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Sample GSM6063489 Query DataSets for GSM6063489
Status Public on May 12, 2022
Title iTCE_D7_pos_rep2
Sample type SRA
Source name TCE_D7_pos
Organisms Homo sapiens; Mus musculus
Characteristics time: D7
cell type: TCE
group: pos
treatment: D7ChemPresent
Treatment protocol For Wnt/FGF pathway stimulation, the medium was then replaced with STEMdiff APEL2 medium (05270, STEMCELL Technologies), supplemented with 2.5 μM of GSK3-inhibitor CHIR99021 (Tocris Bioscience) for 6 days.
Growth protocol hiPSCs alone or in combination with support cell types were prepared for 3D-aggregation by adding a total of 5.5×106 cells per-well in Corning Costar ultra-low attachment 6-well plates (CLS3471, Sigma Aldrich) in STEMdiff APEL2 medium (05270, STEMCELL Technologies) supplemented with 10 μM ROCK inhibitor (Y-27632, 1254, Tocris Bioscience) with constant shaking (Orbi-Shaker CO2, Benchmark Scientific) at 95 rpm at 37 °C and 8% CO2 overnight.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified using Quant-iT Picogreen (Invitrogen, Carlsbad, California, USA) on a Spectramax M2 (Molecular Devices, Sunnyvale, California, USA). Size pattern was controlled using a Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, Santa Clara, California, USA).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description WNT/FGF stimulated three-component embryoids (TCEs)
Data processing Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using gencode.v25.annotation.exon.tls1.tlsNA-nopseudogene.gff3 or Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf.
To eliminate reads that were mapped on genomes from both human and mouse species we used picard tools. Readnames from mouse mapped bam were filtered out of human mapped bam using picard FilterSamReads tools as well as readnames from human mapped bam were filtered out of mouse mapped bam.
Assembly: hs_GRCh38.p2
Assembly: GRCm38
Supplementary files format and content: Comma separated value file including counts per gene (row) for each sample (column)
Submission date Apr 25, 2022
Last update date Jul 06, 2022
Contact name Jerome Feige
Organization name Nestle Institute Of Health Sciences
Department Musculo-Skeletal Health
Street address EPFL Innovation Park, Building H
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platform ID GPL22245
Series (1)
GSE201424 An Engineered Multicellular Stem Cell Niche for the 3D Derivation of Human Myogenic Progenitors from iPSCs
BioSample SAMN27760725
SRA SRX14987763

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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