|
| Status |
Public on Feb 01, 2021 |
| Title |
068_S3011a_IFNpos_B |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: systemic lupus erythematosus (SLE)
cell type surface markers: CD19+, TCRa/b-
cell type: B cells
ifn status: IFNpos
patientuid: S3011
patientid: S3011a
visit number: 1
gender: Female
age: 77
race: White
ethnicity: Hispanic/Latino
|
| Treatment protocol |
NA
|
| Growth protocol |
Cell types were isolated from blood samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from sorted cell populations using miRNAeasy Micro kit (Qiagen, USA) and quantified. 3ng of total RNA was used to generate cDNA following the Smart-seq2 protocol. cDNA was purified using AMPure XP beads (0.8x, Beckman Coulter).
Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)
1ng of cDNA from each sample was used to generate a sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). The libraries were pooled and sequenced on a HiSeq2500 (Illumina) to obtain 50-bp single end reads. Both full-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included after each step to eliminate samples with low quality from downstream process. A detailed protocol has been previously published (Rosales et al. 2018).
Libraries were sequenced on a HiSeq2500 Illumina to obtain a minimum of 10 million 50-bp single-end reads (HiSeq SR Cluster Kit v4 cBot, HiSeq SBS Kit v4).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Bulk_Human_RawCounts.txt
Bulk_Human_TPM.txt
|
| Data processing |
Bulk RNA-seq data (FASTQ files) were mapped against the hg38 genome (GRCh38.p7) reference using TopHat (Trapnell et al. 2009); v2.0.9 (--max-multihits 1 --microexon-search --bowtie1) with FastQC (v0.11.2), and Samtools v0.1.19.0 (Li et al. 2009).
Trimmomatic (v0.36) was used to remove adapters (Bolger et al. 2014).
HTSeq-count with -m union -s no -t exon -i gene_name parameters (part of the HTSeq framework, version v0.7.1 (Anders et al. 2015)) was used for calculating read counts.
Genome_build: hg38
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Bulk_Human_TPM.txt contains Transcript per Million normalized counts
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Feb 01, 2021 |
| Contact name |
Ferhat Ay |
| E-mail(s) |
ferhatay@lji.org
|
| Organization name |
La Jolla Institute for Immunology
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE149050 |
Multi-cell type gene co-expression network analysis reveals coordinated interferon response and cross cell-type correlations in systemic lupus erythematosus |
|
| Relations |
| BioSample |
SAMN14655276 |
| SRA |
SRX8150236 |
