|
| Status |
Public on May 04, 2020 |
| Title |
AT006 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
phenotype: Classic AT
age: 12
% phenotype criteria: 0.67
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PBMCs were isolated using the Ficoll-Paque Plus Method (GE Healthcare Bio-sciences AB) using a process that maintains the viability and a normalized distribution of B and T lymphocytes to account for relative lymphopenia among AT versus control participants. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
Libraries for RNA sequencing were prepared with the NEBNext Ultra I RNA Library Prep Kit for Illumina with poly(A) mRNA selection and sequenced using 1 x 75 single-end reads on an Illumina NextSeq 500 instrument using a NextSeq 500/550 V2 High Output reagent kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using Illumina RTA2 software.
BCL2FASTQ v2.17.1.14 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the hg38 reference genome using Tophat v.2.1.0, and SeqMonk v1.44.0 was used to generate gene and transcript expression levels.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.44.0.
|
| |
|
| Submission date |
Jan 02, 2020 |
| Last update date |
May 04, 2020 |
| Contact name |
Benjamin D. Singer |
| E-mail(s) |
benjamin-singer@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 E. Superior St., Simpson Querrey 5th floor
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE142842 |
DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq] |
| GSE142844 |
DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype |
|
| Relations |
| BioSample |
SAMN13708880 |
