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| Status |
Public on Jun 01, 2024 |
| Title |
H3K4me1, fetal-rumen, 1 (chip-seq) |
| Sample type |
SRA |
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| Source name |
Rumen
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| Organism |
Bos taurus |
| Characteristics |
tissue: Rumen
Sex: male
age: 90 days fetus
genotype: WT
chip antibody: H3K4me1
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| Treatment protocol |
For pluripotent stem cells: The bovine embryonic stem cell line bESCs-F7 was established using the CTFR system. Two treatment methods were employed for bESCs-F7 using MM-102: one involved treating bESCs-F7 with a high concentration (50 μM) of MM-102 for 7 days, followed by normal culturing for 5 passages before characterization, labeled as bESCs-F7-102 (50). The other involved long-term treatment with a low concentration (5 μM) of MM-102, followed by characterization after 5 passages of culturing, labeled as bESCs-F7-102 (5). Bovine induced pluripotent stem cells and the bEPSCs-B18 cell line were established using the LCDM system. And bEPSCs-AGS was using a 500mL system, including 485mL of basic mTeSR1 medium, 5.0 mL of 100×Penicillin-Streptomycin Solution, 0.1 mM 2-mercaptoethanol, 1 μM GSK3β inhibitor CHIR99021, 0.3 μM Lck/Src inhibitor WH-4-023, 5 μM Tankyrase inhibitor XAV939, 5 μM classic WNT signaling pathway inhibitor IWR-1, 50 μg/mL Vitamin C, 10 ng/mL Leukemia Inhibitory Factor (LIF), and 20.0 ng/mL Activin A for culturing bovine Embryonic Pluripotent Stem Cells.
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| Growth protocol |
For tissues, we collected fetal tissues from four healthy pregnant Holstein cows at a slaughterhouse. After the slaughter, we extracted fetal tissues to examine their normal development and measured the crown-rump length (CRL) to estimate gestational age. The gender was identified based on the position of the gonads within the abdominal cavity, anatomical structures, and relationships with adjacent organs (mesonephros and/or kidneys). Two male and two female fetuses were identified (13-16 cm CRL), nine different tissues were collected, including the forebrain, hindbrain, heart, liver, lungs, skeletal muscle (hind limb), kidneys, rumen, and testes.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected by tryple-select enzyme and the lyophilized cells were sent for sequencing. The sequencing was performed by Tianjin Nuohe Zhiyuan Biotechnology Co., LTD, Tianjin, China.
The Simple ChIP®Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (9005, Cell Signaling) was utilized to extract DNA fragments from the cells.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina reads were first mapped to the UCSC bosTau9 reference using bwa-mem (version:0.7.17) with default parameters.
Next, Picard (http://broadinstitute.github.io/picard/, accessed on 12 June 2023, version 2.23.1) was used to mark up the PCR duplicates.
Then, we used macs2 (v2.2.7.1, -nomodel-broad-broad-cutoff 0.1-shift 0-gsize 2.7e9-keep-dup auto) to call the peaks.
H3K4me1 signals were normalized using the MA norm (version: 1.1.4) method for the quantitative comparison of ChIP-seq data, and the significant differential peaks were determined as log10(p-value) < 0 and M-value > 1. Subsequently, the differential peaks were annotated to UCSC bosTau9 using the R package ChIP seeker (version: 1.28.3) and TxDb.Btaurus.UCSC.bosTau9.refGene (version: 3.10.0).
Assembly: UCSC BT9
Supplementary files format and content: bigWig
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| Submission date |
Apr 18, 2024 |
| Last update date |
Jun 01, 2024 |
| Contact name |
jing wang |
| E-mail(s) |
nnlrl@mail.imu.edu.cn
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| Organization name |
Inner Mongolia University
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| Street address |
Zhaojun Road
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| City |
Hohhot |
| State/province |
Nei Mongol |
| ZIP/Postal code |
010000 |
| Country |
China |
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| Platform ID |
GPL26012 |
| Series (2) |
| GSE264336 |
Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ChIP-seq) |
| GSE264346 |
Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions |
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| Relations |
| BioSample |
SAMN41008854 |
| SRA |
SRX24353584 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8216279_fetal-H3K4me1_REP1.bamCompare.bw |
59.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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