|
| Status |
Public on Jun 26, 2018 |
| Title |
AI02 Setd1b HOM (FD/FD; RC/+) |
| Sample type |
SRA |
| |
|
| Source name |
Setd1b HOM (FD/FD; RC/+)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
cell type: Hematopoietic Stem and Progenitor cell (HSPC - LSK compartment)
age: 16 weeks
Sex: male
genotype: Setd1b HOM (FD/FD; RC/+)
treatment: Tamoxifen
|
| Treatment protocol |
Mice were treated with 4.5 mg tamoxifen per mouse per day by gavage (4 days gavage - 3 days pause - 2 days gavage) and sacrificed 3 days after the last treatment. Bone marow cells were isolated, lineage-depleted and the LSK (Lin-, Sca+, Kit+) compartment was stained with fluorescently-labeled antibodies. On a FACSAria III cytometer the LSK compartment (on average 25 x 10^3 cells) was collected and stored at -80°C until further processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Eluted RNA was reverse-transcribed and amplified using the SMARTer Stranded Total RNA-seq Kit – Pico Input Mammalian (Takara) following manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AI02
|
| Data processing |
[basecalling] Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
[alignment] Reads were aligned to the mouse genome assembly (mm10) using GSNAP (2015-12-31; parameters: -d mm10 --gunzip –use-sarray=1 -B 5 -t 8 -N 1 -s EnsemblGene-81.ss.mm10.iit -n 1 -A sam) with known splice sites from Ensembl (v81) as support.
[read counting] Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.0; parameters: -a EnsemblGene-81.mm10.TR.gtf -s 1 -o featureCounts.mm10.e81.csv -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (featureCounts.mm10.e81.csv.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Strand, Gene Length, then all sample counts; comments start with '#'
|
| |
|
| Submission date |
Apr 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Konstantinos Anastassiadis |
| E-mail(s) |
konstantinos.anastassiadis@tu-dresden.de
|
| Phone |
+49 351 46340127
|
| Organization name |
Technische Universitaet Dresden
|
| Department |
Biotechnology Center
|
| Lab |
Stem Cell Engineering
|
| Street address |
Tatzberg 47
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE97976 |
Expression profile of hematopoietic stem and progenitor cells (HSPCs) after conditional deletion of the histone 3 lysine 4 (H3K4) methyltransferase Setd1b in mice |
|
| Relations |
| BioSample |
SAMN06766404 |
| SRA |
SRX2745956 |
