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Sample GSM3436803 Query DataSets for GSM3436803
Status Public on Feb 13, 2019
Title iPax3 RNA-Seq rep1
Sample type SRA
 
Source name PSC-derived myogenic progenitors
Organism Mus musculus
Characteristics cell type: ES-derived myogenic progenitors
Growth protocol iPax3/iPax7 myogenic progenitors were generated thorugh sorting of Vcam1+Flk1- cells from EBs, plated and expanded upon Dox and bFGF administration for 3 passages, then collected with PBS-based dissociation buffer and submitted for downstream analyses.
Extracted molecule total RNA
Extraction protocol Cultured Cells and freshly sorted tissue-derived cells were lysated with buffer RA1+TCEP of kit RNA XS (Machirey-Nagel) and RNA was extracted according to manufacturer's instructions.
Libraries were prepared using Illumina standard protocols (RNA-Seq); Chromium Single Cell 3’ Reagent kit 10X Genomics (single-cell RNA-Seq)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description iPax3_1
Data processing Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using HISAT 2 v2.0.2.
Read assignments were performed by SUBREAD featureCounts v1.4.6.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include SUBREAD assigned raw reads for each sample.
 
Submission date Oct 18, 2018
Last update date Feb 13, 2019
Contact name Tania Incitti
E-mail(s) tincitti@umn.edu
Organization name University of Minnesota
Street address 2231 6th Street SE
City Minneapolis
State/province Minnesota
ZIP/Postal code 55455
Country USA
 
Platform ID GPL21493
Series (2)
GSE121469 Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq]
GSE121639 Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment
Relations
BioSample SAMN10258837
SRA SRX4905887

Supplementary file Size Download File type/resource
GSM3436803_iPax3_1_subread.txt.gz 219.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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