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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 02, 2019 |
| Title |
control rep2 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: CGR8
cell type: embryonic stem cells
transfection: empty ppy-cagg-ires-puro vector
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| Treatment protocol |
mESC are stably transfected with ppy-cagg-ires-puro vector empty or encoding a netrin-1 transgene.
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| Growth protocol |
mESC are grown in serum/LIF conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with Qiagen RNeasy columns.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CGR8 mESC transfected with an empty ppy-cagg-ires-puro vector.
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| Data processing |
Software: All analyses were performed using FastQC version 0.11.5 and fastq_screen version 0.9.5, STAR version 2.5.2b, R version 3.3.2 (2016-10-31), x86_64-apple-darwin13.4.0, Base packages: base, datasets, graphics, grDevices, grid, methods, parallel, stats, stats4, utils,
Read quality: Quality of raw reads was assessed using the FastQC quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Estimation of Contamination: Sample contamination was assessed using the fastq_screen quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen). Bowtie2 indexes for Mus musculus (mm10) and Homo sapiens (GRCh38) were downloaded from the bowtie website.
Mapping and Summarization: The “primary assembly” Mus musculus genome sequence (release GRCm38.p5) and transcriptome annotations (Ensembl release 87) were downloaded from the GENCODE website (files GRCm38.primary_assembly.genome.fa and gencode.vM12.primary_assembly.annotation.gtf, respectively). Raw read data (fastq files) were mapped to these sequences using STAR (with parameters --outFilterType BySJout, --outSAMtype BAM Unsorted, and --quantMode GeneCounts). This last parameter allows direct conversion of the mappings into gene counts.
Normalization: For the quality control representations, the effective library sizes were first computed using function estimateSizeFactors from package DESeq2. The raw count values were then transformed using a variance stabilizing transformation (function varianceStabilizingTransformation from package DESeq2 with parameter blind=TRUE).
Gene filtering: Genes that did not have more than one count per million counts in at least 2 samples were filtered out. Genes were also filtered if their Ensembl description was either empty, “predicted gene”, “predicted pseudogene” or a “RIKEN”.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts_raw.txt: Tab-delimited text file includes raw counts for each sample.
Supplementary_files_format_and_content: counts_normalized.txt : Tab-delimited text file includes normalized counts for the samples.
Supplementary_files_format_and_content: model_fc.txt: Tab-delimited text file includes FC, p-value and adjusted p-value.
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| Submission date |
Jun 25, 2018 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Fabrice Lavial |
| Organization name |
CRCL
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| Street address |
28 rue Laennec
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| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE102826 |
Netrin-1 signalling function in mouse pluripotent stem cells [RNA-seq] |
| GSE102831 |
Netrin-1 signalling function in mouse pluripotent stem cells |
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| Relations |
| BioSample |
SAMN09479730 |
| SRA |
SRX4292369 |
| 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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