis |
|
| Relations |
| BioSample |
SAMN05289828 |
| SRA |
SRX1872762 |
