|
| Status |
Public on Sep 08, 2020 |
| Title |
WT CD8+ splenocyte, Rep.1 |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ splenic T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: CD8+ T cells
genotype: WT
Sex: M
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Splenocytes from two pairs of wildtype and two pairs of H1cTKO;Vav-iCre mice were pooled and T cells were isolated by affinity column depletion. 1.7-2.0 x106 CD8+ T cells were further purified by flow cytometry. Cells were subjected to crosslinking at a concentration of 1x106 cells/mL in PBS, 10% FBS, 2% formaldehyde (final concentration) at room temperature for 10 minutes, before the reaction was quenched by adding 2.5M glycine to a final concentration of 0.2M and the cells were pelleted and flash frozen.
Libraries were prepared using the Arima-HiC+ kit (Arima Genomics) according to the manufaturer’s protocol, and subjected to sequencing.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_CD8pos_M_S1_L001
|
| Data processing |
Sequencing and base calling was performed by NYU Center for Health Informatics and Bioinformatics (https://genome.med.nyu.edu). The sequencing libraries were multiplexed and clustered on a flowcell. After clustering, the flowcell were loaded on the Illumina Novaseq 6000 according to manufacturer’s instructions. The samples were sequenced using a 2x51 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq v. 2.17 program. One mis-match was allowed for index sequence identification.
Hi-C reads from separate lines were concatenated and aligned to mm10 and processed with HiC-Pro (v.2.11.3-beta) using default parameters and genomic bin sizes of 25 and 100 kb.
Replicates were pooled to for A/B compartment analysis with CscoreTool (v. 1.1; https://doi.org/10.1093/bioinformatics/btx802). This program was compiled from https://github.com/scoutzxb/CscoreTool, and Cscores of 100 kb bins were calculated from the intrachromosomal contact matrices.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: HiC-Pro-generated contact matrix and associated genome bed file at 25 kb and 100 kb resolution; Cscore bedGraph track at 25 and 100 kb resolution showing A/B chromatin compartments.
|
| |
|
| Submission date |
Jun 10, 2020 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Boris Bartholdy |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cell Biology
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE141187 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction |
| GSE152176 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [Hi-C] |
|
| Relations |
| BioSample |
SAMN15197730 |
| SRA |
SRX8517406 |
