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Sample GSM1104374 Query DataSets for GSM1104374
Status Public on Mar 26, 2013
Title HeLaS3.siSFMBT1-1_siLSD1-2_siCoREST-1.R
Sample type SRA
Source name HeLa S3
Organism Homo sapiens
Characteristics cell line: HeLa S3
treatment: siRNA against SFMBT1 (#1) + LSD1 (#2) + CoREST (#1)
internal reference: 120123_lane7_VLB4
Extracted molecule total RNA
Extraction protocol RNA was isolated with TRIzol, depleted of polyA+ transcripts with oligo-dT beads, and depleted of rRNA with the Ribominus kit
libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description depleted of polyA+ and rRNA
Data processing Trimmed sequences in 3' to 36 nts
mapped to hg19 with BOWTIE -m40 -v2
assigned counts to gene models in ENS65 with DEGseq
Genome_build: hg19 (HeLaS3) or mm9 (germ cells)
Supplementary_files_format_and_content: RPKM and count table for ENS65
Submission date Mar 22, 2013
Last update date Feb 04, 2022
Contact name Roberto Bonasio
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Bonasio
Street address 3400 Civic Center Blvd - SCTR 9-111
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL11154
Series (2)
GSE45442 SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [RNA-Seq]
GSE45489 SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors
SRA SRX254635
BioSample SAMN01986104

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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