|
Status |
Public on Feb 14, 2024 |
Title |
ZJ31_GFPpos_2 |
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 |
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 |
SAMN38000509 |
SRA |
SRX22241611 |