|
| Status |
Public on Aug 30, 2021 |
| Title |
DC01 at T1 2 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted tetramer positive CD8+ lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Sorted tetramer positive CD8+ lymphocytes
patientid: DC01
patient.category: DC
time.point: T1
replicate: 2
Sex: F
batch: L376_3
ugps: 20788
pct.mitochondrial.transcripts: 13.9372617047621
align.rate: 0.613236655598502
cd4.count: 1138
cell.count: 5000
alignable.reads: 8487746
total.reads: 13840898
total.align: 55864744
|
| Treatment protocol |
CD8 T cells were enriched by magnetic isolation then stained for peptide-HLA tetramer, anti-CD8 and viability dye and sorted by FACS at 4°C.
|
| Growth protocol |
Cryopreserved PBMCs were thawed and rested overnight in RPMI + 10% FBS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Replicate populations of viable tetramer+ CD8+ T cells were sorted into RLT Plus lysis buffer supplemented with 1% betamercaptoethanol and frozen at -80°C. RNA was extracted using QIAGEN AllPrep kits.
Smartseq2 bulk protocol using oligo-dT primers to amplify cDNA from mRNA, followed by Illumina Nextera XT tagmentation and NextSeq 550 sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
DC Patient DC01 Time Point T1 2
A0173.S0059
|
| Data processing |
Illumina sequencing run was deemultiplexed using bcl2fastq veersion 2.19.1.403.
Reads were then mappeed to the hg38 transcriptome using the RSEM pipeline version 1.3.0 with bowtie aligner version 1.2.2. Read counts were calculated as expected counts, and rounded to integer values for analysis with DESeq2, or used without rounding in edgeR.
Differential expression analysis was performed using DESeq2 version 1.26.0 using a model including the following terms: "~ Patient.Category + Batch + UGPS + Pct.Mitochondrial.Transcripts + Align.Rate + CD4.Count"
Prior to differential expression analysis, genes were filtered to have at least 5 expected counts in at least 10% of samples.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: The expected counts matrix (GEO.EC.gz) includes counts for samples and genes listed by their respective ENSEMBL gene IDs and gene symbols, delimited by an underscore. The GEO.sample_metadata.gz file is complete sample metadata including QC evaluations in tab-separated format. A0173.A110X.T3.REST.PCvSC.dv2.rslt.tsv.gz is the DESeq2 result set as tab-separated values.
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Aug 30, 2021 |
| Contact name |
Jonathan Morris Urbach |
| E-mail(s) |
jurbach@mgh.harvard.edu
|
| Organization name |
Ragon Institute of MGH, MIT and Harvard
|
| Lab |
Walker
|
| Street address |
400 Technology Sq Rm 851
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE168296 |
Functional impairment of HIV-specific CD8+ T cells precedes aborted control of viremia |
|
| Relations |
| BioSample |
SAMN18143466 |
| SRA |
SRX10241294 |
