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| Status |
Public on Oct 01, 2020 |
| Title |
I5386F_mA_1 |
| Sample type |
SRA |
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| Source name |
I5386F_mA
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| Organism |
Callithrix jacchus |
| Characteristics |
cell line: Adult marmoset (I5386F)
cell type: Fibroblast-derived induced neurons
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| Treatment protocol |
Fibroblasts transfected with the pPB-tetpA(hBCL2-miR9/9*-124)-iRPT and the TRE-ASCL1 lentivirus were used for neuronal conversion. First day of induction (PID 0), 1.0 × 10^5 cells were seeded on each well of a gelatin-coated 12-well plate (Iwaki) and fed with fibroblast medium containing 2 ug/mL doxycycline (Dox; Wako). On PID 2, cells were fed with fresh fibroblast medium containing Dox. On the PID 4, a 50 uL cell-drop consisted of fibroblast medium and 5.0 × 104 cells was added to each well of a poly-L-ornithine/laminin/fibronectin-coated plate, and fed with fibroblast medium after the cells attached. The following day (PID 5), the medium was switched to a neuronal reprogramming medium composed of a 1:1 mixture of Neurobasal Medium (Thermo Fisher) and DMEM/F-12 (Wako) supplemented with 1% N2 supplement (Thermo Fisher), 2% B27 supplement (Thermo Fisher), 1% non-essential amino acid solution (Sigma Aldrich), 1 mM L-glutamine (Nacalai tesque), 200 uM dbcAMP (Sigma Aldrich), 10 uM Forskolin, 10 uM Y-27632 (Wako), 3 uM CHIR99021 (Axon), 1 uM PD-0325901 (Wako), 0.5 uM A83-01 (Santa Cruz), 10 ng/mL recombinant human Leukemia inhibitory factor (Oriental Yeast), 1 mM valproic acid (Wako), 10 ng/mL Brain-derived neurotrophic factor (Peprotech), 10 ng/mL Glial cell line-derived neurotrophic factor (Peprotech), 10 ng/mL Neurotrophin-3 (Peprotech), 200 uM Ascorbic acid (Sigma Aldrich), 1 uM Retinoic acid (Sigma Aldrich), supplemented with Dox and penicillin/streptomycin. Medium was changed every four days.
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| Growth protocol |
Fibroblasts were cultured in fibroblast medium consisting of DMEM supplemented with 10% inactivated FBS and 1% penicillin/streptomycin solution.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 14, 2020 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Sho Yoshimatsu |
| E-mail(s) |
yoshima@a7.keio.jp
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| Organization name |
Keio University School of Medicine
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| Department |
Physiology
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| Lab |
Hideyuki Okano's Lab
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| Street address |
35 Shinanomachi
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| City |
Shinjuku |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
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| Platform ID |
GPL28659 |
| Series (1) |
| GSE152433 |
Rapid and efficient conversion of common marmoset fibroblasts into mature and functional neurons by overexpression of ASCL1 and microRNA-9/9*-124 |
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| Relations |
| BioSample |
SAMN15233209 |
| SRA |
SRX8542823 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4615570_I5386F_mA_1.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
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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