 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 03, 2017 |
| Title |
hNES-WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
hNES cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPS-derived neural progenitor cells
genotype: WT
|
| Treatment protocol |
Cells were transduced with an MOI 1 and allowed to expand 10days prior to FACS (FACSAria, BD sciences). GFP+ cells were snap frozen before isolation of RNA.
|
| Growth protocol |
AF22 (iPS-derived, hNES) were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 supplement (1x, Thermo Fisher Scientific), B27 (0.05x, Invitrogen) , EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). Cells were grown on NuncTM T25 or T75 flasks pre-coated with Poly L-Ornithine (15µg/ml, Sigma) and Laminin (2mg/ml, Sigma). Cells were passaged every 2-3 days using TryplLETM Express enzyme (Life Technologies) and Defined Trypsin Inhibitor (Life Technologies) and plated at a density of 6x104 per cm2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
miRNeasy Micro Kit (Qiagen)
KAPA stranded RNA-seq with RiboErase kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Processed data in hg38.d10.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt
|
| Data processing |
RNA-seq reads were mapped to the human genome assembly hg38 using STAR aligner v4.1. For mRNA analysis, default parameters were used. For analysis of retrotransposons we used the --outFilterMultimapNmax 1 to only report uniquely mapping reads
ChIP-seq reads were mapped to the human genome assembly hg38 using Bowtie2 with --very-sensitive. All alignments with MAPQ < 10 were discarded.
ChIP-seq peaks were called with MACS2 normalizing against IN. H3K9me3 peaks were called using --broad, TRIM28 peaks were called with default parameters. A cutoff of -q 0.05 was used for both data sets.
mRNA and non-coding RNAs were quantified using the subread package FeatureCounts (--primary) and iGenome NCBI annotation. Retrotransposons were quantified using the RepeatMasker track from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-Seq: Matrix of quantification of non-exonic retroelements using featureCounts.
Supplementary_files_format_and_content: ChIP-Seq: Bed files with called peaks.
|
| |
|
| Submission date |
Jul 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Per Brattas |
| Organization name |
Lund University
|
| Lab |
Clinical Genomics
|
| Street address |
Sölvegatan 17
|
| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE84259 |
TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells |
|
| Relations |
| BioSample |
SAMN05372132 |
| SRA |
SRX1925737 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
