|
| Status |
Public on Feb 14, 2024 |
| Title |
GFPpos_ZG41_22 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: liver
cell type: Macrophage
treatment: Stem cell transplant
|
| Treatment protocol |
Autologous transplantation with barcoded lentivirally-transduced CD34+ HSPCs was performed
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Up to 10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour. The mix was then incubated with proteinase K for 30 minutes at 40°C.
High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over ?? million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
Assembly: RheMac10
Supplementary files format and content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Supplementary files format and content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
|
| |
|
| Submission date |
Oct 26, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Jason Brenchley |
| E-mail(s) |
jbrenchl@niaid.nih.gov
|
| Organization name |
NIAID
|
| Street address |
4 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL27943 |
| Series (2) |
| GSE246348 |
Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques [ATAC-seq] |
| GSE246351 |
Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques |
|
| Relations |
| BioSample |
SAMN37999845 |
| SRA |
SRX22240997 |
