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Status |
Public on Sep 20, 2020 |
Title |
CM33_2 week neuron_Gorilla |
Sample type |
SRA |
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Source name |
2 week neuron
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Organism |
Gorilla |
Characteristics |
individual: 75 Sex: F sh: none
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Treatment protocol |
No additional treatment was performed
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Growth protocol |
Established iPSC colonies were kept in feeder-free conditions indefinitely and passed using mechanical dissociation. To obtain NPCs from iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with the addition of Noggin. Rosettes were collected after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10 ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were obtained after 1-2 passages with accutase under the same conditions. To obtain neurons, NPCs were cultured in DMEM/F12 plus N2 and B27 with the addition of laminin (1 µg/ml), BDNF (20 ng/ml), GDNF (20 ng/ml) and cyclic AMP (500 µg/ml) for up to 8 weeks.
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions. PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
processed data file: Linker_Marchetto_Gage_count.txt Linker_Marchetto_Gage_tpm.txt CM33_R2
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Data processing |
RNA and ChIP-Seq: trim raw FASTQ files, SolexaQA++ RNA: alignment to hg19, STAR RNA: alignment to panTro4, STAR RNA: alignment to gorgor3, STAR RNA: alignment to rhemac2, STAR RNA: join all alignments for each sample and sort by read id RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species) RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq RNA: Transform counts to TPM ChIP-Seq: Alignment to hg19, bowtie ChIP-Seq: Peak Calling, HOMER Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0) Supplementary_files_format_and_content: tab-delimited text file
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Submission date |
Sep 20, 2018 |
Last update date |
Sep 20, 2020 |
Contact name |
Fred H Gage |
E-mail(s) |
gage@salk.edu
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Organization name |
The Salk Institute for Biological Studies
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Street address |
10010 N Torrey Pines Rd
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platform ID |
GPL25594 |
Series (1) |
GSE120271 |
RNA-seq and ChIP-seq for human-specific regulation of neural maturation identified by cross-primate transcriptomics |
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Relations |
BioSample |
SAMN10098227 |
SRA |
SRX4723322 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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