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| Status |
Public on Feb 14, 2019 |
| Title |
Bono_01086_c1, NPC, Bonobo (bulk RNA-seq) |
| Sample type |
SRA |
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| Source name |
NPC
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| Organism |
Pan paniscus |
| Characteristics |
sample id: 1086
gender: M
cell type: iPS-derived neural progenitor cells (NPCs)
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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.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total cellular RNA was extracted from ~5x10e6 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
RNA-seq: PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit. scRNA: library was prepared according to the 10X protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Bono_01086_c1
Marchetto_Gage_count.txt
Marchetto_Gage_tpm.txt
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| Data processing |
bulk RNA: trim raw FASTQ files, SolexaQA++
bulk RNA: alignment to hg19, STAR
bulk RNA: alignment to panTro4, STAR
bulk RNA: alignment to gorgor3, STAR
bulk RNA: alignment to rhemac2, STAR
bulk RNA: join all alignments for each sample and sort by read id
bulk RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
bulk RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
bulk RNA: Transform counts to TPM
single-cell RNA: cellranger v2.0.0
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 files report TPMs and counts.
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| Submission date |
Jan 06, 2019 |
| Last update date |
Feb 14, 2019 |
| 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 |
GPL17238 |
| Series (1) |
| GSE124706 |
Species-specific maturation profiles of human, chimpanzee and bonobo neural cells |
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| Relations |
| BioSample |
SAMN10697411 |
| SRA |
SRX5212493 |
| 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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