|
Status |
Public on Feb 07, 2017 |
Title |
C51sh3plus |
Sample type |
SRA |
|
|
Source name |
breast cancer cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line name: Cal51 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 |
SAMN05187207 |
SRA |
SRX1808071 |