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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 25, 2024 |
| Title |
IECs, CD1dKO2 |
| Sample type |
SRA |
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| Source name |
Proximal small intestine
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| Organism |
Mus musculus |
| Characteristics |
tissue: Proximal small intestine
cell type: Epithelial cell
genotype: CD1d1/2 KO
treatment: na
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| Treatment protocol |
na
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| Growth protocol |
na
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (QIAGEN). RNA was then quantified using with Nanodrop and submitted for RNA-sequencing.
Library preparation and whole transcriptome profiling was performed by The Francis Crick Institute Advanced sequencing facility. Sequencing libraries were prepared with 100ng total RNA with RN integrity (RIN) values of more than 7. The KAPA mRNA HyperPrep Kit for Illumina sequencing (Roche) was used to prepare the sequencing libraries following manufacturer’s instructions. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
DEL2304A2
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| Data processing |
Sample quality was assessed with FastQC with MultiQC used to inspect all samples together. Fastq files were trimmed using Cutadapt with a quality threshold of 10
Trimmed sequence reads were mapped to GRCm39 mouse reference genome using Hisat2
QC of alignment was performed with Picard Tools (MarkDuplicates, CollectAligmentSummaryMetrics and CollectRnaSeqMetrics tools) to generate alignment metrics that were then inspected with MultiQC
FeatureCounts program from the subread package was used to aggregate the total read counts for each gene or exon. The raw count data was then imported into R and analysed using DESeq to identify differentially expressed genes (false discovery threshold(FDR) of 0.05) between treatment groups.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample
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| Submission date |
Mar 26, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
Patricia Barral |
| E-mail(s) |
[email protected]
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| Organization name |
King's College London
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| Department |
CIBCI
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| Lab |
Barral lab
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| Street address |
Great Maze Pond
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| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE262532 |
Comparing the transcriptome of small intestinal epithelial cells in CD1d-KO vs WT mice |
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| Relations |
| BioSample |
SAMN40622113 |
| SRA |
SRX24067956 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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