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| Status |
Public on Jun 08, 2017 |
| Title |
S25020_FluTmrposCD8pos_C74 |
| Sample type |
SRA |
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| Source name |
Tmr-positive CD8+ sorted T-cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Tmr-positive CD8+ sorted T-cells
samplelabel: lib4061
sampleID: S25020
samplename: 1_FluTmr+CD8+_C74
libraryid: lib4061
cdnasynthesis: C1+SMARTer v1
libraryprep: C1+NexteraXT
projectid: P85-3
seqsite: BRI
c1plateid: 1771023180
c1capturesite: C74
c1captureannotation: single cell
flowcellid: C4WKJACXX
runchemistry: TruSeq SBS Kit v3
lane: 8,7
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were captured on a C1 system, using a 5-10 um mRNA Seq IFC according to manufacturer’s instructions (Fluidigm, South San Francisco, CA). Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in three steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2; SMARTer adapter sequence trimming with fastq-mcf (FastqMcf tool, v.1.0.0); 3) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: PF_ALIGNED_BASES>3.5e6, MEDIAN_CV_COVERAGE<=2.0 & MEDIAN_CV_COVERAGE >=0.4, PCT_USABLE_BASES>=0.25, log10(MEDIAN_3PRIME_BIAS+1)<=0.4 & log10(MEDIAN_3PRIME_BIAS+1)>=0.1, and >=1 detected in-frame rearranged TCR junction.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_influenza_CD8.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
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| Submission date |
Mar 13, 2017 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
[email protected]
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 9th Ave
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| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE96564 |
Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD8+ influenza-reactive T cells) |
| GSE96569 |
Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes |
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| Relations |
| BioSample |
SAMN06565289 |
| SRA |
SRX2637152 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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