|
| Status |
Public on May 01, 2021 |
| Title |
Sample 8_Aiolos_Ikzf3_WT_thymus_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ikzf3+/+_thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Ikzf3+/+
tissue: thymus
cell type: thymocytes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample 1-6: Bone marrow B220+ cells were purified using anti-CD45R coated MACS beads (Miltenyi Biotec) following manufacturer’s instruction. Pre-pro B cell (B220+AA4.1+IgM-CD43+CD24-) and pre-B cell (B220+AA4.1+IgM-CD43-CD24+) were isolated by flow cytometry. Total RNA was extracted by TRIzol reagent (Thermo Fisher Scientific), followed by DNA digestion by RNA Clean & Concentrator-5 (ZYMO RESEARCH), and mRNA was obtained by poly (A) selection with mRNA DIRECT kit (Thermo Fisher Scientific). RNA-seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol.
Sample7-16: Lysates were purified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Sample 1-6: Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)
Sample7-16: Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls were performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq sequences were aligned on mm10 using Hisat2 (version 2.1.0) with default parameters, and read counts were calculated using Htseq (version 0.12.4) using RefGenes as the reference.
ChIP-seq sequences were aligned on mm9 using BWA (Burrows-Wheeler Aligner, version 0.7.17) with default parameters.
Peaks were called using MACS2 (version 2.1.1) with default parameters.
Genome_build: mm10 for RNA-seq and mm9 for ChIP-seq
Supplementary_files_format_and_content: tab-delimited text file include raw read count for each RNA-seq sample. BED6+3 format file for each ChIP-seq sample.
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
May 02, 2021 |
| Contact name |
Motoi Yamashita |
| E-mail(s) |
myamashita.ped@tmd.ac.jp
|
| Organization name |
Tokyo Medical and Dental University
|
| Street address |
1-5-45, Yushima
|
| City |
Bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8519 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE167487 |
A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS |
|
| Relations |
| BioSample |
SAMN18053890 |
| SRA |
SRX10166886 |
