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Sample GSM3123890 Query DataSets for GSM3123890
Status Public on Dec 21, 2018
Title LymeDisease Pt18 Visit7
Sample type SRA
 
Source name Peripheral Blood Mononuclear Cells
Organism Homo sapiens
Characteristics cell type: Peripheral Blood Mononuclear Cells
timepoint: 2 years post-treatment
disease group: Lyme disease
treatment response: Responder
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.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description LD18_V7
Amplicon mixture
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.
 
Submission date May 01, 2018
Last update date Dec 21, 2018
Contact name Lisa K Blum
E-mail(s) lkblum@gmail.com
Phone 805-234-7162
Organization name Stanford University
Lab William H. Robinson
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (2)
GSE113938 Heavy chain immunoglobulin sequencing of Lyme disease PBMCs
GSE114310 Immunoglobulin sequencing of Lyme disease individuals
Relations
BioSample SAMN09008894
SRA SRX4019013

Supplementary file Size Download File type/resource
GSM3123890_Lyme_bulk_processed_LD18_V7.fastq.gz 1.2 Mb (ftp)(http) FASTQ
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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