|
| Status |
Public on Jul 01, 2016 |
| Title |
1_oWT_10dBNF_2 |
| Sample type |
SRA |
| |
|
| Source name |
oWT_10dBNF_small intestinal organoids
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVB
genotype/variation: WT
treated with: beta-naphthoflavone for 10 days
tissue/cell type: small intestinal organoids
run id: Run 385
|
| Treatment protocol |
Organoids were grown from either isolated AhCre or AhCre;Eedf/f crypts and treated with bNF for 10 days, after which the organoids were removed from Matrigel with ice-cold medium, washed, and lysed in TRIzol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from samples using TRIzol and further purified using the Qiagen MinElute Cleanup Kit.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2941_6_AhCre-bNF_2__A_GCCAATA
|
| Data processing |
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 0.12.9/1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Prior to analysis the provided processed data files were only normalized for sequencing depth, using the DESeq2 package, and normalized for batch effects (ex: sequencing run) if necessary using ComBat, as described in the paper.
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples; format: 2 tab-separated text files corresponding to the two sequencing runs, 385 and 440
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martijn Koppens |
| E-mail(s) |
[email protected]
|
| Organization name |
NKI-AVL
|
| Department |
Molecular Genetics
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE81576 |
Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [RNA-seq] |
| GSE81578 |
Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts |
|
| Relations |
| BioSample |
SAMN05007709 |
| SRA |
SRX1771675 |
