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Sample GSM1087891 Query DataSets for GSM1087891
Status Public on Nov 21, 2013
Title 13289-100mers-GM12878-243-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78339)
Sample type SRA
Source name GM12878
Organism Homo sapiens
Characteristics labexpid: 13289
cell line: GM12878
Growth protocol
Extracted molecule polyA RNA
Extraction protocol Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description ****************************
GSM1087891 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78339
Data processing Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end.
Submission date Feb 25, 2013
Last update date May 15, 2019
Contact name Diane E Trout
Organization name California Institute of Technology
Department Biology
Lab Wold
Street address 1200 E California Blvd M/C 156-29
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
Platform ID GPL11154
Series (1)
GSE44618 Single Cell RNA-Seq
Superseded by GSE78339
SRA SRX245469
BioSample SAMN01924728

Supplementary file Size Download File type/resource
GSM1087891_13289-genes.fpkm_tracking.gz 1.3 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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