|
| Status |
Public on Jan 22, 2025 |
| Title |
Ectoderm_H3K4me3_ChIP_Xencode_Group3_1 |
| Sample type |
SRA |
| |
|
| Source name |
ectoderm
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: ectoderm
cell type: ectoderm_stage21
genotype: WT
batch: 1
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As described in Hörmanseder et al 2017.
ChIP-seq library preparation with the TruSeq DNA kit (Illumina, FC-121-2001).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group3_1
|
| Data processing |
Raw ChIP-seq data were aligned to the Xenopus laevis genome (v10.1) using BWA (v0.7.17-foss-2018b).
Low-quality mapped reads (MAPQ < 10) were discarded using samtools (v1.16.1), and PCR duplicates were removed with sambamba (v0.8.2). Coverage track files (.bigwig) were generated using deepTools (v3.5.1), with normalization to Counts Per Million (CPM).
Assembly: Xenopus laevis 10.1
Supplementary files format and content: bigwig coverage tracks, merged replicates with input subtracted
|
| |
|
| Submission date |
Dec 22, 2024 |
| Last update date |
Jan 22, 2025 |
| Contact name |
Eva Hoermanseder |
| E-mail(s) |
eva.hoermanseder@helmholtz-munich.de, antonio.scialdone@helmholtz-munich.de
|
| Organization name |
Helmholtz Center Munich
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Lab |
Hoermanseder Lab
|
| Street address |
Feodor-Lynen-Str. 21
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21046 |
| Series (1) |
| GSE285205 |
‘Digital Reprogramming’ Decodes Epigenetic Barriers of Cell Fate Changes and Identifies p300 Inhibitors as Facilitators [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN45942618 |
| SRA |
SRX27164021 |
