title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD012_indexed

status: Public on Sep 02 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male

tag: age

tag: strain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD002_indexed


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title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E2_AD002_indexed


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title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E10_AD007_indexed


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title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_H5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G3_AD001_indexed


title: 20-piohfd_diet_KO

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

library_source: transcriptomic

data_processing:
Basecalls performed using RTA Version 2.7.3
Sequence reads were aligned to the GRCm38 genome assembly using STAR version 2.0.4b
Gene counts were computed from uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Genome_build: Ensembl release 76 top-level assembly (GRCm38)

molecule: total RNA

source_name: liver

extract_protocol:
As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284
As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284

treatment_protocol: Mice were fed either control diet or high fat diet supplemented with Pio or vehicle.

tag: gender

value: 5 months

tag: tissue

value: liver

tag: treatment

value: High Fat Diet with Pioglitazone


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD012_indexed


title: 19-piohfd_diet_KO


title: 17-piohfd_diet_KO


title: 16-piohfd_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD006_indexed


title: 14-pio_diet_KO

value: Control Diet with Pioglitazone


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G1_AD006_indexed


title: 9-hfd_diet_KO

value: High Fat Diet


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G1_AD002_indexed


title: 12-pio_diet_KO


title: 13-pio_diet_KO


title: 11-pio_diet_KO


title: 10-hfd_diet_KO


title: 15-pio_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD007_indexed


title: 8-hfd_diet_KO


title: 7-hfd_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD010_indexed


title: 6-hfd_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G1_AD012_indexed


title: 4-control_diet_KO

value: Control Diet


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD012_indexed


title: 18-piohfd_diet_KO


title: 5-control_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD006_indexed


title: 2-control_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD004_indexed


title: 1-control_diet_KO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD001_indexed


title: 841-Pio_diet_WT


title: 842-Pio_diet_WT


title: 845-Pio_diet_WT


title: 840-HFD_Pio_diet_WT


title: 843-Pio_diet_WT


title: 839-HFD_Pio_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD002_indexed


title: 844-Pio_diet_WT


title: 838-HFD_Pio_diet_WT


title: 835-control_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD010_indexed


title: 836-HFD_Pio_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD002_indexed


title: 834-control_diet_WT


title: 3-control_diet_KO


title: 837-HFD_Pio_diet_WT


title: 833-control_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_G10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD002_indexed


title: 832-control_diet_WT


title: 831-control_diet_WT


title: 830-HFD_diet_WT


title: 828-HFD_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F9_AD001_indexed


title: 827-HFD_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD007_indexed


title: 829-HFD_diet_WT


title: 826-HFD_diet_WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD006_indexed


title: Pio_Diet_input_KO_2

data_processing:
Basecalls performed using RTA Version 2.7.3
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign version V3.04.06 with harclipping (-H) and adapter stripping (-a)
Peaks were called using MACS  version version 2.1.1 (20160309) using a paired input control
Genome_build: mm10
Supplementary_files_format_and_content: Bed files: The bed files contain the called peaks, the 5th column is the standard MACS -10*log10pvalue; Xls files: contain the peaks with additional information, such as position of peak summit, number of tags in peak region, fold enrichment and FDR

source_name: Knockout Mouse fed control diet with pioglitazone for 12 weeks

tag: genotype

value: PPARg knockout

tag: chip antibody

value: none - not applicable


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD010_indexed


title: Pio_Diet_input_KO_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD001_indexed


title: Pio_Diet_input_KO_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD004_indexed


title: Pio_Diet_input_KO_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD008_indexed


title: Pio_Diet_input_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD010_indexed


title: Pio_Diet_RXR_KO_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD004_indexed


title: Pio_Diet_RXR_KO_2


title: Pio_Diet_RXR_KO_3


title: Pio_Diet_RXR_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD007_indexed


