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Sample GSM8312347 Query DataSets for GSM8312347
Status Public on Jun 20, 2024
Title MDMs monoculture donor 1 replicate 1
Sample type SRA
 
Source name PMBCs
Organism Homo sapiens
Characteristics tissue: PMBCs
cell type: MDMs
Growth protocol MDMS were generated from freshly isolated CD14+ cells by cultiring in high attachment plates RPMI supplemented with human Ab serum for 5 days. Medium was changed for RPMI supplemented with IFNg and LPS for 48h before co-cuclture establishment. Freshly isolated PBMCs were culture for 24h in RPMI supplemented with FBS, GlutaMax and IL-2 before HIV infection with 0.1 MOI.
Extracted molecule total RNA
Extraction protocol Extraction kit: QIAGEN RNeasy mini kit. Protocol according to manufacturer instructions.
Illumina Stranded mRNA Prep, Ligation (https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/illumina-stranded-mrna-prep-data-sheet-m-gl-02143/illumina-stranded-mrna-prep-data-sheet-m-gl-02143.pdf)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq X
 
Data processing The raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.23.4). Reads with length <18nt after trimming were additionally filtered out.
Sequence pseudo alignment of the resulting high-quality reads to the Human reference genome and quantification of gene level expression (gene model definition from GENCODE release 42) was carried out using Kallisto (Version 0.46.1)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited transcript abundances
 
Submission date Jun 06, 2024
Last update date Jun 20, 2024
Contact name Genome Informatics
E-mail(s) fgcz.gi@gmail.com
Organization name ETH ZURICH / University of Zurich
Department Functional Genomics Center Zurich (FGCZ)
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
 
Platform ID GPL34281
Series (1)
GSE269285 Macrophages show unprecedented anti-HIV activity in HIV-infected iHMD-NSG mice
Relations
BioSample SAMN41720254
SRA SRX24828830

Supplementary file Size Download File type/resource
GSM8312347_EM1.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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