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| Status |
Public on Jun 08, 2017 |
| Title |
S19596_413aCD3_bulk_lib2377 |
| 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: lib2377
sampleID: S19596
samplename: HiAff_aCD3_Bulk
status: HiAff_aCD3_Bulk
stim: aCD3
replicate: 3
numcellssorted: 1000
libraryid: lib2377
cdnasynthesis: SMARTer v3
libraryprep: NexteraXT
projectid: P48
seqsite: BRI
flowcellid: C3523ACXX
runchemistry: TruSeq SBS Kit v3
lane: 4,8
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| Extracted molecule |
total RNA |
| Extraction protocol |
Full-length cDNA was prepared from 500-1000 cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v3 according to manufacturer’s instructions (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.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
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_clone_bulk.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) |
| GSE96563 |
Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (bulk 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 |
SAMN06565400 |
| SRA |
SRX2637133 |
| 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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