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Sample GSM1722195 Query DataSets for GSM1722195
Status Public on Jun 25, 2018
Title Cytosolic Spt5 KD control
Sample type SRA
Source name HeLa_Cytosolic Spt5 KD control
Organism Homo sapiens
Characteristics cell line: HeLa
genotype/variation: Spt5 KD
treated with: none
molecule subtype: cytoplasmic RNA
Treatment protocol HeLa cells were transfected with control Spt5 RNAi plasmids along with a plasmid direcing puromycin resistant gene. Transfected cells were selected with puromycin. 72 hours post transfection cell were trearted with TNFα for one hour.
Growth protocol Hela cells were grown using standard growth conditions
Extracted molecule total RNA
Extraction protocol Cells were separated into cytosol and chromatin fractions which were then subjected to RNA extraction and DNAseI tretment
Cytosolic and chromatin associated RNA samples were depleted of ribosomal RNA using Ribozero gold rRNA depletion kit (Epicentre). RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina)without poly A capturing. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 4 samples on one lane. Paired-end 101 bp reads were sequenced on Illumina HiSeq 2500 rapid mode with cBot on HiSeq Rapid Flow Cell v1 HCS:
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Demultiplexing and base calling was done with CASAVA 1.8.2 (RTA
Reads were aligned to the hg19 genome built using Tophat (v2.0.04) with an annotation file (refSeq from igenomes UCSC).
Raw gene read counts were calculated by HTSeq using refSeq gene annotations (igenomes).
Normalized gene counts were calculated with DESeq. Chromatin and cytosol samples were analysed separately.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing gene counts
Submission date Jun 25, 2015
Last update date May 15, 2019
Contact name Rivka Dikstein
Organization name The Weizmann Institute of Science
Street address 2 Hertzl st.
City Rehovot
ZIP/Postal code 76100
Country Israel
Platform ID GPL16791
Series (1)
GSE70268 RNA-seq of cytosolic and chromatin-associated transcripts following TNFα and Spt5 KD
BioSample SAMN03794768
SRA SRX1073579

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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