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Sample GSM1126516 Query DataSets for GSM1126516
Status Public on Apr 22, 2013
Title T11_RNA-Seq
Sample type SRA
Source name T11, 1st pair, 1st individual
Organism Homo sapiens
Characteristics cell type: CD14 cells
individual identifier: T11
Extracted molecule total RNA
Extraction protocol For RNA-seq, 200 ng of total RNA was used to prepare RNA-seq libraries using the TruSeq RNA kit from Illumina following the instructions provided in the supplier's manual, and sequenced on an Illumina GAIIx instrument.

Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description PE72
Data processing ChIP-seq reads were aligned to the reference sequence using bwa-0.6.6 then sorted and indexed using samtools
Read pairs with quality scores >=10 were extracted and the number of read pairs overlapping each probe on the Illumina HumanMethylation450K array were counted.
RNA-seq was aligned with TopHat 1.3.1 and FPKM values were generated using CuffLinks 1.0.3
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Fragment coverage across Illumina HumanMethylation450K probes (GEO Platform GPL13534) for ChIP data.
Supplementary_files_format_and_content: Transcript FPKM numbers for nearest TSS for RNA-seq data.
Submission date Apr 19, 2013
Last update date May 15, 2019
Contact name Thomas A Down
Organization name University of Cambridge
Department WT/CRUK Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platform ID GPL10999
Series (2)
GSE46217 Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]
GSE46220 Inactive or moderately active human promoters are enriched for inter-individual epialleles
BioSample SAMN02053618
SRA SRX268696

Supplementary file Size Download File type/resource
GSM1126516_T11_RNA_fpkm.txt.gz 1.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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