|
| Status |
Public on Mar 21, 2024 |
| Title |
P0 Cited1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Nephron progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Nephron progenitor cells
strain: mixed/CD1
genotype: Cited1
age: P0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated kidneys were digested with 2.5 mg/ml collagenase D at 37 degrees celsius for 20-25 minutes. NPCs were sorted by FACS (Sony SH800S) on the basis of GFP-positivity.
Libraries were prepared using Arima-HiC Kit, low input protocol (Arima Genomics) and Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences). Libraries were pooled into a single sample and sequenced on an Illumina NovaSeq 6000 using 150bp paired-end sequencing.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
BAM files utilized for BAC integration analysis were initially mapped to the mm10 reference genome by bwa (version: 0.7.17-r1188) with parameters “bwa mem -SP5M” and samblaster (v0.1.25) to mark the PCR duplicated reads.
Hi-C library sequencing reads were processed with Juicer (v1.5.7). Only high-quality reads (MAPQ>30 with both ends uniquely mapped and no PCR duplication) were utilized for the analysis.
Assembly: mm10
Supplementary files format and content: .hiC
|
| |
|
| Submission date |
Jan 03, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Alison Jarmas Perl |
| Organization name |
CCHMC
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE222062 |
Genome-wide chromatin conformation capture (Hi-C) of primary murine nephron progenitor cells |
|
| Relations |
| BioSample |
SAMN32542820 |
| SRA |
SRX18913296 |
