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| Status |
Public on Jun 08, 2017 |
| Title |
S25517_T1D_CD154pos_C36 |
| Sample type |
SRA |
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| Source name |
Islet antigen-reactive CD4+ sorted T-cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Islet antigen-reactive CD4+ sorted T-cells
samplelabel: lib4278
sampleID: S25517
samplename: 1_T1D_CD154+_C36
status: T1D
pid: T1D2
visit: 1
numcellssorted: 8900
libraryid: lib4278
cdnasynthesis: C1+SMARTer v1
libraryprep: C1+NexteraXT
projectid: P91-3
seqsite: BRI
c1plateid: 1771023185
c1capturesite: C36
c1captureannotation: single cell
flowcellid: C4Y0CACXX
runchemistry: TruSeq SBS Kit v3
lane: 6,7
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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 two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) 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: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<1 & MEDIAN_CV_COVERAGE >0.4.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_T1D_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 |
GPL16791 |
| Series (2) |
| GSE96568 |
Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD4+ pooled islet antigen-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 |
SAMN06565489 |
| SRA |
SRX2637195 |
| 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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