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Sample GSM1223562 Query DataSets for GSM1223562
Status Public on May 29, 2014
Title mouse_tgc_input
Sample type SRA
Source name Trophoblast giant cells - cultured
Organism Mus musculus
Characteristics strain: 129/Sv
chip antibody: None
sample type: Input chromatin
Treatment protocol TSCs were differentiated into trophoblast giant cells (TGCs) by using differentiation media, which consisted of TS media without FGF4, Activin, and Heparin, with the addition of retinoic acid dissolved in ethanol to the media to a final concentration of 5 μM. TSCs were differentiated for five days, replacing media every other day, before harvesting.
Growth protocol Mouse trophoblast stem cells (TSCs) were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).
Extracted molecule genomic DNA
Extraction protocol Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Input chromatin
Data processing Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 using BWA 0.5.9 (-q 10 -I), and filtered using samtools view (-q 10) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.10 with default settings
genome build: = mm9
supplementary files format and content: ChIP-Seq bed files contain peaks called by MACS v2.0.10
Submission date Sep 03, 2013
Last update date May 15, 2019
Contact name Roberta L Hannibal
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL13112
Series (2)
GSE50561 Trophoblast giant cell underrepresentation (sequencing)
GSE50585 Trophoblast giant cell underrepresentation
BioSample SAMN02344593
SRA SRX344648

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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