|
| Status |
Public on Apr 13, 2016 |
| Title |
CC-2 miR-9 KD |
| Sample type |
SRA |
| |
|
| Source name |
control_hiPSC forebrain NPCs
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: C2
diagnosis: Control
gender: male
repository source fibroblast id: GM03440
cell type: forebrain neural progenitor cells (NPCs)
transfected with: miR-9 LNA probes (miR-9 KD)
|
| Biomaterial provider |
https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM03440
|
| Growth protocol |
hiPSC forebrain NPCs were derived as described previously (Brennand et al., 2011). Forebrain NPCs were maintained at high density, grown on Matrigel-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), and 20 ng/ml FGF2 (Invitrogen)) and split approximately 1:3-1:4 every week with Accutase (Millipore).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the miRNeasy Mini Kit (Qiagen), treated on the column with RNAse-free DNAse Kit (Qiagen) and eluted in water.
RNA libraries were prepared for sequencing using standard Illumina protocols (rRNA depleted (ribozero)).
Hi-Seq, 100nt, Paired-End Read, 8 samples per lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3440#5 NPC#A miR-9 KD
|
| Data processing |
The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 8 samples were run per lane using the standard Truseq indices. Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at geneic level for UCSC annotation build.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristen Brennand |
| E-mail(s) |
kristen.brennand@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Psychiatry
|
| Street address |
1425 Madison Ave, 9-20B
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE80163 |
Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells |
| GSE80170 |
Next Generation Sequencing Compares Effects of microRNA-9 perturbation in control and SZ hiPSC NPCs |
|
| Relations |
| BioSample |
SAMN04633569 |
| SRA |
SRX1693140 |
