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Sample GSM3067346 Query DataSets for GSM3067346
Status Public on Mar 01, 2019
Title C4-2B HOXB13 KO1
Sample type SRA
 
Source name prostate cell line
Organism Homo sapiens
Characteristics cell type: Bone-metastatic CRPC cell line C4-2B
type: Androgen-independent
Treatment protocol C4-2B treated with DMSO and or various inhibitors.
HOXB13 pKO genetic deletion were generated by CRISPR/Cas9 strategy
Growth protocol grown in C4-2B specialized media
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from C4-2B using the Qiagen RNeasy kit protocol followed by Dnase I treatment. 1-2ug of total RNA was used for the construction of the libraries.
The Illumina Hi-seq platform with 50 bp single end sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing 1. Reference genome and transcript annotations: hg38 from UCSC
2. Mapping: TopHat splice-aware aligner (Kim et al Genome Biol. 2013)
3. Feature summarization: Expectation-Maximization(EM) approach used to estimate transcript abundance (Jiang and Wong, Bioinformatics, 2009)
4. Normalization:
Within sample: RPKM (reads per kilobase of transcript per million, Mortazavi et al, Nat. Meth. 2008)
Between sample: TMM (Trimmed mean of M values ,Robinson and Oshlack Genome Biol. 2010)
5. Differential test: non-replicates analysis with DESeq software (Anders and Huber Genome Biol 2010)
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Mar 24, 2018
Last update date Mar 01, 2019
Contact name Kiran Mahajan
E-mail(s) kiranm@wustl.edu
Phone 3142737728
Organization name Washington University
Department Surgery
Lab Kiran Mahajan Lab
Street address CB 8242 600 South Euclid Ave
City St. Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL18460
Series (1)
GSE112300 Identification of HOXB13 target genes responsive to BET inhibitors
Relations
BioSample SAMN08793611
SRA SRX3843264

Supplementary file Size Download File type/resource
GSM3067346_C42B_HOXB13_KO1_exp.txt.gz 719.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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