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| Status |
Public on Dec 21, 2018 |
| Title |
LymeDisease Pt24 Visit3 |
| Sample type |
SRA |
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| Source name |
Peripheral Blood Mononuclear Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral Blood Mononuclear Cells
timepoint: 1 month post-treatment
disease group: Lyme disease
treatment response: Responder
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from PBMCs was extracted with Trizol and purified using RNA Clean & Concentrator-5 (Zymo Research) according to the manufacturer’s procedure.
cDNA was tagged with unique-molecular identifier sequences during RT. After a preliminary amplification step (specific for immunoglobulin constant regions), samples were divided into two aliquots and tagged with sequencing adapters in opposing directions (i.e., P5-Gene-P7 and P5-eneG-P7 for each sample), to allow for high quality assembly of UMI contigs. Library was sequenced across two separate HiSeq2500 lanes.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
LD24_V3
Amplicon mixture
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| Data processing |
Matching files from the two HiSeq lanes were concatenated together (e.g., Sample1_Read1_Lane1+Sample1_Read1_Lane2).
Reads were filtered and assembled within UMI groups using MIGEC.
Explanation of the cumulative quality score (CQS) in migec-processed fastq files, and the relationship between CQS and Phred scores is described in the initial migec publication (Shugay et al. 2014, Nature Methods), and further illustrated in Turchaninova et al. 2016, Nature Protocols).
Paired-ends were merged with MITOOLS.
Genome_build: NA
Supplementary_files_format_and_content: *fastq: Fastq files of stitched reads, assembled and collapsed by UMI read group. These processed fastq files represent sequences that were assembled based on unique molecular identifiers (UMIs). The Q scores in these files are calculated based on the number of reads per UMI, as well as the quality of each base in each read.
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| Submission date |
May 01, 2018 |
| Last update date |
Dec 21, 2018 |
| Contact name |
Lisa K Blum |
| E-mail(s) |
lkblum@gmail.com
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| Phone |
805-234-7162
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| Organization name |
Stanford University
|
| Lab |
William H. Robinson
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE113938 |
Heavy chain immunoglobulin sequencing of Lyme disease PBMCs |
| GSE114310 |
Immunoglobulin sequencing of Lyme disease individuals |
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| Relations |
| BioSample |
SAMN09008953 |
| SRA |
SRX4019035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3123912_Lyme_bulk_processed_LD24_V3.fastq.gz |
2.9 Mb |
(ftp)(http) |
FASTQ |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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