|
| Status |
Public on Mar 14, 2016 |
| Title |
C2 NPC |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC forebrain NPCs
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Control
gender: male
repository source fibroblast id: GM03440 (Coriell)
|
| Biomaterial provider |
Coriell Cell Repositories 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 either Matrigel-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), 1 μg/ml Laminin (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 |
Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols
Hi-Seq, 100nt, Paired-End Read, 4 samples per lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3440#5 NPC#A
|
| Data processing |
The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 4 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 both the geneic and exonic levels for UCSC and ensemble annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene
|
| |
|
| Submission date |
Dec 01, 2014 |
| 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) |
| GSE63738 |
Next Generation Sequencing Facilitates Comparisons of Control and Schizophrenia-Patient derived hiPSC-derived NPCs |
| GSE80163 |
Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells |
|
| Relations |
| Reanalyzed by |
GSE81474 |
| BioSample |
SAMN03247078 |
| SRA |
SRX791251 |
