 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2022 |
| Title |
DKO BR1 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell subset: CD4+HSAlowTCRb+
genotype: Tet2-/-Tet3flx/flxCD4cre
treatment: bisulfite conversion
|
| Treatment protocol |
Mice were euthanized by CO2 asphyxiation and thymi were isolated and dissociated to acquire single-cell suspensions. Total thymocytes were depleted of CD24hi cells by staining with biotinylated mouse anti-CD24 (clone:M1/69) purchased from Biolegend. Unwanted cells were depleted by binding to mouse streptavidin magnetic beads (anti-mouse Rapidspheres, cat no 19860, Stemcell Technologies) according to the manufacturer’s instructions. Enriched cells were stained with viability dye (eBioscience) to distinguish live cells from. Cells were stained with aGalactosyl-Ceramide loaded tetramer (conjugated with PE, obtained from NIH tetramer core), TCRb (clone:H57-597) conjugated with PERCP/Cy5.5 (Biolegend), anti-mouse CD4 AF488 (clone:RM4-5), CD8 (clone:53-6.7) conjugated with Brilliant Violet 650 or APC. For the thymic differentiation related studies, live CD4+, CD8-, TCRb+, tetramer - cells were sorted and used in downstream applications. The purity of the samples after sorting was >98%.
|
| Growth protocol |
All mice were bred and maintained under specific pathogen-free conditions at University of North Carolina (UNC) Genetic Medicine building, in a facility managed by the Division of Comparative Medicine at UNC Chapel Hill. The experimental procedures were approved by the UNC Institutional Animal Care and Use Committee.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using Purelink genomic DNA mini kit (invitrogen). DNA was isolated following the manufacturer's instructions and was eluted in 50 ul molecular biology grade water.
A minimum of 1.1 ug of DNA was provided to Biodynami (Huntsville, Alabama) for bisulfite conversion, capture of the murine Zbtb7b locus and upstream region, library preparation and next generation sequencing. Biodynami NGS DNA library prep kit (cat no 30023) was used and methylated adapters were utilized. Bisulfite conversion of genomic DNA was performed with the epitect Bisulfite kit (Qiagen, catalogue number 59104). For the capture of the mm10 chromosome 3: 89,373,714-89,397,292 a Biodynami Custom Capture kit was developed and used.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: CATCH-seq
Adapter trimming and quality filtering of the sequencing libraries was done using trim galore (0.6.2) (--paired).
The sequencing libraries were mapped against mm10 using Bismark (0.22.3). The mapping was done using the Bowtie 2 (2.4.1) backend in the paired-end mode with the following parameter values: --non_directional.
The counts of converted and unconverted cytosines in CpG context were extracted using bismark_methylation_extractor (--bedGraph --counts)
Genome_build: mm10
Supplementary_files_format_and_content: Coverage tracks produced by bismark_methylation_extractor.
|
| |
|
| Submission date |
Dec 06, 2021 |
| Last update date |
Jul 15, 2022 |
| Contact name |
Tarmo Äijö |
| Organization name |
Flatiron Institute
|
| Department |
Center for Computational Biology
|
| Street address |
162 5th Avenue
|
| City |
New York |
| ZIP/Postal code |
10010 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE190227 |
TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner [CATCH-SEQ] |
| GSE206450 |
TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner. |
|
| Relations |
| BioSample |
SAMN23673933 |
| SRA |
SRX13323447 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5718471_SE7362_SA102069_S5_L004_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz |
179.3 Kb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