title: PioHFD_Diet_input_KO_4

source_name: Knockout Mouse fed high fat diet with pioglitazone for 12 weeks


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD002_indexed


title: PioHFD_Diet_input_KO_5


title: PioHFD_Diet_input_KO_3


title: Pio_Diet_RXR_KO_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD006_indexed


title: PioHFD_Diet_input_KO_2


title: PioHFD_Diet_input_KO_1


title: PioHFD_Diet_RXR_KO_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD008_indexed


title: PioHFD_Diet_RXR_KO_3


title: PioHFD_Diet_RXR_KO_2


title: PioHFD_Diet_RXR_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD012_indexed


title: HFD_Diet_input_KO_5

source_name: Knockout Mouse fed high fat diet for 12 weeks


title: HFD_Diet_input_KO_4


title: HFD_Diet_input_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F7_AD002_indexed


title: HFD_Diet_RXR_KO_5


title: PioHFD_Diet_RXR_KO_4


title: HFD_Diet_RXR_KO_4


title: HFD_Diet_RXR_KO_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F6_AD012_indexed


title: Control_Diet_input_KO_5

source_name: Knockout Mouse fed control diet for 12 weeks


title: HFD_Diet_RXR_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F5_AD001_indexed


title: Control_Diet_input_KO_4


title: HFD_Diet_RXR_KO_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD004_indexed


title: Control_Diet_input_KO_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD010_indexed


title: Control_Diet_input_KO_1


title: Control_Diet_input_KO_2


title: HFD_Diet_input_KO_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD006_indexed


title: Control_Diet_RXR_KO_5

value: RXR antibody (sc-774 )


title: HFD_Diet_input_KO_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD008_indexed


title: Control_Diet_RXR_KO_4


title: Control_Diet_RXR_KO_3


title: Control_Diet_RXR_KO_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD002_indexed


title: Pio_Diet_input_WT_5

source_name: Wildtype Mouse fed control diet with pioglitazone for 12 weeks

value: wildtype


title: Control_Diet_RXR_KO_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD010_indexed


title: Pio_Diet_input_WT_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD006_indexed


title: Pio_Diet_input_WT_2


title: Pio_Diet_input_WT_3


title: Pio_Diet_RXR_WT_4


title: Pio_Diet_input_WT_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD008_indexed


title: Pio_Diet_RXR_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F4_AD008_indexed


title: Pio_Diet_RXR_WT_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD001_indexed


title: Pio_Diet_RXR_WT_2


title: Pio_Diet_RXR_WT_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD004_indexed


title: PioHFD_Diet_input_WT_5

source_name: Wildtype Mouse fed high fat diet with pioglitazone for 12 weeks


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F3_AD012_indexed


title: PioHFD_Diet_input_WT_4


title: PioHFD_Diet_input_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F1_AD012_indexed


title: PioHFD_Diet_input_WT_2


title: PioHFD_Diet_input_WT_1


title: PioHFD_Diet_RXR_WT_5


title: PioHFD_Diet_RXR_WT_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD006_indexed


title: PioHFD_Diet_RXR_WT_2


title: PioHFD_Diet_RXR_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD012_indexed


title: HFD_Diet_input_WT_5

source_name: Wildtype Mouse fed high fat diet for 12 weeks


title: HFD_Diet_input_WT_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD002_indexed


title: HFD_Diet_input_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD004_indexed


title: HFD_Diet_input_WT_1


title: HFD_Diet_RXR_WT_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD012_indexed


title: HFD_Diet_RXR_WT_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD004_indexed


title: HFD_Diet_RXR_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E9_AD006_indexed


title: HFD_Diet_RXR_WT_2


title: HFD_Diet_RXR_WT_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD010_indexed


title: PioHFD_Diet_RXR_WT_1


title: Control_Diet_input_WT_4

source_name: Wildtype Mouse fed control diet for 12 weeks


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD008_indexed


title: Control_Diet_input_WT_3


title: Control_Diet_input_WT_2


title: HFD_Diet_input_WT_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD006_indexed


