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Sample GSM4701034 Query DataSets for GSM4701034
Status Public on Oct 30, 2023
Title 839T_siB7H3_2
Sample type SRA
 
Source name Skin
Organism Homo sapiens
Characteristics tissue: Skin
treatment: siRNA B7H3
Treatment protocol Cells were transfected with ON-TARGETplus Non-targeting Control Pool or ON-TARGETplus B7H3 siRNA (Dharmacon) for 72 hours.
Growth protocol Human melanoma cell lines were cultured using standard methods.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from samples using the RNeasy Protect Mini Kit (Qiagen). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA. Total RNA was subjected to ribosomal RNA depletion and further used as input for library construction by the Illumina TruSeq Standard Total RNA library Pre Gold kit (Illumina).
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
 
Description B7H3 specific siRNA treatment to human melanoma cell line 839T, Replicate 2
Data processing Reads were mapped to the human genome using STAR vSTAR_2.5.2a
Counts of reads mapping to each gene were quantified using featureCounts utility from the Subread package v1.4.6-p5
Expression as log(counts per million) was computed using edgeR v.3.30 package for R v.4.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample
 
Submission date Jul 29, 2020
Last update date Oct 30, 2023
Contact name Tiphaine Christiane Martin
E-mail(s) tiphaine.martin@mssm.edu
Phone 2128248403
Organization name Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
Department Oncological Sciences
Lab Parsons
Street address 1470 Madison Ave
City New York
State/province 75459
ZIP/Postal code 10029
Country USA
 
Platform ID GPL18573
Series (2)
GSE155394 Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas [transfection]
GSE161180 Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas
Relations
BioSample SAMN15670606
SRA SRX8845868

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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