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Sample GSM1698411 Query DataSets for GSM1698411
Status Public on Jul 16, 2015
Title P3_D2
Sample type SRA
 
Source name hiF-T cells
Organism Homo sapiens
Characteristics reprogramming time point (day): 4
treatment: 0.1 uM LSD1 inhibitor
Growth protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.
Extracted molecule total RNA
Extraction protocol Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
The 3’-DGE libraries were prepared from 20ng of total RNA according to the Single Cell RNA Barcoding and Sequencing method originally developed for single cell RNA-seq (SCRB-seq (Soumillon et al., 2014) and adapted to extracted total RNA. Briefly, Poly(A)+ mRNA from extracted total RNA are converted to cDNA decorated with universal adapters, sample-specific barcodes and unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Decorated cDNA from multiple samples are then pooled, amplified and prepared for multiplexed sequencing using a modified transposon-based fragmentation approach that enriches for 3’ ends and preserves strand information.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description LSD1i4_R1
Data processing Paired reads were used for analysis if all sixteen bases of the first read had quality scores of at least 10 and the first six bases corresponded exactly to a designed well-barcode. All second sequence reads were aligned to a reference database consisting of all human RefSeq mRNA sequences (hg19) and the ERCC RNA spike-in reference sequences using bwa version 0.7.4 4 with non-default parameter “-l 24”. Reads mapped to multiple genes were excluded from further analysis. Digital gene expression (DGE) profiles were then generated by counting, for each microplate well and RefSeq gene, the number of unique molecular identifiers (UMIs) associated with alignments to that gene in that well.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes UMI values for each sample.
 
Submission date May 29, 2015
Last update date May 15, 2019
Contact name Shannan J Ho Sui
E-mail(s) shosui@hsph.harvard.edu
Organization name Harvard T.H. han Scholol of Public Health
Department Biostatistics
Street address 655 Huntington Ave, Building 2, Rm 437A
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL16791
Series (2)
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
GSE69351 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [SCRB-Seq]
Relations
BioSample SAMN03743503
SRA SRX1042152

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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