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Sample GSM7867553 Query DataSets for GSM7867553
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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