|
| Status |
Public on Jun 01, 2014 |
| Title |
HS_1 (HE007) |
| Sample type |
SRA |
| |
|
| Source name |
neuronal aggregates (day 50) derived from induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: 3-dimensional neuronal aggregates that resemble a first trimester telencephalon
sample group: 39C for 24 hrs
|
| Treatment protocol |
For the HS experiment, a group of 49 day old aggregates was placed in an incubator set at 39 degrees C for 24 hours, while control sets of aggregates were maintained at 37 degrees C. The incubator conditions were otherwise unchanged (ambient O2, 5% CO2, 85% humidity).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, total RNA were extracted to produce cDNA using DT-T7 primers. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
We obtained 101-bp mate-paired reads from DNA fragments of with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8). We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18). The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html. Transcript abundances were measured in Transcripts Per Million (TPM), which is calculated by multiplying the estimated fraction of transcripts made up by a given gene by 106.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Dec 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Herb Lachman |
| E-mail(s) |
herb.lachman@einstein.yu.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Psychiatry
|
| Lab |
Behavioral Genetics
|
| Street address |
1300 Morris Park Ave., F103
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE53667 |
Gene expression profiling in an induced pluripotent stem cell model of the developing human telencephalon: effect of heat shock and its potential impact on the development of neuropsychiatric disorders |
|
| Relations |
| BioSample |
SAMN02486493 |
| SRA |
SRX399548 |
