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Sample GSM1153526

Query DataSets for GSM1153526

Status

Public on Oct 23, 2013

Title

Bonobo AG05253 iPSC-2 A

Sample type

SRA

Source name

induced pluripotent stem cells

Organism

Pan paniscus

Characteristics

cell type: iPSC

Growth protocol

Human iPSC lines WT-33 and ADRC-40 (human IPSC1 and IPSC2 in this work, respectively) and WT-126 were previously described (Marchetto et al., 2010). Fibroblasts from human GM22159 (WT-9), Pan troglodytes (Chimpanzees: PR00818 and PR01209) and from Pan paniscus (Bonobos: AG05253 and PR01086) were acquired from Coriell Cell Repositories (NJ). All fibroblasts were cultured in Minimum Essential Medium (Invitrogen) supplemented with 10% fetal bovine serum (HyClone Laboratories). Retroviral vectors expressing Oct4, c-Myc, Klf4 and Sox2 human cDNAs from Yamanaka's group were obtained from Addgene. Recombinant viruses were produced by transient transfection in 293T cells. Two days after infection, cells were plated on mitotically inactivated mouse embryonic fibroblasts (Chemicon) with hESC medium. After 3 weeks, iPSCs colonies were picked manually and directly transferred to feeder-free conditions on matrigel-coated dishes (BD) using mTeSRTM1 (StemCell Technologies). Established iPSCs colonies were tested for karyotype integrity and expression profile of undifferentiatied markers. Cells were kept in feeder-free conditions indefinitely and passed using mechanical dissociation.

Extracted molecule

polyA RNA

Extraction protocol

Total cellular RNA was extracted from ~5x106 cells using the RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit and analyzed on an Illumina HiSeq 2000 sequencer. (Paired end 2x 100 bp)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

polyA+ RNA-Seq (not strand-specific)
Bonobo iPSC 53A

Data processing

Paired end reads from all libraries were mapped to both the human (hg19, GRCh37) and chimpanzee (panTro3, CGSC 2.1.3) genomes using STAR (v2.2.0c). Due to the lack of annotation in the chimpanzee genome, human gene models (RefSeq) were used to quantify gene expression. To avoid bias introduced by genome insertions and deletions, only reads mapping to both the human and chimpanzee genomes uniquely were used from each sample when comparing gene expression values (~4% of reads mapped to only one genome per sample). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: GRCh37, panTro3
Genome_build: Pan_troglodytes-2.1.3
Supplementary_files_format_and_content: File "rpkm.txt.gz" (linked as a supplementary file to the Series record) is a tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq protein-coding genes (hg19 assembly)

Submission date

Jun 04, 2013

Last update date

May 15, 2019

Contact name

Christopher Benner

E-mail(s)

cbenner@ucsd.edu

Organization name

University of California, San Diego (UCSD)

Department

Medicine