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Sample GSM2735188 Query DataSets for GSM2735188
Status Public on Jul 15, 2018
Title PolyA_Gatad2a-/-_Day2
Sample type SRA
 
Source name Gatad2a-/- cell line, Day2 post DOX induction
Organism Mus musculus
Characteristics cell line: Gatad2a-/- cell line
stage of reprogramming: Day2
Treatment protocol Reprogramming dynamics samples were generated by adding Dox to Secondary MEF. ES and iPSC samples were harvested after 3-4 days of growth in N2B27 2i\LIF medium. Reprogramming samples of days 3-8, ES and iPSC samples were plated on irradiated human foreskin fibroblasts (HFF).
Growth protocol Maintenance and reprogramming (Day 3 and beyond) of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:
N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).
KSR media: 500 ml DMEM (Invitrogen) , 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).
Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated from indicated cell lines, and extracted from Trizol pellets by Direct-zol RNA MiniPrep kit (Zymo) according to manufacturer’s manual.
RNA was extracted from Trizol pellets, and utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description PolyA RNA-seq from Gatad2a-/- system, Day2
Data processing We used Illumina CASAVA 1.8.2 software to generate fastq files.
Tophat software version 2.0.10 was used to align reads to mouse mm10 reference genome
FPKM values were calculated over all genes in mm10 assembly GTF (UCSC, December 2011), using cufflinks version 2.2.1.
Genome_build: mm10
 
Submission date Aug 08, 2017
Last update date May 15, 2019
Contact name Noa Novershtern
E-mail(s) noa.novershtern@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL19057
Series (2)
GSE102348 High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [RNA-Seq]
GSE102518 High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems
Relations
BioSample SAMN07460297
SRA SRX3070390

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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