|
| Status |
Public on Feb 14, 2024 |
| Title |
DBv1_Ctrl_3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: liver
cell type: Macrophage
treatment: none
|
| Treatment protocol |
Autologous transplantation with barcoded lentivirally-transduced CD34+ HSPCs was performed
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from pelleted cells resuspended in Buffer RLT Plus (Qiagen) with 1% BME. RNA was extracted using RNeasy Micro kit (Qiagen).
SMART-Seq® v4 Ultra® Low Input RNA was used for mRNA library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq samples were sequenced as 101bp paired-end libraries on a Novaseq S4. All samples had over 70 million reads.
Reads were trimmed using Cutadapt (v1.18) and aligned to the Mmul_10/RheMac10 reference genome and Gencode (Ensembl release 108) using STAR (v2.7.6a) in 2-pass basic mode. Expression levels were quantified with RSEM (v1.3.3) before being converted into FPKM values.
Assembly: RheMac10
Supplementary files format and content: RSEM_genes_expected_counts.tsv
Supplementary files format and content: RSEM.genes.FPKM.all_samples.txt
|
| |
|
| 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) |
| GSE246350 |
Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques [RNA-seq] |
| GSE246351 |
Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques |
|
| Relations |
| BioSample |
SAMN38000508 |
| SRA |
SRX22241612 |
