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Sample GSM3790265 Query DataSets for GSM3790265
Status Public on Nov 22, 2019
Title Fetal_HeliosKO_IL2iTreg_3
Sample type SRA
 
Source name Fetal spleenocytes
Organism Homo sapiens
Characteristics donorid: F83
genotype: Helios Knockout
age: 22.2 weeks
Sex: Male
Treatment protocol For fetal iTreg cells,CRISPR-Cas9 editing via nucleofection of Cas9 complex with the Helios gRNA1 (HeliosKO) or non-targeting guide (HeliosWT) was carried out prior to Treg differentiation
Growth protocol Treg differentiation - Cells were stimulated with anti-CD3/CD28/CD2 tetratmers (Stemcell) in culture media supplemented with with 10ng/mL IL-2 (Peprotech) in the presence of absence of 50ng/mL TGFb (Peprotech)
Extracted molecule total RNA
Extraction protocol Cells were harvested on Day 6 of culture, and total RNA was extracted from 25,000 cells using the Nucleospin XS RNA kit (Machery Nagel)
Libraries were constructed using a standard Illumina protocol following manufactorer instructions using the NEBNext® Ultra™ II Directional RNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Sequencing batch 1
TMM_normalizedreads_iTregHeliosKOvsWT.txt
Data processing Fastq files were mapped to hg19 with Bowtie 2
Read counts per gene was obtained using RSEM
TMM normalization and differential expression analysis performed using EdgeR package for Bioconductor
Separate comparisons were performed for adult and fetal iTreg cells, and fetal HeliosKO and HeliosWT iTreg cells using generalized linear models
TMM read counts for HeliosKO versus HeliosWT comparisons are normalized for paired samples and batch effects due to two sequencing runs carried out, and are supplied as log2 read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Generalized linear model output with fold change and FDR in text files for both comparisons. TMM normalized read counts for both comparisons in txt files.
 
Submission date May 21, 2019
Last update date Nov 24, 2019
Contact name Melissa Ng
E-mail(s) melissa.ng@ucsf.edu
Organization name University of California, San Francisco
Lab Burt Lab
Street address 35 Medical Centre Way, Regeneration Medicine Building 903B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL20301
Series (2)
GSE110472 Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells.
GSE131589 Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells [RNA-Seq - induced Treg cells].
Relations
BioSample SAMN11810110
SRA SRX5879648

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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