|
| Status |
Public on Mar 15, 2018 |
| Title |
ZT36.CLKkd.3 (hi2500) |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neural progenitor cells
line: OF4106
Sex: F
age: --
|
| Treatment protocol |
Tissue culture was performed as previously described (PMID: 21647150). Lentivirus was delivered via pZIP shRNA constructs (Transomics).
|
| Growth protocol |
Differentiated human neural progenitor cell lines were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen’s miRNeasy kit according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. 2ug of total RNA were enriched for mRNA with poly-A selection beads. Libraries were prepared using previously published methods (PMID: 25662462)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (hg38, Gencode v.24). HiSeq 2500 and NextSeq 500 counts per gene were further added into a final count to calculate RPKM values and downstream analysis.
RNA-seq RPKM values were then quantified using in-home scripts, providing gene definitions (hg38, Gencode v.24).
Gene-level RPKMs quantifications were used for all downstream processing.
tab-delimited text file include RPKM values for each Sample.
Genome_build: Human hg38
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Genevieve Konopka |
| E-mail(s) |
gena@alum.mit.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Neuroscience
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE96659 |
Novel transcriptional networks regulated by CLOCK in human neurons |
|
| Relations |
| BioSample |
SAMN06604833 |
| SRA |
SRX2642515 |
