|
| Status |
Public on Jul 13, 2023 |
| Title |
org_fetal_rep2_cage |
| Sample type |
SRA |
| |
|
| Source name |
small intestinal epithelium derived organoids
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestinal epithelium derived organoids
developmental state: E16.5
strain: C57BL/6J
treatment: untreated
|
| Growth protocol |
Fetal spheroids and adult organoids derived from E16.5 fetal epithelial fragments or scraped adult crypts harvested from proximal small intestine using 2mM EDTA were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with 50 ng/ml EGF, 100 ng/ml Noggin, and 500 ng/ml, R-Spondin1, 3 µM CHIR99021 and 10 mM Nicotinamide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from established fetal and adult organoid cultures using Qiagen® RNEasy MicroKit.
CAGE libraries for three biological replicates of fetal spheroids and adult organoids were prepared as previously described (Takahashi et al., 2012, Nat Protoc, doi:10.1038/nprot.2012.005) with an input of 3000 ng of total RNA. After individually preparing CAGE libraries for each sample, three samples with unique barcodes (CTT, GAT, and ACG) were pooled per sequencing lane and 30% Phi-X was spiked-in to each lane. Sequencing was done with Illumina HiSeq2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes
After removal of linker sequences and filtering, the reads were mapped to the mm10 assembly with Bowtie2 and only uniquely mapping reads not mapping to chrM were retained for further analysis.
5’ ends of CAGE tags (CTSSs) supported by only a single read were excluded from the analysis. CTSSs were subsequently Tags Per Million (TPM) normalised (CAGE reads per total mapped reads in library times 106). CTSSs on the same strand within 20bp of each other were merged into tag clusters (TCs) and quantified in all samples (single read CTSSs were included for the quantification). A summit was identified in each TC, defined as the single base-pair position within the TC with highest total TPM coverage across all samples.
Genome_build: mm10
Supplementary_files_format_and_content: CAGE bigwig files where the score represents strand-specific per-base genome coverage normalized to the library size.
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Laura Maarit Pikkupeura |
| Organization name |
University of Copenhagen
|
| Department |
BRIC
|
| Lab |
Jensen lab
|
| Street address |
Ole Maaloes vej 5
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE160449 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I] |
| GSE228519 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation |
|
| Relations |
| BioSample |
SAMN16596955 |
| SRA |
SRX9401590 |
