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| Status |
Public on May 20, 2019 |
| Title |
day 0 treatment, rep 2 |
| Sample type |
SRA |
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| Source name |
HA1800, ScienCell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human fetal cortical astrocytes
passages: p10 - p15
time point: day 0
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA were extracted according to protocols accompanying with Macherey-Nagel NucleoSpin RNA kit, then sent to sequencing center for polyA enrichment
libraries were constructed using KAPA RNA kit at UCLA Technology Center for Genomics & Bioinformatics
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
D0_2
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| Data processing |
quality check using FastQC v0.11.3
reads were aligned to hg19 using HISAT2 version 2.0.4
counts summarized using featureCounts v1.5.1 (count) or StringTie v1.3.4 (RPKM)
differential analysis by DESeq2 v1.16.1
Genome_build: hg19
Supplementary_files_format_and_content: a txt file containing read count from all samples generated by featureCounts
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| Submission date |
Nov 19, 2018 |
| Last update date |
May 20, 2019 |
| Contact name |
Gong Chen |
| Organization name |
Penn State University
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| Street address |
Old Main
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE122701 |
Transcriptome analysis of small molecule-mediated astrocyte-to-neuron reprogramming |
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| Relations |
| BioSample |
SAMN10441198 |
| SRA |
SRX5026195 |
| 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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