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Sample GSM6176818

Query DataSets for GSM6176818

Status

Public on Aug 30, 2023

Title

M6516, Lymph Nodes, Day 2

Sample type

SRA

Source name

Lymph Nodes

Organism

Macaca mulatta

Characteristics

tissue: Lymph Nodes
time: Day 2
cell type: LNMC
virus: SIVmac251
group: No Rebound
treatment: ART

Extracted molecule

total RNA

Extraction protocol

Cell-associated RNA was collected from PBMCs and tissue biopsied LNMCs two weeks prior to infection as a baseline control, the timepoints that each group of monkeys-initiated ART (6 hours for group I, day 1 for group II, day 2 for group III and day 3 for group IV) and week 24 before ART discontinuation.
Total RNA was extracted from these samples and libraries were prepared for Illumina NextSeq 500 Next-Gen Sequencing Paired-End 75bp (PE75).
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

X20180531_d2_6516_PTL5537.2of3_S4
geo_1511_may19_LN_countMatrix.csv

Data processing

Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis.
Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos).
Trimmed reads were aligned to the Macaca mulatta genome using STAR. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools.
Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Normalized expression counts were used for visualizations purposes using PCA and heatmaps where indicated.
Assembly: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary files format and content: CSV file (read count matrix), geo_1511_may19_PBMC_countMatrix.csv, md5: ce95b4b9ab3f959a82c4097ea956ab5e
Supplementary files format and content: CSV file (read count matrix), geo_1511_may19_LN_countMatrix.csv, md5: 2bec57edf8a2704046e620229a69b8e1

Submission date

May 23, 2022

Last update date

Aug 30, 2023

Contact name

Dan Barouch

Organization name

BIDMC

Department

CVVR

Lab

Barouch Lab