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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 27, 2018 |
| Title |
H9 miR-146a Diff 2 |
| Sample type |
SRA |
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| Source name |
Human neural stem cell
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| Organism |
Homo sapiens |
| Characteristics |
passage: 2
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| Growth protocol |
GIBCO® human neural stem cells (H9 hESC-Derived) was purchased commercially (N7800100, ThermoFisher Scientific). Cells were cultured in flasks or plates previously coated for at least 1H with GelTrex™ LDEV-Free, hESC-qualified, reduced growth factor basement membrane matrix (A1413302, ThermoFisher Scientific). Cells were maintained in Complete StemPro® NSC SFM medium (growth media) consisting of KnockOut™ D-MEM/F-12 (12660012, ThermoFisher Scientific) supplemented with 2% StemPro® Neural Supplement (A1050901, ThermoFisher Scientific), 20 ng/mL EGF (PHG0315, ThermoFisher Scientific), 20 ng/mL bFGF (GF003, ThermoFisher Scientific), 2 mM GlutaMax™-I (35050038, ThermoFisher Scientific) and 10 μg/mL Penicillin-Streptomycin (15140122, ThermoFisher Scientific). For passaging, cells were washed once with DPBS (14190169, ThermoFisher Scientific) and detached from the surface by StemPro™ Accutase (A1110501, ThermoFisher Scientific), centrifuged at 1500 RPM for 5 minutes, and replated in fresh growth media. To initiate spontaneous differentiation, H9 cells were plated at a density of 20-25000 cells/cm2 in growth media for 24H, after which media was replaced with differentiating media (growth media without growth factors). Differentiating media was changed every 2-3 days during the course of the differentiation process.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRizol reagent (15596026, ThermoFisher Scientific) and RNeasy Mini Kit (74104, QIAGEN) with DNase I treatment step (79254, QIAGEN) following the manufacturer’s protocol. The integrity of RNA was determined by RNA ScreenTape (5067-5576, Agilent Technologies) on the Agilent 4200 TapeStation (Agilent Technologies).
RNAseq libraries were prepared starting from 600 ng of total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) as recommended by the manufacturer. Half of the oriented cDNA produced from the poly-A+ fraction were PCR amplified (11 cycles). The RNAseq libraries were sequenced on an Illumina HiSeq2500 (Paired-End sequencing 130x130 bases, High Throughput Mode). A minimum of 10 million of paired-end reads was produced per library sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
H9 Processed File.txt
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| Data processing |
Sequence reads were aligned to the human HG19 or mouse mm9 reference genome using the Burrows-Wheeler Alignment version 0.6.2.13.
Gene expression was analyzed by three different tools: limma, Deseq and EdgeR. Differentially expressed genes were determined by threshold P<0,05 and fold change >1,5 for H9 cells and 1,2 for mouse brains.
Genome_build: HG19 or mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample as analyzed by EdgeR for reference.
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| Submission date |
Jun 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lam Son Nguyen |
| E-mail(s) |
[email protected]
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| Organization name |
INSERM U1163
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| Department |
Institute Imagine
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| Street address |
24 Bld du Montparnasse
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| City |
Paris |
| State/province |
IDF |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE100670 |
Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders |
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| Relations |
| BioSample |
SAMN07302114 |
| SRA |
SRX2971914 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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