title: Control_Diet_input_WT_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD004_indexed


title: Control_Diet_RXR_WT_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_F10_AD007_indexed


title: Control_Diet_RXR_WT_4


title: Control_Diet_RXR_WT_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD002_indexed


title: Control_Diet_RXR_WT_1


title: Control_Diet_RXR_WT_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD001_indexed


title: Control_Diet_input_WT_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD008_indexed


title: Plp2mn1

city: New York

first: Sarah

last: Moyon

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

data_processing:
Library strategy: RRHP
RRHP libraries were prepared from 200ng input DNA per biological replicate, as described (ZymoResearch, D5440)
The raw sequencing reads were aligned to the mouse reference genome (mm10).
DNA hydroxymethylation levels were calculated as the relative ratio of cytosine reads for each individual CpG site, for each sample, compared to all the replicates.
Determination of differential hydroxymethylation was performed at the single base level, using only CpG dinucleotides. Differentially hydroxymethylated CpGs were selected at a q-value < 0.05.
Differentially hydroxymethylated regions (DMR) were defined by 2 kb genomic regions containing at least 2 concordantly hydroxymethylated CpGs (in the same direction).
Genome_build: mm10
Supplementary_files_format_and_content: counts, .txt files

source_name: Brain

extract_protocol:
DNA were obtained from FAC-sorted P60 oligodendrocyte progenitor cells and from P60 myelinating oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. DNA quality was checked using a NanoDrop and aQubit Fluorometric quantitation (Thermo Fisher).
RRHP libraries were prepared following ZymoReseacrch protocol ZymoResearch, D5440)

tag: development stage

value: Post-natal day 60

value: Primary FAC-sorted PDGFRa-EGFP+ cells


title: Plp2mn3


title: Plp2mn2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD004_indexed


title: Pdgfra2mn3


title: Pdgfra2mn1


title: Pdgfra2mn2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD004_indexed


title: NT C57BL/6_2

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
LPS_rechallenge_exp_wt11_nt_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt c57bl6_normalized.txt

data_processing:
UTAP analysis (https://doi.org/10.1186/s12859-019-2728-2)
Demultiplexing
Low-quality trimmng
UMI counting
Normalization
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts, for all genes which are expressed in at least one sample

source_name: Mouse brain

extract_protocol:
Brain homogenization and microglia enrichment
Mars-seq (DOI: 10.1126/science.1247651)

treatment_protocol: 2.5mg/kg LPS injection

value: Brain

tag: cell type

value: Microglia

value: Steady state

value: WT C57BL/6


title: 48 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_2

description:
AS_DKO_LPS_2ndexp_156_DKO_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt

value: 48hrs post LPS i.p


title: NT C57BL/6_4

description:
LPS_rechallenge_exp_wt9_nt_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt c57bl6_normalized.txt


title: NT C57BL/6_1

description:
LPS_rechallenge_exp_wt10_nt_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt c57bl6_normalized.txt


title: 48 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_4

description:
DKO_post_LPS_128
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD010_indexed

value: MOp

value: male


title: NT C57BL/6_3

description:
LPS_rechallenge_exp_wt12_nt_4
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt c57bl6_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD001_indexed


title: 48 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_1

description:
AS_DKO_LPS_2ndexp_112_DKO_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E6_AD001_indexed


title: 48 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_3

description:
DKO_post_LPS_126
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_6

description:
DKO_post_LPS_158
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt

value: 6hrs post LPS i.p


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_5

description:
DKO_post_LPS_156
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD008_indexed


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_4

description:
AS_DKO_LPS_2ndexp_132_DKO_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E5_AD002_indexed


