|
| Status |
Public on Nov 28, 2023 |
| Title |
Sox4 hepatocytes, replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: Hepatocyte
genotype: Sox4
treatment: AAV8-TBG-HA-Sox4-P2A-Cre injected; harvested 4 days post injection
|
| Treatment protocol |
AAV8-TBG-Cre (EV) or AAV8-TBG-HA-Sox4-P2A-Cre (Sox4) were retro-orbitally injected. 4 days post injection, hepatocytes were harvsted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from sorted cells using a solution of 10 mM Tris-HCl pH 7.4/10 mM NaCl/3 mM MgCl2/0.1% IGEPAL CA-630.
Immediately following isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 30 minutes at 37 °C.
Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded, and PCR amplified for xx cycles using NEBNext High Fidelity 2x PCR master mix (New England Biolabs), and then the libraries were purified with AMPure XP beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
After alignment, 3 bam files were merged into one file, and converted to bigwig files
ATAC_Sox4_3rep_merged_RPGC.bw
|
| Data processing |
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by aligning the sequence tags to mm10 by bowtie2 with default parameters and converting the bam files to bigwig using bamCoverage by RPGC normalization.
Supplementary files format and content: Peak calling was performed using MACS2 with the options ‘--nomodel --extsize 200 --shift -100’.
|
| |
|
| Submission date |
Nov 30, 2022 |
| Last update date |
Nov 28, 2023 |
| Contact name |
Takeshi Katsuda |
| E-mail(s) |
tkatsuda412@gmail.com
|
| Phone |
+1-215-746-5559
|
| Organization name |
University of Pennsylvania
|
| Department |
Perelman School of Medicine
|
| Lab |
Gastroenterology Division
|
| Street address |
421 Curie Blvd, BRB II/III Rm531
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE219052 |
Influence of Sox4 on chromatin accessibility of adult hepatocytes [EV and Sox4] |
| GSE221225 |
Sox4 in adult hepatocytes |
|
| Relations |
| BioSample |
SAMN31942526 |
| SRA |
SRX18428106 |
