|
| Status |
Public on Feb 20, 2018 |
| Title |
iTreg_NT_72h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cord blood CD4+ cells 72h after activation and polarization towards iTreg with control siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cord blood
cell type: CD4+ T cell
biological replicate: 2
transfection: control siRNA
time: 72h
|
| Growth protocol |
Human CD4 positive T cells were isolated from cord blood using dynal CD4 positive T cell isolation kit. Control (NT) or HIC1 (HicSi) targeting siRNA transfections were performed with Amaxa nucleofector device. After 24h, resting cells were activated with plate bound anti-CD3 and soluble anti-CD28 in presence of IL2, TGF beta and ATRA for 48/72 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated with RNeasy mini kit (QIAGEN).
Library was prepared following illumina Truseq protocol and were sequenced by HiSeq3000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Exp4D2_iTreg_NT_72h_S65
|
| Data processing |
Paired-end reads were aligned with Tophat (version 2.1.1) and Bowtie2 (version 2.2.5) to human reference genome (hg19) and Gencode transcriptome (v19). Based on calculation for one million reads, we set the mean insert size and standard deviation for each sample separately.
Read counts were determined using HTSeq-count (version 0.6.1) with parameters “--stranded no --order name”
Bioconductor package edgeR was used for differential expression calling. Genes with RPKM <3 in at least two samples in both conditions were filtered out before differential expression calling.
Genome_build: hg19
Supplementary_files_format_and_content: Estimated RPKM values (txt)
|
| |
|
| Submission date |
Nov 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sini Rautio |
| Organization name |
Aalto University
|
| Street address |
Konemiehentie 2
|
| City |
Espoo |
| ZIP/Postal code |
02100 |
| Country |
Finland |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE90468 |
Retinoic Acid Induced Transcriptional Repressor HIC1 is Required for Suppressive Function of Human Induced Regulatory T cells [RNA-Seq 1] |
| GSE90570 |
Transcriptional repressor HIC1 contributes to suppressive function of human induced regulatory T cells |
|
| Relations |
| BioSample |
SAMN06050886 |
| SRA |
SRX2370309 |
