|
| Status |
Public on Feb 07, 2017 |
| Title |
HCC1954sh3plus |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line name: HCC1954
doxycycline added: plus dox
gene target of shrna: SF3B1
|
| Treatment protocol |
for doxycycline samples, treated with 100 ng/mL for 4 days to induce SF3B1 suppression
|
| Growth protocol |
RPMI 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiangen RNA easy extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, FASTQ files were aligned using TOPHAT v1.4 with parameters "--mate-inner- dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam -p 4" and aligned to hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RNASeqMetrics 44
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in .gct file format
|
| |
|
| Submission date |
May 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Brenton Paolella |
| Organization name |
Dana-Farber Cancer Institute
|
| Lab |
Rameen Beroukhim
|
| Street address |
450 Brookline Ave. Smith 1010
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE81978 |
Effect of SF3B1 suppression in cancer cells with different SF3B1 copy-number levels |
|
| Relations |
| BioSample |
SAMN05187214 |
| SRA |
SRX1808078 |
