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Sample GSM6742879 Query DataSets for GSM6742879
Status Public on Sep 29, 2023
Title P53 KO IPSCS 2
Sample type SRA
 
Source name BJFF.6 iPSC
Organism Homo sapiens
Characteristics cell type: BJFF.6 iPSC
genotype: Trp53 null iPSCs
Extracted molecule total RNA
Extraction protocol For tumors, tumor samples were manually dissected from normal surrounding tissue.
For sorted cells, tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA from tumors was harvested using miRNeasy mini plus kit (Qiagen) and RNA from sorted cells was harvested using miRNeasy micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description p53 KO BJFF.6 iPSCs p5 - 2440991
Data processing Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60), mapped to human (hg38) or mouse (mm10) genome assembly (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (human release 31 for human sampls or mouse release 22 for mouse samples).
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM text file
 
Submission date Nov 18, 2022
Last update date Sep 29, 2023
Contact name Hongjian Jin
E-mail(s) hongjian.jin@STJUDE.ORG
Organization name St Jude Children's Research Hospital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38015
Country USA
 
Platform ID GPL24676
Series (2)
GSE218274 PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity
GSE218357 PAX3-FOXO1 drives tumor formation from multiple lineages [RNA-seq]
Relations
BioSample SAMN31792170
SRA SRX18312888

Supplementary file Size Download File type/resource
GSM6742879_2440991_MEH505.RSEM.genes.counts.txt.gz 733.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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