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Status |
Public on Jul 12, 2023 |
Title |
GMP_WT_B_HIC |
Sample type |
SRA |
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Source name |
BM GMPs
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Organism |
Mus musculus |
Characteristics |
isoloation markers: Lin- cKIT+Sca1-CD16/32+CD150- strain: C57BL/6J developmental stage: Adult (4-6 weeks old) tissue: Bone Marrow genotype: Control (Runx1f/f)
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Treatment protocol |
Cells were harvested and were sorted on the same day as harvest
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Extracted molecule |
genomic DNA |
Extraction protocol |
200,000 cells were sorted from BM and Hi-C experiments were performed according to the Arima-Hi-C protocol (A510008). NEBNext Ultra II DNA library Prep kit was used for sequencing library preparation. Briefly, proximally-ligated DNA was fragmented, and an adaptor was added followed by limited-cycle PCR to enrich and add an index to the fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on the NovaSeq 6000.
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Hi-C data was first demultiplexed by Bcl2Fastq v2.20 and then processed using software HiCPro v3.1.0. The ligation sites were obtained by running HiCPro utils script digest_genome.py with option ‘-r ^GATC,G^ANTC’. The reads were aligned to mm10 mouse genome. HiCPro was executed in a sequential mode with modules -s mapping -s proc_hic -s quality_checks for each sample. Valid pairs from different biological replicates were then put into the same folder followed up by running -s merge_persample. The contact matrices were constructed by running -s build_contact_maps and normalized by running -s ice_norm modules. The contact matrix was built in 50-kb resolution for downstream analysis. Hi-C compartments were identified at 50-kb resolution using a “sliding window” strategy. First, the expected matrix was calculated by averaging Hi-C contacts at the same distance. Then, the observed/expected matrix was obtained by summing the observed Hi-C contacts within a window of 500 kb centered at each bin divided by the sum of expected Hi-C contacts in the same window. The observed/expected matrix was then transformed into a Pearson’s correlation matrix. The principal components were then obtained by calculating the covariance matrix of the Pearson’s correlation matrix followed by eigenvector decomposition with the ‘eigen’ function in R. PC1 was used to assign the A and B compartment: regions with positive PC1 values corresponded to the A compartment and negative values corresponded to the B compartment based on their association with gene density. Assembly: mm10 Supplementary files format and content: The iced.matrix files provided are outputs of the ice_norm module of HiCPro and are normalized contacts between any pair of genomic bins Supplementary files format and content: The bed file provided genomic coordinates of each bin of the genome for the iced.matrix files
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Submission date |
Jun 13, 2023 |
Last update date |
Jul 12, 2023 |
Contact name |
Alexandra Zezulin |
E-mail(s) |
Alexandra.zezulin@pennmedicine.upenn.edu
|
Organization name |
University of Pennsylvania
|
Lab |
Speck Lab
|
Street address |
421 Curie Blvd 544 BRB II/III
|
City |
Philadelphia |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE221427 |
Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils. |
GSE234847 |
Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [HI-C] |
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Relations |
BioSample |
SAMN35725409 |
SRA |
SRX20671946 |