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Sample GSM2443533

Query DataSets for GSM2443533

Status

Public on Feb 16, 2018

Title

HeLa_RSF1_KD_RNA-seq

Sample type

SRA

Source name

human HeLa cell

Organism

Homo sapiens

Characteristics

genotype: RSF1 KD
cell line: HeLa
passages: 25-30

Treatment protocol

10 nM siRNA was transfetced into cells. 48 hrs later, total RNAs were extracted.

Growth protocol

DMEM, 10%FBS

Extracted molecule

total RNA

Extraction protocol

Samples for mRNA were prepared following the Illumina mRNA sequencing sample preparation guide. Briefly, total RNA was extracted with Trizol (Cat # 15596026, Invitrogen, Carlsbad, CA, USA).
mRNA was specifically enriched from total RNA using oligo(dT) beads and hydrolyzed into small pieces. The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis using DNA polymerase I. The short cDNA strands were ligated with 3’- and 5’-adapters for amplification and sequencing (Illumina HiSeq v4 (pair end,50 bp, 50 M reads) in the HudsonAlpha Institute for Technology (Huntsville, AL, USA). Primer sequences are available upon request.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

processed data file: HeLa_RNA-seq_FPKM.txt

Data processing

For RNA-seq data, reads were mapped to hg19 or mm10 using STAR version 2.5.1b. Differentially expressed genes (q-value≤0.05) were identified with Cuffdiff. The log2 fold change is a direct output from Cuffdiff. For visualization, the mapped reads were converted into BedGraph format using BEDTools. For ChIP-seq data, reads were mapped to hg19 or mm10 using bowtie version 1.1.2. Bam files are sorted by Samtools and PCR duplicates were removed using Picard (http://picard.sourceforge.net). Peak calling was perform using MACS-1.4.2. For MNase-seq, Reads were analyzed and profiled using Danpos.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample or wig file

Submission date

Jan 03, 2017

Last update date

May 15, 2019

Contact name

Hengbin Wang

E-mail(s)

hbwang@uab.edu

Phone

2059345286

Organization name

University of Alabama at Birmingham