|
| Status |
Public on Oct 18, 2021 |
| Title |
H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.H3K27ac.replicate.1 |
| Sample type |
SRA |
| |
|
| Source name |
H1 FOXA1/2 Exon Deletion
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: differentiated hESCs
developmental stage: Gut tube
chip antibody: Rabbit anti-H3K27ac
antibody manufacturer: Active Motif
antibody catalog number: 39133
|
| Growth protocol |
CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019). iAEC2 cells were maintained and differentiatied as previously described (Hurley et al 2020)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Histone marker
|
| Data processing |
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Oct 18, 2021 |
| Contact name |
Maike Sander |
| E-mail(s) |
masander@ucsd.edu
|
| Organization name |
UC San Diego
|
| Street address |
2880 Torrey Pines Scenic Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE148368 |
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors |
|
| Relations |
| BioSample |
SAMN14567227 |
| SRA |
SRX8089882 |
