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Sample GSM5577292 Query DataSets for GSM5577292
Status Public on Feb 04, 2022
Title CA1 cNESCs P22/D10 6F-2F rep1
Sample type SRA
Source name CA1 hESCs-derived cNESCs
Organism Homo sapiens
Characteristics cell type: cNESCs
growth conditions: Differentiated from hESCs grown in normal growth conditions
treatment: Grown 10 days in 4F medium
Treatment protocol H1JA and CA1 cNESCs were cultured 10 days in either 6F medium (NES supplemented with 6F) or in 4F medium (NES supplemented with only 10ng/ml FGF2, 3μM CHIR99021, 1μM SB431542, 100nM LDN193189)
Growth protocol H1 and CA1 human pluripotent stem cells (hPSCs) were routinely cultured on mitomycin C treated mouse embryonic fibroblast feeder cells in KSR media with 10ng/ml FGF2. KSR media contains 80% DMEM-F12 (GIBCO), 20% Knockout serum replacement (GIBCO), 0.1mM 2-mercaptoethanol, 2mM Glutamax, 0.1mM Non-essential amino acids. Prior to neural differentiation hPSCs were transferred to geltrex (GIBCO) coated surface in the absence of feeders and were cultured in mTESR2 (Stem cell technologies) media. On the day of neural induction, hPSCs were replated on geltrex coated surface in N2B27 media supplemented with 10µM SB431542 and 100nM LDN193189 and 10µM Y27632. Neural cultures were detached from Geltrex first on day 8-10 with Accutase or PBS-EDTA, and replated on laminin (Sigma) coated surface, in neural maintenance media (NES) supplemented with 10µM Y27632 at 3x105 cells per cm2 and 6F : 10ng/ml FGF2, 3μM CHIR99021, 1μM SB431542 (Peprotech), 100nM LDN193189, 100nM K02288 (Selleckchem), 100nM AKTiVIII, 75nM MK2206 (Selleckchem), and 1 μM XAV939 (Selleckchem). NES media contains 50% DMEM-F12, 50% Neurobasal, 0.1mM 2mercaptoethanol, 2mM Glutamax, 1x N2 supplement, 0.05x B27 minus vitamin A supplement (GIBCO).
Extracted molecule polyA RNA
Extraction protocol Cell lysates were homogenized in QIAshredder columns (QIAGEN #79654) and total RNA was extracted with Rneasy mini columns (QIAGEN). RNA was DNase treated using TURBO DNase (ThermoFisher Scientific #AM2238). RNA quality was verified on a 2100 Bioanalyzer (Agilent Technologies) and polyadenylated RNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB # E7490L)
Libraries were generated using 100 ng of poly(A)+ RNA and Oxford Nanopore Technologies’ Direct cDNA Sequencing Kit (ONT SQK-DCS109), with each sample barcoded with the Native Barcoding Expansion kits (ONT EXP-NBD104 and ONT EXP-NBD114), according to the manufacturer’s specifications. Barcoded samples were pooled, loaded on a MinION sequencer on R9 Flow Cells (ONT FLO-MIN106D), and sequenced using the MinKNOW software v19.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MinION
Data processing Raw fast5 files were basecalled using Guppy v.4.2.2 with the guppy_basecaller command and the dna_r9.4.1_450bps_fast.cfg configuration file and default settings. Output fast5 files were generated with the --fast5_out argument.
Barcodes were detected and reads were demultiplexed with the guppy_barcoder using the default settings.
The resulting FASTQ reads were aligned to the GRCh38 human reference with Minimap2 using the following parameters: -aLx splice --cs=long.
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode.
EdgeR R-package (v3.12.1) was then used to normalize the data, calculate RNA abundance (as counts per million reads (CPM), and perform statistical analysis. Briefly, a common biological coefficient of variation (BCV) and dispersion (variance) were estimated based on a negative binomial distribution model. This estimated dispersion value was incorporated into the final EdgeR analysis for differential gene expression, and the generalized linear model (GLM) likelihood ratio test was used for statistics, as described in EdgeR user guide. Differential gene expression was established as genes with a fold change ≥ 1.5, p-value ≤0.05 and FDR ≤0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Varga_et_al_lrRNAseq_DE_CPM.txt contains CPM values for each samples obtained from EdgeR, as well as differential expression comparisons for each sets of replicates. EdgeR output contains the log2(Fold Change of expression between samples), log2(CPM), as well as the Likelihood ratio (LR), P-values and False discovery rates (FDR). For more information, please refer to the EdgeR package manual.
Submission date Sep 14, 2021
Last update date Feb 04, 2022
Contact name Samer M.I. Hussein
Organization name CHU de Québec - Université Laval
Department Departement of medecine
Lab Hussein Lab
Street address 9 rue Mcmahon
City Quebec City
State/province Quebec
ZIP/Postal code G1R 3S3
Country Canada
Platform ID GPL24106
Series (1)
GSE184081 Signal requirement for cortical potential of transplantable human neuroepithelial stem cells
BioSample SAMN21424538
SRA SRX12177281

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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