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| Status |
Public on Apr 30, 2024 |
| Title |
WT_Th2_K4me1_R1 |
| Sample type |
SRA |
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| Source name |
Spleen and lymph nodes
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen and lymph nodes
cell line: Primary LCMV TCRtg CD4+ Thy1.1+ cells
cell type: CD4 T cells
genotype: Wild type
treatment: Th2 conditions
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| Treatment protocol |
Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)).
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| Growth protocol |
Adoptively transferred WT, Tbx21+/-, Tbx21-/- LCMV‑TCRtg CD4+ Thy1.1+ cells from LCMV-challenged mice were isolated and MACS-sorted on day 10 of infection. Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)). On day 4 of the second round of stimulations the cells were harvested and processed for Chip-Seq.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were incubated for 10min at room temperature with 1% formaldehyde. Cross-linking was terminated by addition of glycine to a final concentration of 125mM. ChIP was performed using iDeal ChIP-seq Kit (Diagenode) according to the manufacturer’s instructions. Antibodies against H3K4me3 (ab8580, Abcam), H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K27me3 (ab6002, Abcam) and H3K9me3 (ab8898, Abcam) were used.
10ng of chromatin-immunoprecipitated DNA was end-repaired and dA-tailed. Subsequently, adaptor was ligated to the dA-tailed DNA. DNA was cleaned up using AMpure XP beads after each step. Adaptor-ligated DNA was size selected with AMpure XP beads using different DNA to beads ratio to an average fragment size of 200bp. At last step, size-selected and adaptor-ligated DNA was enriched by PCR with different index primers and cleaned up using AMpure XP beads. Purified library DNA was quantified with Qubit 2.0 and fragment size was assessed using Bioanalyzer (Agilent high sensitivity chip).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
NA
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| Data processing |
# Bowtie v1.2.1.1 bowtie -t -m 1 -S -q -p 8 <Genome Location > <FASTQ File > <SAM File Output >
# SICER v1.1 ( modified script )
SICER_modified.sh <Input file folder > <Input file name > <Control file name > <Output
folder > t mm10 1 200 150 0.8
# SICER params: ["InputDir"] ["bed file"] ["control file"] ["OutputDir"] ["Species"] ["redundancy threshold"] ["window sizes (bp) - submit multiple window sizes in quote"] ["fragment size"] ["effective genome fraction"] ["number of background islands for evalue (def: 1000)"]
Assembly: mm10
Supplementary files format and content: bed files: for K4me3 histone modifications the params are W200-G200-FDR0.01; for all others the params are W200-G600-FDR0.01
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| Submission date |
Apr 29, 2024 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Ahmed Nabil Hegazy |
| Organization name |
Charité - University Medicine Berlin
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| Department |
Department of Gastroenterology, Infectious Diseases and Rheumatology
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| Lab |
Hegazy Lab
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| Street address |
Hindenburgdamm 30
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| City |
Berlin |
| ZIP/Postal code |
12203 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE266175 |
Plasticity and lineage commitment of individual Th1 cells are determined by stable T-bet expression quantities (ChIP-Seq) |
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| Relations |
| BioSample |
SAMN41127162 |
| SRA |
SRX24402539 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8241936_37wt_Th2_1_K4me1_ATCACG_merged.bam-W200-G600-FDR0.01-island.bed.gz |
277.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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