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_2

description:
AS_DKO_LPS_2ndexp_124_DKO_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_1

description:
AS_DKO_LPS_2ndexp_122_DKO_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT  DKO CX3CR1CreER:IL10Rafl:TNFfl_5

description:
DKO_post_LPS_116
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD002_indexed


title: NT  DKO CX3CR1CreER:IL10Rafl:TNFfl_4

description:
DKO_post_LPS_114
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD012_indexed


title: 6 hrs LPS  DKO CX3CR1CreER:IL10Rafl:TNFfl_3

description:
AS_DKO_LPS_2ndexp_126_DKO_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS  'WT' IL10RaflTNFfl_7

description:
DKO_post_LPS_142
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS  'WT' IL10RaflTNFfl_6

description:
DKO_post_LPS_130
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS  'WT' IL10RaflTNFfl_4

description:
AS_DKO_LPS_2ndexp_144_cont_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT  DKO CX3CR1CreER:IL10Rafl:TNFfl_3

description:
DKO_post_LPS_112
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD002_indexed


title: NT  DKO CX3CR1CreER:IL10Rafl:TNFfl_2

description:
AS_DKO_LPS_2ndexp_158_DKO_nt
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT  DKO CX3CR1CreER:IL10Rafl:TNFfl_1

description:
AS_DKO_LPS_2ndexp_148_DKO_nt
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS  'WT' IL10RaflTNFfl_1

description:
AS_DKO_LPS_2ndexp_114_DKO_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD010_indexed


title: 48 hrs LPS  'WT' IL10RaflTNFfl_3

description:
AS_DKO_LPS_2ndexp_142_cont_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD006_indexed


title: 48 hrs LPS  'WT' IL10RaflTNFfl_5

description:
AS_DKO_LPS_2ndexp_146_cont_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E4_AD008_indexed


title: 6 hrs LPS  'WT' IL10RaflTNFfl_5

description:
DKO_post_LPS_162
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 6 hrs LPS  'WT' IL10RaflTNFfl_4

description:
DKO_post_LPS_102
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD012_indexed


title: 6 hrs LPS  'WT' IL10RaflTNFfl_3

description:
AS_DKO_LPS_2ndexp_134_cont_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT 'WT' IL10RaflTNFfl_6

description:
DKO_post_LPS_846
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD001_indexed


title: 6 hrs LPS  'WT' IL10RaflTNFfl_2

description:
AS_DKO_LPS_2ndexp_130_cont_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD007_indexed


title: NT 'WT' IL10RaflTNFfl_5

description:
DKO_post_LPS_844
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS  'WT' IL10RaflTNFfl_2

description:
AS_DKO_LPS_2ndexp_116_cont_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 6 hrs LPS  'WT' IL10RaflTNFfl_1

description:
AS_DKO_LPS_2ndexp_128_cont_6h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT 'WT' IL10RaflTNFfl_4

description:
DKO_post_LPS_118
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD007_indexed


title: NT 'WT' IL10RaflTNFfl_3

description:
AS_DKO_LPS_2ndexp_140_cont_nt
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT 'WT' IL10RaflTNFfl_2

description:
AS_DKO_LPS_2ndexp_138_cont_nt
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E1_AD002_indexed


title: 48 hrs LPS MUT CX3CR1CreER:IL10Rafl_5

description:
AS_DKO_LPS_2ndexp_3_IL10R_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: NT 'WT' IL10RaflTNFfl_1

description:
AS_DKO_LPS_2ndexp_120_cont_nt
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 48 hrs LPS MUT CX3CR1CreER:IL10Rafl_3

description:
AS_3rd_LPS_7B4_IL10R_8_mut2_48h_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 48 hrs LPS MUT CX3CR1CreER:IL10Rafl_4

description:
AS_DKO_LPS_2ndexp_2_IL10R_48h
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_DKO_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD008_indexed


title: 24 hrs LPS MUT CX3CR1CreER:IL10Rafl_5

description:
Anat_LPSchallenged_7B4_IL10R_P_24h_110
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt

value: 24hrs post LPS i.p


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD002_indexed


title: 48 hrs LPS MUT CX3CR1CreER:IL10Rafl_1

description:
AS_3rd_LPS_7B4_IL10R_10_mut3_48h_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD010_indexed


