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Sample GSM849950 Query DataSets for GSM849950
Status Public on Dec 20, 2012
Title mES_H3K4me3_shluc_ctrl_for_MLL4KD
Sample type SRA
Source name mouse ES cells, shluc control, H3K4me3 ChIP
Organism Mus musculus
Characteristics cell line: R1
cell type: embryonic stem cells
condition: shluc control for shMLL4 mES cells
antibody (vendor: catalog#, or reference): anti-H3K4me3 antibody (Millipore: 17-614)
Treatment protocol Lentiviral Infections: The RNA interference construct targeting mouse H2A.Z was generated by inserting the cDNA sequence of H2A.Z (or MLL4) into pGreenPuro Lentivector (containing a GFP marker) as described in the manual (System Biosciences). The lentiviral particles were packaged by transfecting 293T cells with the shRNA constructs or shLuciferase constructs for 2 days, and lentiviral supernatants were then harvested. Mouse ES cells were transduced with the lentiviral supernatants. After 4 days, 10-50 GFP+ cells were sorted and plated into a feeder coated 6-well plate. One week later, individual colonies were selected, expanded, and knockdown efficiency was analyzed by RT-PCR and Western blot.
Growth protocol CMTi-1 and R1 murine ES cell lines were routinely cultured on feeder-coated dishes in ES-qualified DMEM (Cat #SLM-220-B; Millipore) supplemented with 20% ES-qualified FES (Cat #SCRR-30-2020; ATCC), 2mM L-glutamine (Cat #TMS-002-C; Millipore), 100 units/ml penicillin/streptomycin (Cat #TMS-AB2-C; Millipore), 0.1mM non-essential amino acids ( Cat # TMS-001-C; Millipore), 0.1mM2-mercaptoethanol (Cat #ES-007-E; Millipore), 1mM sodium pyruvate (Cat #25-000-CI; Cellgro), and 1,000 units/ml LIF (Esgro, Cat #ESG1107; Millipore). The cells were trypsinized and replated or re-fed every second day. To generate EBs, ES cells were dissociated into a suspension of single cells using trypsin and then diluted to 10,000 cells/ml in 6-well petri dishs (Corning) in ES medium (see growth conditions for ES cells) lacking leukemia inhibitory factor (LIF). Cultures were maintained in a humidified chamber under 5% CO2 at 37C. EBs were allowed to grow for up to 14 days.
Extracted molecule genomic DNA
Extraction protocol Library constructions for BNase-Seq, ChIP-Seq, MNase-Seq and RNA-Seq follow the protocols as described previously in (Epigenetics Chromatin. 2012 5:10. PMID: 22734930), (Cell. 2007 May 18;129(4):823-37. PMID: 17512414), (Cell. 2008 Mar 7;132(5):887-98. PMID: 18329373) and (Nucleic Acids Res. 2009 Sep;37(16):e106. PMID: 19528076), respectively.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K4me3.
Data processing GA2971-mouse-R1-shHLuc-H3K4me3-r490l8-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
Submission date Dec 15, 2011
Last update date May 15, 2019
Contact name Gangqing Hu
Organization name West Virginia University
Department MicroBiology, Immunology, and Cell Biology
Lab 2072A, HSC North, Floor 2
Street address 64 Medical Center Drive
City Morgantown
State/province West Virginia
ZIP/Postal code 26506-9177
Country USA
Platform ID GPL11002
Series (1)
GSE34483 H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-renewal and Differentiation
SRA SRX111891
BioSample SAMN00765727

Supplementary file Size Download File type/resource
GSM849950_GA2971-mouse-R1-shHLuc-H3K4me3-r490l8-m1_noDup.bed.gz 84.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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