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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
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
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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