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_7

description:
Anat_LPSchallenged_7B4_IL10R_P_6h_106
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD008_indexed


title: 24 hrs LPS MUT CX3CR1CreER:IL10Rafl_3

description:
Anat_LPSchallenged_7B4_IL10R_P_24h_107
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 24 hrs LPS MUT CX3CR1CreER:IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_501_mut_24h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 48 hrs LPS MUT CX3CR1CreER:IL10Rafl_2

description:
AS_3rd_LPS_7B4_IL10R_48_mut1_48h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 24 hrs LPS MUT CX3CR1CreER:IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_508_mut_24h_4
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_6

description:
Anat_LPSchallenged_7B4_IL10R_P_6h_102
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD004_indexed


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_5

description:
Anat_LPSchallenged_7B4_IL10R_P_6h_100
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E11_AD001_indexed


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_4

description:
AS_2nd_exp_7B4_IL10R_LPS_610_mut_6h_4
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_605_mut_6h_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_3

description:
AS_2nd_exp_7B4_IL10R_LPS_608_mut_6h_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD002_indexed


title: 6 hrs LPS MUT CX3CR1CreER:IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_602_mut_6h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD008_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_9

description:
Anat_LPSchallenged_7B4_IL10R_P_nt_18
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: NT MUT CX3CR1CreER:IL10Rafl_6

description:
AS_3rd_LPS_7B4_IL10R_4_mut1_nt_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD010_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_7

description:
Anat_LPSchallenged_7B4_IL10R_IL10R_P_nt_20
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_E10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD008_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_5

description:
AS_3rd_LPS_7B4_IL10R_24_mut3_nt_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD004_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_4

description:
AS_3rd_LPS_7B4_IL10R_20_mut2_nt_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: NT MUT CX3CR1CreER:IL10Rafl_8

description:
Anat_LPSchallenged_7B4_IL10R_P_nt_17
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: NT MUT CX3CR1CreER:IL10Rafl_3

description:
AS_2nd_exp_7B4_IL10R_LPS_513_mut_nt_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD001_indexed


title: day 7 LPS  IL10Rafl_4

description:
IL10R_LPS_d7_493_flox_4
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt

value: 7days post LPS i.p


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD012_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_512_mut_nt_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD001_indexed


title: day 7 LPS  IL10Rafl_2

description:
IL10R_LPS_d7_481_flox_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt


title: 48 hrs LPS  IL10Rafl_5

description:
AS_3rd_LPS_7B4_IL10R_46_cont4_48h_4
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: day 7 LPS  IL10Rafl_1

description:
IL10R_LPS_d7_474_flox_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D9_AD002_indexed


title: 48 hrs LPS  IL10Rafl_6

description:
AS_3rd_LPS_7B4_IL10R_54_cont5_48h_5
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD006_indexed


title: NT MUT CX3CR1CreER:IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_510_mut_nt_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 48 hrs LPS  IL10Rafl_3

description:
AS_3rd_LPS_7B4_IL10R_38_cont2_48h_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 48 hrs LPS  IL10Rafl_2

description:
AS_3rd_LPS_7B4_IL10R_32_cont6_48h_6
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 48 hrs LPS  IL10Rafl_1

description:
AS_3rd_LPS_7B4_IL10R_30_cont1_48h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD002_indexed


title: 48 hrs LPS  IL10Rafl_4

description:
AS_3rd_LPS_7B4_IL10R_42_cont3_48h_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 24 hrs LPS  IL10Rafl_4

description:
Anat_LPSchallenged_7B4_IL10R_M_24h_109
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD004_indexed


title: 24 hrs LPS  IL10Rafl_3

description:
AS_2nd_exp_7B4_IL10R_LPS_502_cont_24h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD001_indexed


title: 24 hrs LPS  IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_509_cont_24h_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 24 hrs LPS  IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_511_cont_24h_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD008_indexed


