|
| Status |
Public on Feb 19, 2022 |
| Title |
Input rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
developmental stage: E16.5
genotype: wildtype
chip antibody: none
chip antibody vendor/cagalog number: none
|
| Treatment protocol |
E16.5 kidneys were isolated in PBS + Ca and Mg on ice and crosslinked, washed, and homogenized in lysis buffer.
|
| Growth protocol |
In utero mouse kidney growth to E16.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
E16.5 kidney chromatin was extracted from isolated nuclei and sheared to 100-1000bp. Primary antibody was incubated overnight for ChIP reactions. Crosslinks were reversed by adding NaCl and heating at 65 °C for 15 h, RNase A was added and incubated for 2 h at 37 °C, and Proteinase K added and incubated 2 h at 63 °C. DNA was isolated using the MinElute PCR Purification Kit (Qiagen 28004). 2 ng DNA was sheared to 100–300 bp.
Libraries were constructed using the Ion Plus Fragment Library Kit (Thermofisher Scientific 4471269) according to (Dorsett and Misulovin, Methods Mol Biol. 2017; 1515:125-139).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Reads were aligned to the mm10 mouse genome using the TMAP aligner map4 algorithm without soft clipping (-g 3 option).
Genome at each base pair for Input and each ChIP sample was calculated using BEDtools genomecoveragebed (-d option).
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Dorsett and Misulovin, Methods Mol Biol. 2017; 1515:125-139. Coverage in each window was normalized to total genome coverage prior to normalization to Input.
ChIP enrichment was averaged for all replicates to generate final processed data files.
Final sgr files were converted to BigWig files using the UCSC bedGraphToBigWig utility.
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: BigWig files for each antibody (Brg1, Sall1, H3K4me1, H3K27ac, and RNAPol2S2) of enrichment over Input.
|
| |
|
| Submission date |
Feb 18, 2022 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Jeannine M Basta |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Internal Medicine/Nephrology
|
| Lab |
Rauchman
|
| Street address |
660 S Euclid Ave, MSC 8126-0012-08
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE196995 |
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation [ChIP-seq] |
| GSE196997 |
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation |
|
| Relations |
| BioSample |
SAMN26082963 |
| SRA |
SRX14222480 |
