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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 11, 2020 |
| Title |
RNAseq_45 mir-802fl/fl |
| Sample type |
SRA |
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| Source name |
Enterocytes isolated from upper jejunum
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| Organism |
Mus musculus |
| Characteristics |
strain: B6.SJL-Tg(Vil-cre)997Gum/J * B6.mir802tm1(fl/fl)MS
genotype: Intestinal miR-802 WT
cell type: Upper jejunum enterocytes
age: 18 weeks (adult)
Sex: Female
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from jejunum enterocytes isolated from 18-week-old mice using Trizol (Sigma-Aldrich) followed by column purification using the RNeasy column purification kit (Qiagen), with on-column DNase (Qiagen) digestion for all samples. 1ug of total RNA was used for library preparation.
Illumina TruSeq stranded mRNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Total RNA was extracted from samples. PolyA-enrichment.
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| Data processing |
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
Reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
Reads mapped and quantified with RSEM 1.2.22.
Differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text file with the following columns: 1. Identifier (Ensembl TranscriptID), 2. gene_id (= Ensembl GeneID) , 3. gc (=transcript gc-content), 4. width (= transcriptLength in [nt]), 5. transcriptCout (= raw counts), 6.-7. TPM/FPKM (= normalized counts), 8.-10. Applying PosteriorEstimates to previous count information.
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| Submission date |
Apr 06, 2020 |
| Last update date |
Dec 12, 2020 |
| Contact name |
Algera Goga |
| Organization name |
ETH Zurich
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| Department |
Biology
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| Lab |
Markus Stoffel
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| Street address |
Otto-Sttern-Weg 7
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| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
Zurich 8093 |
| Country |
Switzerland |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE148198 |
MicroRNA-802 regulates the innate immune response through Paneth cell expansion and Wnt signaling |
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| Relations |
| BioSample |
SAMN14546363 |
| SRA |
SRX8068456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4456008_45_female_wt.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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