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| Status |
Public on Jul 10, 2024 |
| Title |
nt-hg-2 |
| Sample type |
SRA |
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| Source name |
pancreatic beta cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic beta cell
cell line: EndocbetaH5
cell type: primary
genotype: wild type
treatment: none
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from EndoCβH5 cells using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany), following manufacturer’s recommendations
NextFlex Poly(A) Bead 2.0 (v21.01; PerkinElmer Waltham, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
nt-hg-VS-nti-hg.tsv
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| Data processing |
Raw data from Illumina Novaseq have been demultiplexed using bcl2fastq v2.20.0.422 (Illumina). An adapters trimming step has been executed using trimmomatic version 0.39 (MINLEN:35 AVGQUAL:20). Mapping has been done using STAR version 2.7.3a with hg38 genome. Raw and normalized counting steps were done using RSEM v1.3.1 using a GTF from encode version 39 (hg38), and Ensembl version 105 for genes names annotations. The differential analysis was performed in R version 3.6.3 with DESeq2 v1.24.0.
Assembly: the human genome GRCh38
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes Differential expression for nt-hg-VS-nti-hg
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| Submission date |
Jul 10, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Souhila amanzougarene |
| E-mail(s) |
bioinfo-good@listes.egid.fr
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| Organization name |
CNRS
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| Department |
Nord
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| Lab |
EGID
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| Street address |
1 place de Verdun
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| City |
Lille |
| ZIP/Postal code |
59045 |
| Country |
France |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE271922 |
RNA-seq in EndoCbetaH5 under high glucose, treated or not with naltrindole |
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| Relations |
| BioSample |
SAMN42395684 |
| SRA |
SRX25265387 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8389145_nt-hg-2_Ensembl-105.genes.results.gz |
1.8 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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