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| Status |
Public on Dec 15, 2021 |
| Title |
1_T1D10_C54_T1D_T1D10 lib15710_CAHY7ANXX_tophat_alignments |
| Sample type |
SRA |
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| Source name |
Islet-reactive CD4+ sorted T-cell
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| Organism |
Homo sapiens |
| Characteristics |
library id: lib15710
study group: T1D
donor: T1D10
age: 30
Sex: female
lib prep method: C1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were captured on a C1 system or plate sorted. C1 capture was done 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). For plate sorting, single cells were sorted into wells of a 96-well plate. Full-length cDNA was prepared using a SMARTer V4 kit with half-volume reactions.
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 NextSeq 500 |
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| Description |
1_T1D10_C54_T1D_T1D10
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| Data processing |
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCh38
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| Submission date |
Aug 26, 2021 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
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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 |
GPL18573 |
| Series (1) |
| GSE182870 |
Germline-like TCR alpha chains dominate shared self-reactive T cell receptors in type 1 diabetes |
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| Relations |
| BioSample |
SAMN21003029 |
| SRA |
SRX11928387 |
| 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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