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Sample GSM1602563 Query DataSets for GSM1602563
Status Public on Feb 09, 2017
Title G401-sg1-HOXB13
Sample type SRA
Source name rhabdoid tumor of the kidney
Organism Homo sapiens
Characteristics tissue: kidney
tumor type: rhabdoid
cell line: G401
Growth protocol G401 cells were grown in RPMI + 15% FBS and harvested at 80% confluency
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy kit
Extracted RNA was enriched using the Ribominus™ Eukaryote Kit (Invitrogen). The Ion PI™ Template OT2 200 Kit (Invitrogen) was used to prepare the RNA library for sequencing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Data processing Torrent Suite™ Software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie
Fragments Per Kilobase of exon per Million reads (FPKM) were calculated using TopHAT and Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: Excel files contain FPKM counts of each cell line
Submission date Feb 05, 2015
Last update date May 15, 2019
Contact name Paul-Joseph P Aspuria
Organization name Cedars-Sinai Medical Center
Department Women's Cancer Program
Lab Sandra Orsulic
Street address 8400 Beverly Blvd.
City Los Angeles
State/province California
ZIP/Postal code 90048
Country USA
Platform ID GPL17303
Series (1)
GSE65655 The effect of HOXB13 CRISPR knockout on the transcriptome in G401 cells
BioSample SAMN03329689
SRA SRX866292

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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