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Sample GSM3011767 Query DataSets for GSM3011767
Status Public on Feb 15, 2019
Title B9: LN2 CD69- RNA-seq
Sample type SRA
 
Source name CD8+ T cells
Organism Homo sapiens
Characteristics passages: FACS purified cells
tissue: mesenteric lymph node
cell type: CD8+ T cells
Extracted molecule total RNA
Extraction protocol RNA-seq: 250 cells per subset were sorted using a FACSAriaII (BD Biosciences) directly into lysis buffer provided with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and snap frozen.
RNA-seq: RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s protocols. Briefly, 3’ SMART-Seq CDS (oligo-dt) Primers were hybridized to the poly(A) tail of all the mRNA and reverse transcribed with the SMARTScribe RT enzyme. cDNA was pre-amplified using SeqAmp DNA polymerase and frozen. Amplified material was purified using Agencourt AMPure XP beads (Beckman) and cDNA quantity was assessed on a Qubit 3.0 (Thermo) and fragment size was evaluated on a 2100 BioAnalyzer (Agilent). The PCR products were next indexed using the Nextera XT DNA Library Prep Kit (Illumina) according to manufacturer’s protocol. Briefly, products were tagmented using the Amplicon tagment mix, containing Tn5 transposase, and indexed using Nextera index 1 (i7) and index 2 (i5) primers. The libraries were again cleaned-up with Agencourt AMPure XP beads, pooled, quantified and sequenced across 75 base pairs (bp) using a paired-end strategy with a 150-cycle high output flow cell on a NextSeq 550 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Data processing RNA-seq: Fastq files from three sequencing runs were concatenated and aligned using STAR 2.5.2a and hg38 to generate a final unique paired mapped read depth ranging from 8 million to 13.6 million reads per sample. The aligned files were normalized using Deseq2.
Genome_build: mm10
 
Submission date Feb 15, 2018
Last update date Nov 14, 2019
Contact name Marcus Buggert
E-mail(s) marcus.buggert@ki.se
Organization name Karolinska Institutet
Department Microbiology
Street address C2:94; Karolinska Universitetssjukhuset Huddinge
City Stockholm
State/province PA
ZIP/Postal code 141 86
Country Sweden
 
Platform ID GPL21697
Series (1)
GSE110684 Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue
Relations
BioSample SAMN08545559
SRA SRX3703072

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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