|
| Status |
Public on Jun 16, 2021 |
| Title |
BRA71 |
| Sample type |
SRA |
| |
|
| Source name |
minor salivary glands
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: minor salivary glands
diagnosis: primary Sjogren's syndrome
gender: Female
age: 49
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Minor salivary glands were obtained from study participants and stored in RNAlater (Qiagen) until RNA extraction. Samples were homogenized with a Bullet-Blender (Next Advance) or an Omni TH (Omni International). Total RNA was extracted with an RNeasy Mini kit according to the instructions of the manufacturer (Qiagen). The quality of RNA was measured using a 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ribosomal RNA ratio of 1.7 and an RNA integrity number of ≥ 6.5 were used for the arrays.
The cDNA libraries were produced by the Genomics and Computational Biology Core (GCBC) using the Nextera XT method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PS_10
|
| Data processing |
Samples were run on an Illumina NextSeq500 configured for 37 x 37 PE reads.
FASTQ files were extracted using bcl2fastq, and the FASTQ files were further processed using this SNAKEMAKE_FILE pipeline using the snakemake/3.8 utility in the Biowulf2 cluster.
Quality of the reads was evaluated using the FastQC software. The reads satisfy all critical parameters and are deemed of sufficient quality to proceed with further processing and analysis.
Read mapping against a recent ENCODE human release was performed using the STAR v2.5.2a aligner using the standard mode with mapping parameters derived from the GENCODE project
For read counting we used the quantMode utility of the STAR aligner.
Supplementary_files_format_and_content: The counts are generated during mapping, producing one count file per sample, which are then merged as RAWCOUNTFILE.
Supplementary_files_format_and_content: Normalized counts per gene (CPM, or counts per million reads) in the TMMNORMALIZEDCOUNTS file
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Thomas John Pranzatelli |
| E-mail(s) |
thomas.pranzatelli@nih.gov
|
| Phone |
3013671203
|
| Organization name |
National Institute of Dental and Craniofacial Research
|
| Department |
Molecular Physiology and Therapeutics Branch
|
| Lab |
Chiorini
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE154926 |
Bulk RNA sequencing in minor salivary glands of Brazilian patients with primary Sjögren’s syndrome (SS) and healthy volunteers |
|
| Relations |
| BioSample |
SAMN15608711 |
| SRA |
SRX8801308 |