title: 6 hrs LPS  IL10Rafl_5

description:
Anat_LPSchallenged_7B4_IL10R_M_6h_112
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D8_AD006_indexed


title: 6 hrs LPS  IL10Rafl_6

description:
Anat_LPSchallenged_7B4_IL10R_M_6h_113
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS  IL10Rafl_4

description:
Anat_LPSchallenged_7B4_IL10R_M_6h_111
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS  IL10Rafl_3

description:
AS_2nd_exp_7B4_IL10R_LPS_604_cont_6h_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD008_indexed


title: 6 hrs LPS  IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_601_cont_6h_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: NT IL10Rafl_6

description:
AS_3rd_LPS_7B4_IL10R_2_cont1_nt_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D7_AD002_indexed


title: NT IL10Rafl_5

description:
AS_3rd_LPS_7B4_IL10R_22_cont3_nt_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D4_AD006_indexed


title: NT IL10Rafl_3

description:
AS_2nd_exp_7B4_IL10R_LPS_609_cont_nt_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 6 hrs LPS  IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_603_cont_6h_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD006_indexed


title: NT IL10Rafl_4

description:
AS_3rd_LPS_7B4_IL10R_18_cont2_nt_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D6_AD007_indexed


title: NT IL10Rafl_2

description:
AS_2nd_exp_7B4_IL10R_LPS_607_cont_nt_2
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: NT IL10Rafl_1

description:
AS_2nd_exp_7B4_IL10R_LPS_606_cont_nt_1
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt, UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD012_indexed


title: total_RNA_MCM2_2A_mESC rep2

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

source_name: mESC

growth_protocol: Mouse E14 ES cells (a gift from Dr. Tom Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. Yeast cells were synchronized and cultured following the standard protocol (Dunham et al., 2015).

extract_protocol:
eSPAN in yeast was performed exactly as previously described (Yu et al., 2014). Total RNA samples were purified the same as for RT-PCR. OK-seq was performed as previously described with some modifications (Petryk et al., 2016).
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.
RNA-Seq, ChIP-Seq, CUT&TAG, OK-Seq, eSPAN

tag: experiments


title: total_RNA_POLA1_hbm_mESC


title: H3K9me3_CUT_MCM22A_mESC

data_processing:
Library strategy: CUT&TAG
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.


title: total_RNA_MCM2_2A_mESC


title: total_RNA_WT_mESC

value: WT


title: H3K9me3_CUT_POLA1_hbm_mESC


title: H3K9me3_CUT_POLA1_hbm_mESC rep2


title: H3K9me3_CUT_WT_mESC


title: H4K20me2_eSPAN_MCM22A_mESC 50k

data_processing:
Library strategy: eSPAN
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

tag: condition

value: 50k cell


title: H4K20me2_eSPAN_POLA12A_mESC 50k


title: total_RNA_POLA1_hbm_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD007_indexed


title: H3K9me3_CUT_WT_mESC rep2


title: H4K20me2_eSPAN_WT_mESC 50k


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD010_indexed


title: total_RNA_WT_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD006_indexed


title: H4K20me2_eSPAN_WT_mESC 100k

value: 100k cell


title: 24 hrs LPS MUT CX3CR1CreER:IL10Rafl_4

description:
Anat_LPSchallenged_7B4_IL10R_P_24h_108
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl vs mut_normalized.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D3_AD008_indexed


title: H3K36me3_eSPAN_POLA12A_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD012_indexed


title: H3K36me3_eSPAN_WT_mESC rep2


title: H3K36me3_eSPAN_WT_mESC


title: H4K12ac_eSPAN_POLA12A_mESC rep2


title: H3K36me3_eSPAN_POLA12A_mESC


title: H4K12ac_eSPAN_POLE4_KO_mESC rep2


title: H4K12ac_eSPAN_POLE4_KO_mESC


title: H4K12ac_eSPAN_POLE3_KO_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD002_indexed