|
| Status |
Public on Jun 12, 2017 |
| Title |
3-D1-Th1_S3_L001_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cell Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 1
t-helper like treg: TH1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS-sorted Th-like Tregs (2x105 per well) were activated with CD3/CD28 beads (ratio 1:4) for 72h. Cells were lysed in Trizol (Thermo Fisher Scientific) and RNA was isolated with Direct-Zol RNA MicroPrep w/Zymo-Spin columns (Cambridge Bioscience). RNA sequencing was performed using The Human Inflammation & Immunity Transcriptome RNA targeted panel (Qiagen). Samples were quantified with Agilent High Sensitivity DNA Kit (Agilent Technologies) and sequenced with Illumina MiSeq using MiSeq Reagent Kit v3 (150-cycle). 100ng of RNA was used to construct libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols provided but with kits procided by Qiagen
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
qiagen analysis pipeline for targeted RNAseq panels was used (http://www.qiagen.com/shop/genes-and-pathways/data-analysis-center-overview-page/?akamai-feo=off0
RNAseq was a targeted panel. Only targeted with primers at some 500 immunology genes.
adaptors trimmed, reads< 55bp droped, first 12bp dropped form every read (as they cointain molecular tags) and ampped using STAR RNA read mapper. Non mapped reads were dropped
bam files were then imported into PARTEk genomics suite for generation of RPKM values
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text file (reubenmcg_RNASeq_results.gene.rpkm) includes RPKM values for each Sample
|
| |
|
| Submission date |
Jun 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Reuben McGregor |
| E-mail(s) |
reubenmcgregor88@gmail.com
|
| Organization name |
Kings College London
|
| Street address |
Great Maze Pond
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE99733 |
Targeted next generation sequencing of 589 genes identifies complementary responses in t-helper-like T regulatory cells |
|
| Relations |
| BioSample |
SAMN07199567 |
| SRA |
SRX2888456 |
