|
| Status |
Public on Jul 29, 2020 |
| Title |
CS18_12456_H3K4me1_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Heart Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: CS18
chip antibody vendor: Diagenode
antibody catalog number: C15410194
|
| Treatment protocol |
Cotney and Noonan, CSHL Protocols 2015.
|
| Growth protocol |
Samples flash frozen immediately after collection by HDBR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cotney and Noonan, CSHL Protocols 2015.
ChIP-seq libraries were prepared using the SMARTer® ThruPLEX® DNA-seq 48S Kit, Cat No. R400427, Takara Bio USA.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
CS18_12456_25state.bigBed
CS18_12456_18state.bigBed
CS18_12456_15state.bigBed
12456_DNase.imputed.bigWig
12456_H2A.Z.imputed.bigWig
12456_H3K27ac.imputed.bigWig
12456_H3K27me3.imputed.bigWig
12456_H3K36me3.imputed.bigWig
12456_H3K4me1.imputed.bigWig
12456_H3K4me2.imputed.bigWig
12456_H3K4me3.imputed.bigWig
12456_H3K79me2.imputed.bigWig
12456_H3K9ac.imputed.bigWig
12456_H3K9me3.imputed.bigWig
12456_H4K20me1.imputed.bigWig
|
| Data processing |
Align to genome using bowtie 2.3.1
Generate bam format and normalize with samtools 1.3.1
Sort bam with samtools 1.3.1
Index bam with samtools 1.3.1
Merged bams from alignment for 3 Replicates of 2N and 4N respectively to prepare for ChromImpute
Convert to tagAlign format for size estimation of combined and single replicates
Estimate fragment size using phantompeakqualtools for combined and single replicates
Call peaks with MACS2 2.1.1.20160309 for combined and single replicates
Convert combined bedGraph to binary for ChromImpute 1.0.3
Generate global distance measurements for ChromImpute
Generate features for training
Generate trained predictors
Generate imputed signal track
Convert imputed signals to ChromHMM singal format using DeepTOOLS 2.0
Binarize imputed signals for ChromHMM
Generate Chromatin State Segmentation with ChromHMM 1.12
Generate files for UCSC genome browser based on published Roadmap Epigenome Conventions
Convert segmentation beds to bigBed format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are the imputed bigWigs that are the output imputed signal tracks from ChromImpute, bigBed files are the 25 State chromatin segmentations that come from ChromHMM
|
| |
|
| Submission date |
Sep 19, 2019 |
| Last update date |
Oct 27, 2023 |
| Contact name |
Jennifer VanOudenhove |
| Organization name |
Yale University
|
| Department |
Internal Medicine - Section of Hematology
|
| Lab |
Halene Lab
|
| Street address |
300 George St RM 786
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE137731 |
Epigenomic Atlas of Embryonic Human Heart Development |
|
| Relations |
| BioSample |
SAMN12788141 |
