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Sample GSM2402464 Query DataSets for GSM2402464
Status Public on Feb 20, 2018
Title iTreg_NT_48h_rep1
Sample type SRA
Source name Cord blood CD4+ cells 48h after activation and polarization towards iTreg with control siRNA
Organism Homo sapiens
Characteristics tissue: Cord blood
cell type: CD4+ T cell
biological replicate: 1
transfection: control siRNA
time: 48h
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 Exp4D1_iTreg_NT_48h_S59
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
BioSample SAMN06050879
SRA SRX2370304

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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