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| Status |
Public on Dec 06, 2016 |
| Title |
S32812_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C86 |
| Sample type |
SRA |
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| Source name |
CD8+ sorted T-cells
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| Organism |
Homo sapiens |
| Characteristics |
samplelabel: lib9402
sampleID: S32812
status: R
itn name: AbATE_106306
area_under_the_curve: 2.490464688
baseline_area_under_the_curve: 1.541891094
auc_percent_of_baseline: 161.5201422
studysiteshort: UCSF
age: 12
gender: Female
treatmentgroup: hOKT3
race: American Indian or Alaska Native; White
trunkbarcode: 927496
siteandparticipantcode: 106306
visitnumber: 19
visitnumber: 6
four_hour_auc_percent_of_baseline: 161.5201422
sortmarkers: CD8+ CD45R0+ TIGIT- KLRG1-
stim: anti-CD3 anti-CD28 Stimulated
numcellssorted: 750
samplebarcode: 927496-31
libraryid: lib9402
cdnasynthesis: C1+SMARTer v1
libraryprep: C1+NexteraXT
projectid: P54-8
seqsite: BRI
c1plateid: 1771029186
c1capturesite: C86
c1captureannotation: single cell +debris
flowcellid: C81KDANXX
runchemistry: HiSeq SBS Kit v4
lane: 1
flowcellid: C81KDANXX
runchemistry: HiSeq SBS Kit v4
lane: 1
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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) adapter trimming to remove SMARTer adapter sequences (FastqMcf tool, v1.0.0); 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 ht-seq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<2 & MEDIAN_CV_COVERAGE >0.4; PCT_USABLE_BASES>0.35; and at least one in frame TCR CDR3 junction identified by IMGT/HighV-QUEST.
Genome_build: GRCh38
Supplementary_files_format_and_content: AbATE_single_cell_profile_raw_counts.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.
Supplementary_files_format_and_content: metrics_AbATE_single_cell_libs.txt is a tab-delimited matrix. The first column contains library ID, remaining columns include RNA sequencing and alignment metrics.
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| Submission date |
Aug 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott Presnell |
| E-mail(s) |
SPresnell@benaroyaresearch.org
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 Ninth Avenue
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE85527 |
Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (single-cell RNA-seq of sorted CD8+ T-cells) |
| GSE85573 |
Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes |
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| Relations |
| BioSample |
SAMN05570933 |
| SRA |
SRX2018309 |
| 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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