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Sample GSM3397326 Query DataSets for GSM3397326
Status Public on Sep 20, 2020
Title Chimp_00818_c5_NPC_Chimp
Sample type SRA
 
Source name NPC
Organism Pan troglodytes
Characteristics individual: 818
Sex: F
sh: none
Treatment protocol No additional treatment was performed
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Chimp_00818_c5
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
 
Submission date Sep 20, 2018
Last update date Sep 20, 2020
Contact name Fred H Gage
E-mail(s) gage@salk.edu
Organization name The Salk Institute for Biological Studies
Street address 10010 N Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL16809
Series (1)
GSE120271 RNA-seq and ChIP-seq for human-specific regulation of neural maturation identified by cross-primate transcriptomics
Relations
BioSample SAMN10098238
SRA SRX4723301

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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