|
| Status |
Public on Sep 06, 2023 |
| Title |
12.5_dpc_H3K27me3_ChIPseq [GAIIx] |
| Sample type |
SRA |
| |
|
| Source name |
neural progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: ICR
Stage: 12.5 dpc
cell type: neural progenitor cells (NPCs)
chip antibody: H3K27me3 (Millipore, 07-449)
|
| Treatment protocol |
RNA-seq: For Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-, cells were stained with CD133 antibody and highly positive fraction was isolated as neural stem cells.
|
| Growth protocol |
ChIP-seq: Neocortical NSCs were isolated either by fluorescent activated cell sorting (FACS) from mice expressing the NSC marker, Nestin-d4-Venus, or by manual dissection of the ventricular zone of the neocortex.
RNA-seq: Neocortical NSCs were isolated by fluorescent activated cell sorting (FACS) either from mice expressing the NSC marker, Nestin-d4-Venus or from Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to Illumina's instructions accompanying the Truseq ChIP Prep Kit.
RNA-seq: Total RNA was extracted from cell lysates.
RNA libraries were prepared according to Illumina' s instructions accompanying the Truseq RNA Prep Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 12.5 dpc stage of mouse NPCs (manually dissected).
|
| Data processing |
Basecalls performed using Illumina CASAVA version 1.4 at GAIIx and Illumina bcl2fastq-1.8.4 at Hiseq2000/Hiseq2500.
Sequenced reads were aligned to the mm9 reference genome using ELAND v2 software (Illumina).
The bigWig file generated by Homer software using makeTagDirectory and makeUCSCfile.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Sep 06, 2016 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Yukiko Gotoh |
| Organization name |
University of Tokyo
|
| Street address |
7-3-1 Hongo, Bunkyo-ku
|
| City |
Tokyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE86461 |
Genome-wide analysis of HMGA2 and H3K27me3 deposition in neocortical neural stem cells and transcriptome of Wild Type and Ring1 KO neocortical neural stem cells |
|
| Relations |
| BioSample |
SAMN05730873 |
| SRA |
SRX2140460 |
