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Sample GSM1467497 Query DataSets for GSM1467497
Status Public on Aug 08, 2014
Title PNFF-ev
Sample type SRA
Source name human PN patient cells
Organism Homo sapiens
Characteristics subject status: poikiloderma with neutropenia (PN) patient
cell type: foreskin fibroblasts from PN patient (PNFF)
genotype/variation: PNFF-ev
Growth protocol Logarithmically growing yeast cells in liquid YES media at 30°C, shaking at 150 rpm; PNFF-derived cells were maintained in DMEM supplemented with 20% fetal bovine serum, non-essential amino acids, penicillin/streptomycin
Extracted molecule total RNA
Extraction protocol Hot phenol RNA dextraction protocol (Schmitt ME, Brown TA & Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 3091–3092); Trizol reagent was used to isolate total RNA from human cells.
10 µg of total RNA was ligated to Thaliana_lig_2 adaptor oligonucleotides (rArGratcggaagagcgtcgtgtagggaaagag-ddT where r denotes ribonucleotides) using Thaliana tRNA ligase. RNA was purified and treated with 20 U of rSAP (Affymetrix) in rSAP buffer (25 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1 mM ATP (NEB)) at 37°C for 1 hour in order to remove 2’ phosphates remained on ligated RNA. RNA was fragmented with RNA fragmentation reagent (Ambion). The fragmented RNA was then reverse transcribed using primers complementary to the ligated RACE adaptor. the obtained cDNA was used to construct sequencing library.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description GQY35
Data processing Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the human or yeast genome using RUM version 2.0.4
A reference collection consisting of RNA features and (for human samples) features from the RepeatMasker database ( was created
Each aligned read was if possible assigned to one of these features with HTSeq-count, using the "union" method to handle read alignments overlapping multiple features
Reads aligning to multiple positions in the genome were defined to contribute "1/N read" to each position
Genome_build: ASM294v1.17 (yeast), hg19 (human)
Supplementary_files_format_and_content: txt files containing the estimated expression level of each quantified feature
Submission date Aug 07, 2014
Last update date May 15, 2019
Contact name Claus M Azzalin
Organization name ETH Zürich
Department Institute of Biochemistry
Street address Otto-Stern-Weg 3
City Zürich
ZIP/Postal code 8093
Country Switzerland
Platform ID GPL16791
Series (2)
GSE60197 Global 3' RACE in yeast and humans
GSE60198 The Mpn1 exonuclease defines a novel spliceosomal snRNA decay pathway dependent on Rrp6 and Lsm2-8 complex
BioSample SAMN02954388
SRA SRX671725

Supplementary file Size Download File type/resource
GSM1467497_GQY35_featurecounts_method1_union.txt.gz 178.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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