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| Status |
Public on Nov 21, 2016 |
| Title |
S13158_666079_hOKT3_R_24mo_WB |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Homo sapiens |
| Characteristics |
samplelabel: lib1566
sampleID: S13158
status: R
itn name: AbATE_666079
area_under_the_curve: 0.959796563
baseline_area_under_the_curve: 0.789331563
auc_percent_of_baseline: 121.5961211
studysiteshort: PNRI
age: 16
gender: Male
treatmentgroup: hOKT3
race: White; American Indian or Alaska Native
trunkbarcode: 928876
siteandparticipantcode: 666079
visitnumber: 42
visitmonth: 24
four_hour_auc_percent_of_baseline: 121.5961211
libraryid: lib1566
libraryprep: TruSeq RNA v2
projectid: P54-1
seqsite: Covance
flowcellid: D1G9TACXX
runchemistry: TruSeq SBS Kit v3
lane: 5
flowcellid: D1G9TACXX
runchemistry: TruSeq SBS Kit v3
lane: 5
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was globin reduced with GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the TruSeq RNA Sample Preparation kit v2 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 2000 |
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| Data processing |
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 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: GRCh37
Supplementary_files_format_and_content: combined_ABATE_raw_counts_after_qc_063016_not_collapsed.txt is a tab-delimited matrix. The first column contains the Ensembl gene ID. 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_after_qc_063016.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 |
GPL11154 |
| Series (2) |
| GSE85531 |
Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (whole blood RNA-seq) |
| 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 |
SAMN05570788 |
| SRA |
SRX2018957 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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