|
| Status |
Public on Apr 20, 2022 |
| Title |
IgG_miR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN |
| Sample type |
SRA |
| |
|
| Source name |
fetal liver cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Doxycycline 1μg/mL for 48h
strain: B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J
developmental stage: day E12.5-13.5 p.c.
transgene1: sgGata1
transgene2: miR-125b
transgene3: Arid3a-FLAG (doxycycline inducible)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed CUT&RUN as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018). On day 2 post-induction, 0.2 million cells were sorted and incubated with the following antibodies: rabbit anti-DRIL-1 (abcam), rabbit anti-GATA1 (Abcam), rabbit anti-SMAD2 and anti-SMAD3 (Cell Signalling) and rabbit anti-IgG (Diagenode). pAG/MNase nuclease (Addgene 123461) was produced and purified as previously described, after removal of the HA tag.
Illumina libraries were constructed from the cleaved DNA as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018), and sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CnR_15_EKDL210002156-1a_H57Y5DSX2
|
| Data processing |
library strategy: CUT&RUN
Raw reads were processed using Trimmomatic v0.39 to remove adapter sequences. Parameters: -phred33 ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25.
Kseq (Zhu et al., Genome Biol 2019) was to trim reads containing ≤6 bp of adapter sequence, which are not effectively handled by Trimmomatic.
Trimmed reads were aligned to murine reference genome mm10 using bowtie v2.3.5.1
Aligned reads were sorted and indexed using Samtools v1.3.1.
Normalized bigWig files were generated using bamCoverage from deepTools v3.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw pileups as bigWig tracks for each sample
|
| |
|
| Submission date |
Aug 06, 2021 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Jan-Henning Klusmann |
| E-mail(s) |
jan-henning.klusmann@kgu.de
|
| Organization name |
Goehte University Frankfurt
|
| Department |
Pediatric Hematology and Oncology
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE181568 |
The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis [CUT&RUN] |
| GSE181570 |
The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis. |
|
| Relations |
| BioSample |
SAMN20601284 |
| SRA |
SRX11661814 |
