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Sample GSM2064469 Query DataSets for GSM2064469
Status Public on May 31, 2017
Title Control RNAi batch 5
Sample type SRA
 
Source name luci_1
Organism Homo sapiens
Characteristics cell line: HeLa Kyoto cells
treatment: control siRNA
experimental batch: 5
Treatment protocol 2 x 10^5 HeLa Kyoto cells were seeded into 6-well plates 24 h prior to transfection to reach a confluence of 30 – 40%. Small interfering RNA (siRNA) stock solutions (100 µmol in 1xUniversal Buffer) were diluted 1:5 in sterile water. 4 µl Oligofectamine transfection reagent was diluted in 11 µl Opti-MEM and incubated at RT for 5 min. Meanwhile, 10 µl of siRNA dilution was mixed with 175 µl Opti-MEM. 15 µl transfection reagent dilution was added and incubated for 20 min at RT. Cells were washed twice with sterile PBS, growth medium replaced by 800 µl DMEM not containing FCS or antibiotics and the transfection mix added drop wise. After 4 h at 37°C in the incubator 500 µl DMEM supplemented with 30% FCS was added. Cells were harvested and analyzed 2 to 3 days after transfection.
Growth protocol HeLa Kyoto cells were grown in DMEM medium (PPA), supplemented with 10% FCS (Sigma-Aldrich) and 1% penicillin / streptomycin (PAA) at 37°C and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA from HeLaK cells subjected to PWWP2A siRNAs and control siRNAs was isolated utilizing the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. The quality of the RNA (amount and integrity) was assessed using the BioAnalyzer and a RNA 6000 pico kit (Agilent). mRNA isolation, fragmentation, first and second strand cDNA synthesis and end repair were carried out using the NEBNext Ultra RNA library prep kit for Illumina (NEB) following the manufacturer’s instructions
cDNA sequencing libraries were established with the MicroPlex Library Preparation Kit (Diagenode) as described above
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.4.1c
Gene-level expression quantitation was performed using rsem version 1.2.22
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for each sample with gene id, transcript ids, length, effective length, expected count, TPM, FPKM
 
Submission date Feb 17, 2016
Last update date May 15, 2019
Contact name Tobias Straub
E-mail(s) tstraub@med.uni-muenchen.de
Organization name LMU Munich
Department Biomedical Center, Bioinformatics
Street address Großhadener Str. 9
City Martinsried
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL18460
Series (2)
GSE78003 Multivalent binding of PWWP2A to H2A.Z-marked transcriptional active chromatin regulates mitosis and organ development [RNA-seq]
GSE78009 Multivalent binding of PWWP2A to H2A.Z-marked transcriptional active chromatin regulates mitosis and organ development
Relations
SRA SRX1589776
BioSample SAMN04503793

Supplementary file Size Download File type/resource
GSM2064469_luci_1.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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