|
| Status |
Public on Apr 15, 2024 |
| Title |
E11.5_Ikba_CD31_2 [Cut&Tag] |
| Sample type |
SRA |
| |
|
| Source name |
AGM
|
| Organism |
Mus musculus |
| Characteristics |
developmental time: E11.5
tissue: AGM
cells: CD31+
antibody: rabbit anti IkB-a
ab description: C-21, santa cruz
|
| Treatment protocol |
none
|
| Growth protocol |
Primary E14.5 fetal liver LT-HSCs and AGM CD31+ cells were obstained by disecting fetal liver or AGMs from E14.5 or E11.5 embryos folled by FACS sorting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cut and tag experiments were performed on lightly fixed cell suspension and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with unique index primers and NEBNext HiFi 2x PCR Master mix (cat#M0541S) as decribed in bentop cut and tag v3.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Read length: 75bp
|
| Data processing |
Followed steps for data preprocessing (i) Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap.
(ii) Trimmed reads were aligned to GRCm38 reference genome with Bowtie2 aligner tool (v2.4.4) (Langmead & Salzberg, 2012). Reference genome was retrieved from Ensembl FTP site (http://ftp.ensembl.org/pub/release-102/).
(iii) Bowtie2 was executed with following parameters: --no-mixed –no-discordant –dovetail –very-sensitive-local. Multi-mapped reads and those reads showing MAPQ < 20 were filtered out.
(iv) [Only applicable for H3K27me3 samples] Peak calling was performed with SEACR (v1.3) in stringent mode without considering IgG control sample (Meers et al., 2019). For this purpose, required input bedgraph files were obtained from deduplicated BAM files using bedtools (v2.30) following SEACR authors guidelines (Quinlan & Hall, 2010). The top 0.5% of peaks were retrieved for downstream analysis.
(v) BigWig files were obtained from BAM files with duplicates using deepTools (v3.5.1)
Assembly: mm10
Supplementary files format and content: BigWig files and detected SEACR peaks in .bed files (only applicable for H3K27me3 experiments)
Library strategy: Cut&Tag
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Anna Bigas |
| E-mail(s) |
abigas@imim.es
|
| Phone |
+34933160440
|
| Organization name |
Institut Hospital del Mar d'Investigacions Mèdiques
|
| Department |
Cancer Research
|
| Lab |
Stem Cells and Cancer
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE188524 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development [Cut&Tag] |
| GSE188525 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development |
|
| Relations |
| BioSample |
SAMN40203031 |
| SRA |
SRX23795577 |
