|
| Status |
Public on Aug 31, 2023 |
| Title |
mm_chip_spreb_NIPBL-ATPneg.2 |
| Sample type |
SRA |
| |
|
| Source name |
Small_Pre-B_cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Small_Pre-B_cell
genotype: ATPneg
chip antibody: NIPBL
matched input_for_chip_samples: mm_input_spreb_WT
|
| Treatment protocol |
For ATPneg (ATP depleted) sampleas small pre-B cells were isolated from WT mouse bone marrow and cultured in presence of 126nM of Oligomycin A for 2hrs before performimg ChIP sample preparation
|
| Growth protocol |
No cultured cells were used. All cells used are primary small pre-B cells isolated from bone marrow of WT or BRWD knock out mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from flow-sorted small pre-B cells (2x10^6) from WT and Brwd1-/- mice, and WT small pre-cells treated with Oligomycin A, were used for each ChIP experiment with anti-H3K4me1 (07-436, Millipore-Sigma), anti-H3K27Ac (07-360, Millipore-Sigma), anti-CTCF (Millipore Sigma, 07-729) , anti-RAD21 (Abcam, ab154769), anti-SMC3 (Abcam, ab9263), anti-NIPBL (Proteintech, 18792-1-AP) and anti-WAPL (Proteintech, 16370-1-AP) antibodies.
Libraries were prepered by University of Chicago Core facility using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Primary flow purified small pre-B cells from WT mouse bone marrow treated with ologomycin for 2hrs
|
| Data processing |
Genome alignment and peak calling, for processed files 1 and 2: The sequences were aligned to the mm9 reference genome (National Center for Biotechnology Information build mm9_NCBI_build_37.1) with BWA MEM and PCR duplicates were removed using Picard MarkDuplicates (Version 1.107). Peaks for ChIP-seq samples were called using MACS2. Normalized bedgraph tracks were generated using the SPMR flag and converted to bigwig using the UCSC tool bedGraphToBigWig. Peaks with a score >5 were retained.
For processed files 3 to 6: Quantification steps were carried out separately for each ChIP-seq mark; we did not perform these steps on the ATPneg genotype samples. First, peak calls from replicates in both WT and Brwd1-/- groups were merged using bedtools merge. Peak and input enrichment counts in merged peaks was computed using featureCounts; replicate inputs were combined prior to quantification. Input counts were subtracted from peak counts after adjusting for differences in sequencing depth for each library. Normalized enrichment was computed using edgeR as CPM with TMM normalization factors.
Assembly: mm9
Supplementary files format and content: BED file of peak calls from Macs2 with Q<1e-5
Supplementary files format and content: BigWig file of normalized enrichment from Macs2, normalized with --SPMR (signal per million reads)
Supplementary files format and content: BED file of merged peak calls over all ChIP samples of the same mark, merged using bedtools merge
Supplementary files format and content: Read counts per merged peak for all ChIP samples of the same mark plus input sample(s), quantified using featureCounts. Peak IDs match the coordinates provided in merged bed files (processed data file 3). Input replicates were combined prior to quantification: mm_input_spreb_BRWD1KO is the sum of mm_input_spreb_BRWD1KO.1 and mm_input_spreb_BRWD1KO.2, and mm_input_spreb_WT is the sum of mm_input_spreb_WT.1 and mm_input_spreb_WT.2. mm_input_spreb.2 is the counts from previously-submitted input sample GSM2753125.
Supplementary files format and content: Read counts per merged peaks for all ChIP samples of the same mark, after subtracting input counts from the matched input sample. Input counts were up- or down-sampled stochastically to account for differences in the total number of alignments between input and ChIP samples.
Supplementary files format and content: Normalized counts per merged peak for all ChIP samples of the same mark, units of counts per million and including TMM normalization with edgeR.
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Mark Maienschein-Cline |
| E-mail(s) |
mmaiensc@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Research Resources Center
|
| Lab |
Center for Research Informatics
|
| Street address |
1819 W Polk Ave, Rm 336 M/C 789
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE221518 |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes (ChIP-Seq) |
| GSE221519 |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes |
|
| Relations |
| BioSample |
SAMN32352791 |
| SRA |
SRX18809563 |
