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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 01, 2018 |
| Title |
iMPC-Pax7-nGFP-minus |
| Sample type |
SRA |
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| Source name |
Sorted for Pax7-nGFP- cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Induced myogenic progenitors cells
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| Growth protocol |
Reprogramming of MEFs and TTFs into iMPCs was performed using “iMPC medium” containing KnockOut-DMEM (ThermoFisher Scientific, catalog number 10829-018) supplemented with 10% FBS (HyClone catalog number SH30396.03), 10% KnockOut Serum Replacement (ThermoFisher Scientific, Catalog number 10828028), 1% GlutaMAX (Catalog number 35050061), 1% non-essential amino acids (ThermoFisher Scientific, Catalog number 11140050), 1% penicillin-streptomycin (ThermoFisher Scientific, catalog number 15140122), 0.1% β-mercaptoethanol (ThermoFisher Scientific, catalog number 21985-023) and 10ng/ml basic FGF (R&D 233-FB). Forskolin (Sigma-Aldrich F6886) and RepSox (Sigma-Aldrich, R0158) were added at a concentration of 5μM each. For some experiments, 3μM of the GSK3β inhibitor CHIR99021 (Tocris) was used. Doxycycline (Sigma-Aldrich, D9891) was added at a final concentration of 2μg/ml. For all reprogramming experiments, cells were reprogrammed in “iMPC medium” with and without Forskolin, RepSox and GSK3βi. Expanded bulk cultures as well as iMPC clones were cultured in iMPC medium without dox and supplemented with Forskolin (5μM), RepSox (5μM), and GSK3 inhibitor (3μM).
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| Extracted molecule |
total RNA |
| Extraction protocol |
DNase I-treated total RNA was extracted using RNeasy Mini or Micro Kit (74004) according to the manufacturer’s instructions (Qiagen).
PolyA selection followed by library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Pax7-nGFP- iMPCs (sorted)
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| Data processing |
PICARD, Version: 1.100
STAR, version 2.3.0
HTSeq, version 0.6.0 (unstranded) using Ensembl release 67 transcript annotations
EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files with whole-genome RNA-seq coverage; spreadsheets of gene expression values for each sample
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| Submission date |
Dec 26, 2017 |
| Last update date |
May 01, 2018 |
| Contact name |
Ori Bar-Nur |
| E-mail(s) |
ori.bar-nur@mail.huji.ac.il
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| Organization name |
Harvard University
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| Department |
Center of Regenerative medicine
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| Lab |
Hochedlinger
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| Street address |
185 Cambridge st.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE108543 |
Direct reprogramming of mouse fibroblasts into functional skeletal muscle progenitors |
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| Relations |
| BioSample |
SAMN08244572 |
| SRA |
SRX3515527 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2904731_iMPC-Pax7-nGFP-min.genes.counts.txt.gz |
145.9 Kb |
(ftp)(http) |
TXT |
| GSM2904731_iMPC-Pax7-nGFP-min_RNAseq.bw |
59.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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