|
| Status |
Public on Feb 11, 2017 |
| Title |
NSC-1 (miRNA) |
| Sample type |
SRA |
| |
|
| Source name |
neural stem cell (NSC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NSC differentiated from LCL-reprogrammed iPSC
|
| Treatment protocol |
The six LCLs were reprogrammed into iPSCs using episomal plasmids encoding reprogramming factors (i.e. OCT3/4, SOX2, KLF4, L-MYC, LIN28) and mouse p53DD - p53 carboxy-terminal dominant-negative fragment as described in Okita et al., 2012. The reprogrammed iPSCs were then differentiated into neural stem cells (NSC). Both iPSC reprogramming and NSC inductions were confirmed by immunocytochemistry.
|
| Growth protocol |
The six de-identified LCLs were cultured in RPMI 1640 complete media at 37 oC, 5% CO2 and atmospheric O2 for 1-2 passages to obtain the appropriate number of viable cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
smallRNA Sequencing: The Illumina® TruSeq® Small RNA Sample Preparation Kit was used to prepare small RNA sequencing libraries from 1 μg of total RNA.
Total RNA was extracted from cell pellets (~5x106 cells) snap-frozen from LCLs immediately before nucleofection with reprogramming factors; from stable iPSC lines after at least five but less than ten passages; and from validated NSC lines after 3-4 passages.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
iPSC-NSC-miRNA.txt
|
| Data processing |
Raw fastq sequence files were generated and de-multiplexed using the Illumina CASAVA v1.8 pipeline.
After pre-alignment QCs, sequences were aligned to human genome build 19 (hg19) and mapped to UCSC transcripts using Strand NGS software v2.1 (Strand Genomics Inc.). The small RNA reads were also mapped to small RNA annotations as implemented in Strand NGS v2.1 (Strand Genomics Inc.) and reads mapping only to miRNAs were retained for further analysis.
The aligned reads were then filtered based on read quality metrics, so that only perfect alignments were retained and then quantification was performed using NGS software v2.1 (Strand Genomics Inc.).
The expression values (read counts) were log transformed and ‘DESeq’ normalization was applied.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include DESeq normalized abundance measurements for six LCLs-iPSC and six iPSC-NSC pairs, formatted as matrix tables.
|
| |
|
| Submission date |
Oct 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Satish Kumar |
| E-mail(s) |
[email protected]
|
| Phone |
+1-956-665-6477
|
| Organization name |
University of Texas Rio Grande Valley
|
| Department |
Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine
|
| Street address |
5300 North L Street (MBMRF-2.219)
|
| City |
McAllen |
| State/province |
Texas |
| ZIP/Postal code |
78504 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE74289 |
Improved LCL to iPSC reprogramming: RNA Analysis of LCLs, reprogrammed iPSCs, and differentiated NSCs reveal potential regulatory and functional processes involved in these cellular transitions. |
|
| Relations |
| BioSample |
SAMN04209954 |
| SRA |
SRX1369785 |
