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Sample GSM3633239 Query DataSets for GSM3633239
Status Public on Dec 31, 2021
Title bulk_RNA-seq_PT1_day_16_replicate_2
Sample type SRA
 
Source name forebrain neural progenitors
Organism Pan troglodytes
Characteristics time point: day_16
cell type: iPSC-derived forebrain neural progenitors
Growth protocol iPS cells were differentiated into forebrain neural progenitor cells using the following protocol: The iPSCs were plated at 10.000 cells/cm2 in N2 medium (1:1 DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), 0.2% penicillin/streptomycin (Gibco)) with dual SMAD-inhibition (10 µM SB431542 (Axon), 100 ng/ml noggin (Miltenyi)) as well as ROCK inhibitor (10 µM Y27632) on LN111 coated Nunc delta surface multidishes (1.14 µg/cm2; Biolamina). The media was changed every 2-3 days to N2 medium with SMAD-inhibitors up until day 9 of differentiation when only N2 medium was used. On day 11 the cells were dissociated using StemPro accutase (75 µl/cm2; Gibco) and replated at 800,000 cells/cm2 on LN111-coated Nunc plates in B27 medium (Neurobasal supplemented with 1% B28 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) supplemented with 10 µM ROCK inhibitor, BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2mM; Sigma-Aldrich). The cells were then harvested at day 13, 14, 15, or 16.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted with RNeasy mini kit (Qiagen) for bulk RNA-seq
Libraries for bulk RNA-seq were prepared withTruSeq RNA Library prep kit v2 (Illumina). Single cell libraries were prepared with Chromium Single Cell 3' Library & Gel Bead kit v2 (10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt
pantro6.s2.multi.Gencode27.Exon.sjdb.v2.txt
Data processing bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the genome (GRCh38 and PanTro6) using STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
The Subread package FeatureCounts was used to quantify the reads overlapping Gencode v27 gene annotations. The human Gencode annotation was lifted over to PanTro6 using UCSC LiftOver tool.
single cell fastqs:
I1 Technical: Index read
R1 Technical: 16 bp Barcode and 10bp UMI
R2 Biological
Genome_build: GRCh38 and PanTro6
Supplementary_files_format_and_content: matrix.mat: raw read counts
Supplementary_files_format_and_content: Exon.sjdb.txt: featureCounts
 
Submission date Feb 27, 2019
Last update date Dec 31, 2021
Contact name Johan Jakobsson
Organization name Lund University
Lab Molecular Neurogenetics
Street address Sölvegatan 17, building A11
City Lund
ZIP/Postal code 221 84
Country Sweden
 
Platform ID GPL21121
Series (1)
GSE127253 Post-transcriptional mechanisms distinguish human and chimpanzee forebrain progenitors
Relations
BioSample SAMN11027136
SRA SRX5444594

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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