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Sample GSM818940 Query DataSets for GSM818940
Status Public on Nov 01, 2011
Title Sox2 ChIP-Seq in neural progenitor cells, biol repl 2
Sample type SRA
Source name Neural progenitor cells
Organism Mus musculus
Characteristics cell type: ES-derived neural progenitor cells
differentiation specificity: 4 days in differentiation conditions with retinoic acid
chip antibody: Sox2 (Millipore)
Treatment protocol Formaldehyde 1% crosslink 9min at 37°C. Cells were mechanically dissociated from the surface before lysis.
Growth protocol Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2. C2C12 cells were cultured with serum unless for 3h during lipofectamine transfection.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit (1003473).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against Sox2
Data processing Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.
Submission date Oct 18, 2011
Last update date May 15, 2019
Contact name Rickard Sandberg
Organization name Karolinska Institutet
Department Department of Cell and Molecular Biology
Street address Berzelius vag 35
City Stockholm
ZIP/Postal code 17177
Country Sweden
Platform ID GPL11002
Series (2)
GSE33024 Sequentially acting Sox transcription factors in neural lineage development
GSE33059 Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq]
SRA SRX101688
BioSample SAMN00739991

Supplementary file Size Download File type/resource
GSM818940_GAU14b_Sox2_NPC_chipseq.bed.gz 98.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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