|
| Status |
Public on Nov 05, 2023 |
| Title |
Input_rep2_9463 |
| Sample type |
SRA |
| |
|
| Source name |
kidney cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney cortex
developmental stage: 2 month
genotype: Mta2flx/flx
|
| Treatment protocol |
Two month old kidneys (2 biological replicates) were harvested and isolated kidney cortex was cross-linked with 2 mM Di (N succinimidyl) glutarate (DSG, Proteo Chem C1104) in PBS for 30 min followed incubation in 1% formaldehyde (Thermo Scientific 28906) for an additional 10 min at room temperature and quenched with 125 mM glycine for 5 min.
|
| Growth protocol |
Mouse kidney growth to 2 months old.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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).
Libraries were made using NEBNext Ultra II Library Kit (E7645) and sequenced on an Illumina Nova Seq at a depth of 100 million paired end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the mm10 mouse genome using the Bowtie2 read aligner.
RPKM noralized Bigwig files were made using Deeptools bamCoverage.
Genome coverage was calculated for ChIP and input samples using Deeptools bamCoverage.
ChIP peaks were called using Macs2 standard peak calling parameters using input samples as control.
Called peaks were assigned to genomic features (promoters, enhancers, introns, or exons) using Bedtools based on peak overlap with a defined feature. Genomic features (active/inactive promoters and predicted enhancers) were defined using published ENCODE (50) datasets for H3K4me3 (ENCSR000CAN), H3K27ac (ENCSR000CDG), H3K4me1 (ENCSR000CAF) and DNase-seq (ENCSR000CNG).
Assembly: mus musculus mm10
Supplementary files format and content: Merged (rep1 and rep2) BigWig files for each antibody (Mta2, Mbd3, Zbtb7a).
Supplementary files format and content: Merged (rep1 and rep2) narrowPeak files for each antibody (except Input).
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Nov 05, 2023 |
| Contact name |
Jeannine M Basta |
| E-mail(s) |
jbasta@wustl.edu
|
| 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 |
GPL24247 |
| Series (2) |
| GSE246693 |
Deletion of NuRD component Mta2 in nephron progenitor cells causes developmentally programmed FSGS [2month.ChIPseq] |
| GSE246695 |
Deletion of NuRD component Mta2 in nephron progenitor cells causes developmentally programmed FSGS |
|
| Relations |
| BioSample |
SAMN38052750 |
| SRA |
SRX22322340 |
