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| Status |
Public on Jun 08, 2017 |
| Title |
S13240_413Unstim_C39 |
| Sample type |
SRA |
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| Source name |
T-cell clone BRI4.13
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| Organism |
Homo sapiens |
| Characteristics |
tissue: T-cell clone BRI4.13
samplelabel: lib1108
sampleID: S13240
samplename: 1_413UNST_C39
stim: Unstimulated
numcellssorted: 1000
libraryid: lib1108
cdnasynthesis: C1+SMARTer v1
libraryprep: C1+NexteraXT
projectid: P48
seqsite: BRI
c1plateid: 1772030045
c1capturesite: C39
c1captureannotation: single cell
flowcellid: C24YKACXX
runchemistry: TruSeq SBS Kit v3
lane: 4,8
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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 HiScanSQ |
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| Data processing |
Base-calling was performed using CASAVA v.1.8.2.
Reads were aligned using Omicsoft Sequence Aligner (OSA, v.1.7.3) with OShell (v.6.1.0.2) using default parameters and a gene models index provided for Ensembl version 66.
Read counts per Ensembl gene ID were estimated using htseq-count (v.0.5.4p3).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files 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_clone_single_cell.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 |
GPL15456 |
| Series (2) |
| GSE96562 |
Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of T-cell clone) |
| 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 |
SAMN06565640 |
| SRA |
SRX2636986 |
| 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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