|
| Status |
Public on Jan 21, 2022 |
| Title |
NOTCHWT_TCFKO_3 [Tcf7-Tg-3_S10] |
| Sample type |
SRA |
| |
|
| Source name |
BM LSK (Lin- Sca1+ cKit+)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J; Sv/129
transgene: Tcf7 lox/lox Mx1Cre
cre: Mx1Cre induction 2ug/g b.w. poly(I:C)
facs sorting: Target population from bone marrow: Lin- Sca1+ cKit+
group: NOTCHWT_TCFKO
replicate: 3
batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated from sorted bone marrow LSK and RNA was harvested using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) according to manufacturer’s instructions
We performed cDNA library with the "Illumina TruSeq RNA Library Prep kit"
We then performed a Nextera XT library prep according to Illumina protocol 15031942 Rev. E. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation 4200. We performed a single end 75nt sequencings on NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed. Reads were aligned to mouse genome build mm10 using HISAT2, v2.0.3beta aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR(3.28.0) TMM method and log2 transformed with voom (limma3.42.0).
Batch effect was removed using ComBat (sva3.34.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID.
|
| |
|
| Submission date |
Mar 17, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Nadine Fournier |
| E-mail(s) |
nadine.fournier@sib.swiss
|
| Organization name |
Agora Cancer Research Center & Swiss Institute of Bioinformatics
|
| Lab |
Translational Data Science Facility
|
| Street address |
Agora Cancer Research Center, Bugon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE169116 |
Gene expression profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [RNA-seq] |
| GSE169121 |
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology. |
|
| Relations |
| BioSample |
SAMN18340982 |
| SRA |
SRX10372483 |
