|
| Status |
Public on Jan 15, 2022 |
| Title |
Generation of Hematopoietic TF-rDNA Atlas in Human and Mouse |
| Sample organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences.
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Data processing steps:
FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000
Read density across the rDNA sequence was extracted using igvtools
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|
| |
|
| Overall design |
Identification of robust, high-confidence rDNA occupancy of numerous hematopoietic TFs and TF families at canonical TF motif sequences
|
| |
|
| Contributor(s) |
Paralkar VR, George SS |
| Citation(s) |
36113481 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM138035 |
Regulation of rRNA transcription in mammalian tissues |
UNIVERSITY OF PENNSYLVANIA |
Vikram R. Paralkar |
|
| |
| Submission date |
Dec 20, 2021 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Vikram R Paralkar |
| E-mail(s) |
vikram.paralkar@pennmedicine.upenn.edu
|
| Phone |
215-573-9252
|
| Organization name |
University of Pennsylvania Perelman School of Medicine
|
| Department |
Division of Hematology and Oncology, Department of Medicine
|
| Lab |
Paralkar Lab
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| This SubSeries is part of SuperSeries: |
| GSE193651 |
Hematopoietic Transcription Factors Bind rDNA and Regulate rRNA Transcription |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSE191272_SnapGene_Annotation_File__Human_rDNA_with_TF_Peaks_and_motifs.dna.gz |
132.2 Kb |
(ftp)(http) |
DNA |
| GSE191272_SnapGene_Annotation_File__Mouse_rDNA_with_TF_Peaks_and_motifs.dna.gz |
130.2 Kb |
(ftp)(http) |
DNA |
| GSE191272_Track_Images__Human_First_Tier_Factors.zip |
25.6 Mb |
(ftp)(http) |
ZIP |
| GSE191272_Track_Images__Human_IgG.zip |
1.5 Mb |
(ftp)(http) |
ZIP |
| GSE191272_Track_Images__Human_Second_Tier_Factors.zip |
12.6 Mb |
(ftp)(http) |
ZIP |
| GSE191272_Track_Images__Mouse_First_Tier_Factors.zip |
31.2 Mb |
(ftp)(http) |
ZIP |
| GSE191272_Track_Images__Mouse_IgG.zip |
1.6 Mb |
(ftp)(http) |
ZIP |
| GSE191272_Track_Images__Mouse_Second_Tier_Factors.zip |
19.7 Mb |
(ftp)(http) |
ZIP |
| GSE191272_rDNA_Atlas_Mapping_Signal_All_Human_Tracks.xlsx |
470.1 Mb |
(ftp)(http) |
XLSX |
| GSE191272_rDNA_Atlas_Mapping_Signal_All_Mouse_Tracks.xlsx |
342.2 Mb |
(ftp)(http) |
XLSX |
| Processed data are available on Series record |
