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Sample GSM675540 Query DataSets for GSM675540
Status Public on Apr 01, 2011
Title R1810A Mutant - Replicate 1
Sample type SRA
 
Source name Raji cells
Organism Homo sapiens
Characteristics cell line: Raji
vector: LS*mock, expressing recombinant, HA-tagged R1810->A RPB1 (amanitin resistant)
Treatment protocol Cells were transfected with the wild-type and (R1810A) Rpb1 expression vectors by electroporation (10 mg of plasmid DNA/107 cells; 960 mF, 250 V). Polyclonal cell batches were established after selection with G418 (1mg/ml) for 6 - 12 days, and subsequently for 10 days with 2 mg/ml a-amanitin (Sigma).
Growth protocol Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 1% penicillin streptomycin (GIBCO, Invitrogen) and 2 mM L-glutamine (GIBCO, Invitrogen) at densities between 2x105 to 106 cells/ml.
Extracted molecule total RNA
Extraction protocol RNA was extracted using peqGOLD Total RNA Kit (PEQLAB Biotechnologie, Erlangen, Germany). Ribosomal RNA was removed using RiboMinusTM Eukaryote Kit for RNA-Seq from Invitrogen (Cat# A10837), starting from 5 µg of total RNA. rRNA-depleted libraries were constructed following Illumina guidelines. Sequences were obtained from an Illumina GAII
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Raji is an Epstein-Barr-virus-positive Burkitt’s lymphoma cell line
Cells expressing R->A mutant CTD
Data processing Fastq file were generated with the Illumina pipeline
For processed data files, rRNA, tRNA, and mtRNA were removed with BOWTIE using a custom index. Remaining reads were mapped to hg19 with BOWTIE settings -v2 -m1 -51 -30. Mapped reads were assigned to the exon union gene set from ENSEMBL v. 59 using the DEGseq bioconductor package for R. Read densities were normalized against the gene size and total mapped reads into RPKM values.
 
Submission date Feb 15, 2011
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 GPL9115
Series (1)
GSE27315 The C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation
Relations
SRA SRX043487
BioSample SAMN00215975

Supplementary file Size Download File type/resource
GSM675540_R1810A_counts_rep1.txt.gz 361.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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