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SRX1871104: GSM2211640: Chimp PR00818 NPC B; Pan troglodytes; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 26.8M spots, 2.7G bases, 1.7Gb downloads

Submitted by: NCBI (GEO)
Study: Modeling human brain evolution using induced pluripotent stem cells: comparative analysis of neuronal development in humans and chimpanzees
show Abstracthide Abstract
Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain represents an important aspect in analyzing the emergence of cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closest living relatives (Pan troglodytes; the common chimpanzee) can shed the light into changes in neuronal morphology compared to the last common ancestor (LCA), opening possibilities for analyses of the timing of their appearance, and the role of evolutionary mechanisms favoring a particular type of information processing in humans. Here, we use induced pluripotent stem cell (iPSC) technology to model neural progenitor cell migration and early development of cortical pyramidal neurons in humans and chimpanzees. In addition, we provide morphological characterization of the early stages of neuronal development in human and chimpanzee transplanted cells, and examine the role of developmental mechanisms previously proposed for the evolutionary expansions of the human brain on the early development of pyramidal neurons in the two species. The strategy proposed here lay down the basis for further comparative analysis between human and non-human primates and opens new avenues for understanding cognitive capability and neurological disease susceptibility differences between species. Overall design: PolyA RNA-Seq profiling of neural progenitor cells (NPCs) and neurons differentiated from human and chimpanzee iPSCs.
Sample: Chimp PR00818 NPC B
SAMN05284436 • SRS1521599 • All experiments • All runs
Organism: Pan troglodytes
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total cellular RNA was extracted from ~1-5x10^6 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions. For RNA library generation from human and chimpanzee NPCs and eight-week-old neurons, polyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit. NPC-derived sequencing libraries were analyzed on an Illumina HiSeq 2000 sequencer at the UCSD Biomedical Genomics Laboratory (BIOGEM). cDNA libraries were prepared from two human and two chimpanzee NPC lines (two clones each) derived from human WT-33 and ADRC-40 iPSC lines and chimpanzee PR00818 and PR01209 iPSC lines, respectively. Libraries were sequenced using single-end 100 bp reads at a depth of 15-30 million reads per library. Sequencing libraries derived from eight-week-old neurons were analyzed on an Illumina HiSeq 2500 sequencer at the Salk Next Generation Sequencing Core. cDNA libraries were prepared from two human (WT-33 and ADRC-40) and two chimpanzee (PR00818 and PR01209) neurons, one clone each. Libraries were sequenced using paired-end 100 bp reads at a depth of 15-30 million reads per library.
Experiment attributes:
GEO Accession: GSM2211640
Links:
Runs: 1 run, 26.8M spots, 2.7G bases, 1.7Gb
Run# of Spots# of BasesSizePublished
SRR371118226,753,3192.7G1.7Gb2016-08-08

ID:
2671954

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