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Sample GSM2123705 Query DataSets for GSM2123705
Status Public on May 27, 2016
Title LEUTX rep 3
Sample type SRA
 
Source name HDF-a_LEUTX
Organism Homo sapiens
Characteristics cell type: Human Adult Dermal Fibroblasts (HDF-a)
transfected with: LEUTX
Biomaterial provider sciencell (#2320)
Growth protocol All cells were grown at 37oC in a 5% CO2 humidified incubator on poly-l-lysine coated plastic in Fibroblast Medium (Sciencell #2301)
Extracted molecule total RNA
Extraction protocol RNA was extracted using a RNeasy Mini Kit following the manufactures instructions with the addition of an on-column DNAse treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq; each library split across two lanes HiSeq4000, 15 half-libraries per lane
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Libraries for all samples were combined in a 15 samples multiplex which were then split across two lanes.
Data processing Reads for each sample were combined and aligned to the reference hg38 genome using the STAR genome aligner with default commands with the addition of --outFilterMultimapNmax 15 --outSAMstrandField intronMotif
Raw read counts for refseq annotated genes were generated using featurecounts using gene annotations from GRCh38.p2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including default output from featurecounts
 
Submission date Apr 14, 2016
Last update date May 15, 2019
Contact name Thomas Dunwell
Organization name University of Oxford
Department Zoology
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3PS
Country United Kingdom
 
Platform ID GPL20301
Series (1)
GSE80282 Evolutionary origin and functional divergence of stem cell homeobox genes in eutherian mammals
Relations
BioSample SAMN04859256
SRA SRX1704925

Supplementary file Size Download File type/resource
GSM2123705_Aligned_LE_3_counts.txt.gz 2.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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