|
| Status |
Public on Mar 04, 2010 |
| Title |
N2_A_p1_1 (Illumina) |
| Sample type |
SRA |
| |
|
| Source name |
Neural differentiation; neural progenitors
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: neural progenitors
|
| Growth protocol |
Two neural differentiation strategies were used. In one approach (A) hESC H1 line was differentiated and cultured using feeder-free chemically defined adherent cell culture system through three stages: N1, an initiation stage; N2, a Neural Progenitor Cell (NPC) stage which produces only neurons upon further differentiation; and N3 which produces both neurons and glial cells. In the second approach (B), neural progenitors (N2-B) were generated from undifferentiated H1 hESCs via embryoid body like neurosphere formation. In each case, standard protocols involving bone morphogenic protein (BMP) signaling antagonists (Noggin) and basic fibroblast growth factor (bFGF) were used
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Solexa sequencing: mRNA was fragmented using 10X Fragmentation Buffer (Ambion) and double-stranded cDNA was synthesized using SuperScript II (invitrogen) reverse transcriptase and random primers. DNA sequencing followed the instructions of the mRNA-Sequencing Sample Prep Kit (Illumina). 454 sequencing: Single-stranded cDNA library was synthesized and adapters were ligated (Supporting Information Appendix) and sequenced using the emPCR II Kit (Amplicon A) and on the 454 Genome Sequencer FLX instrument following the manufacturer’s instructions. GS FLX Titanium cDNA Libraries were prepared and sequenced at the 454 Life Sciences Sequencing Centre (Branford, CT).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNA-Seq; polyA selected mRNA
|
| Data processing |
Reads were obtained and aligned to the human reference genome (hg18) using BOWTIE for Illumina single-end reads, ELAND for Illumina paired-end reads, and BLAT for the long 454 reads. Subsequently, the mapped reads were converted into signal track (WIG) files by counting the number of mapped reads at each nucleotide position. The counts were then normalized by the total number of mapped reads per million.
|
| |
|
| Submission date |
Mar 03, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Lukas Habegger |
| E-mail(s) |
lukas.habegger@yale.edu
|
| Organization name |
Yale University
|
| Street address |
266 Whitney Ave
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE20301 |
Dynamic transcriptomes during neural differentiation of human embryonic stem cells |
|
| Relations |
| SRA |
SRX017377 |
| SRA |
SRX017378 |
| SRA |
SRX017379 |
| BioSample |
SAMN00009669 |
