title: Exon 22, part 4, cisplatin, replicate 2


title: Exon 22, part 1, DMSO, replicate 2

status: Public on Sep 27 2024

type: SRA

city: Frederick

first: Shyam

last: Sharan

state: MD

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

country: USA

institute: National Cancer Institute

library_source: genomic

data_processing:
The reads were demultiplexed using bcl2fastq
SeqPrep was used for adapter trimming and merging the read pairs
The reads were aligned to GRCh38 reference genome using the needleall command from the EMBOSS package
Gaussian mixture-model was applied to HDR counts to get function score
Assembly: GRCh38
Supplementary files format and content: SNV function scores

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cell line expressing a single copy of human BRCA2 [Clone: F7/F7] was cultured with underlying feeder cells (SNLP) that express leukemia inhibitory factor (Lif) and puromycin and neomycin resistance cassettes. The maintenance medium consisted of Knockout DMEM (Gibco) supplemented with 15% FBS (HyClone), penicillin-streptomycin-glutamine (Gibco) and 0.1 mM b-mercaptoethanol. The media was changed every day and cells were trypsinized when ESCs reached 80% confluency.

extract_protocol:
Genomic DNA was extracted from the cell pellets utilizing the Zymo Genomic DNA Extraction kit
The DNA libraries were prepared in line with the protocol specified in the Illumina TruSeq Nano DNA Library Prep kit

tag: cell line

tag: cell type

value: Embryonic stem cell

tag: genotype

value: expressing a single copy of human BRCA2 [Clone:F7/F7]

tag: treatment

value: DMSO

tag: time point

value: Day 14

tag: exon

tag: part

tag: replicate


title: Exon 22, part 2, cisplatin, replicate 1

value: cisplatin


title: Exon 22, part 3, DMSO, replicate 2


title: Exon 22, part 1, olaparib, replicate 1

value: olaparib


title: Exon 21, part 3, olaparib, replicate 2


title: Exon 22, part 1, cisplatin, replicate 2


title: Exon 22, part 1, olaparib, replicate 2


title: Exon 22, part 1, cisplatin, replicate 1


title: Exon 21, part 3, none, replicate 2

value: Day 3


title: Exon 21, part 3, none, replicate 1


title: Exon 21, part 3, DMSO, replicate 1


title: Exon 21, part 3, DMSO, replicate 2


title: Exon 21, part 2, none, replicate 2


title: Exon 21, part 2, none, replicate 1


title: Exon 21, part 2, DMSO, replicate 2


title: Exon 21, part 2, cisplatin, replicate 2


title: Exon 21, part 2, DMSO, replicate 1


title: Exon 21, part 3, cisplatin, replicate 1


title: Exon 21, part 2, cisplatin, replicate 1


title: Exon 21, part 3, cisplatin, replicate 2


title: Exon 21, part 1, none, replicate 2


title: Exon 22, part 1, DMSO, replicate 1


title: Exon 21, part 1, none, replicate 1


title: Exon 25, part 4, olaparib, replicate 2


title: Exon 21, part 1, olaparib, replicate 2


title: Exon 21, part 1, olaparib, replicate 1


title: Exon 21, part 1, DMSO, replicate 1


title: Exon 21, part 1, cisplatin, replicate 2


title: Exon 21, part 1, cisplatin, replicate 1


title: Exon 20, part 4, none, replicate 1


title: Exon 21, part 1, DMSO, replicate 2


title: Exon 20, part 4, none, replicate 2


title: Exon 20, part 4, olaparib, replicate 1


title: Exon 21, part 2, olaparib, replicate 2


title: Exon 20, part 4, DMSO, replicate 2


title: Exon 21, part 3, olaparib, replicate 1


title: Exon 21, part 2, olaparib, replicate 1


title: Exon 20, part 4, DMSO, replicate 1


title: Exon 20, part 4, olaparib, replicate 2


title: Exon 20, part 4, cisplatin, replicate 2


title: Exon 20, part 3, none, replicate 2


title: Exon 20, part 3, none, replicate 1


title: Exon 20, part 3, olaparib, replicate 1


title: Exon 20, part 3, DMSO, replicate 2


title: Exon 20, part 3, olaparib, replicate 2


title: Exon 20, part 3, DMSO, replicate 1


title: Exon 20, part 3, cisplatin, replicate 2


title: Exon 20, part 3, cisplatin, replicate 1


title: Exon 20, part 2, none, replicate 1


title: Exon 20, part 2, olaparib, replicate 2


title: Exon 20, part 2, none, replicate 2


title: Exon 20, part 2, olaparib, replicate 1


title: Exon 20, part 2, DMSO, replicate 2


title: Exon 20, part 2, DMSO, replicate 1


title: Exon 20, part 2, cisplatin, replicate 2


title: Exon 20, part 2, cisplatin, replicate 1


title: Exon 19, part 5, none, replicate 2


title: Exon 19, part 5, olaparib, replicate 1


title: Exon 19, part 5, DMSO, replicate 1


title: Exon 20, part 4, cisplatin, replicate 1


title: Exon 19, part 4, none, replicate 2


title: Exon 19, part 5, cisplatin, replicate 2


title: Exon 19, part 5, DMSO, replicate 2


title: Exon 19, part 5, cisplatin, replicate 1


title: Exon 19, part 4, none, replicate 1


title: Exon 19, part 4, olaparib, replicate 2


title: Exon 19, part 4, olaparib, replicate 1


title: Exon 19, part 4, DMSO, replicate 1


title: Exon 19, part 3, none, replicate 2


title: Exon 19, part 3, none, replicate 1


title: Exon 19, part 3, olaparib, replicate 2


title: Exon 19, part 3, olaparib, replicate 1


title: Exon 19, part 3, DMSO, replicate 2


title: Exon 19, part 3, DMSO, replicate 1


title: Exon 19, part 2, none, replicate 2


title: Exon 19, part 3, cisplatin, replicate 2


title: Exon 19, part 5, none, replicate 1


title: Exon 19, part 2, none, replicate 1


title: Exon 19, part 5, olaparib, replicate 2


title: Exon 19, part 2, olaparib, replicate 2


title: Exon 19, part 2, olaparib, replicate 1


title: Exon 19, part 2, DMSO, replicate 2


title: Exon 19, part 4, DMSO, replicate 2


title: Exon 19, part 2, DMSO, replicate 1


title: Exon 19, part 1, none, replicate 1


title: Exon 19, part 1, none, replicate 2


title: Exon 19, part 2, cisplatin, replicate 1


title: Exon 19, part 1, olaparib, replicate 2


title: Exon 19, part 1, DMSO, replicate 1


title: Exon 19, part 1, olaparib, replicate 1


title: Exon 19, part 2, cisplatin, replicate 2


title: Exon 19, part 1, DMSO, replicate 2


title: Exon 19, part 4, cisplatin, replicate 2


title: Exon 19, part 1, cisplatin, replicate 2


title: Exon 19, part 4, cisplatin, replicate 1


title: Exon 18, part 8, none, replicate 2


title: Exon 18, part 8, none, replicate 1


title: Exon 19, part 1, cisplatin, replicate 1


title: Exon 18, part 8, olaparib, replicate 1


title: Exon 18, part 8, olaparib, replicate 2


title: Exon 18, part 8, DMSO, replicate 1


title: Exon 18, part 8, DMSO, replicate 2


title: Exon 19, part 3, cisplatin, replicate 1


title: Exon 18, part 7, olaparib, replicate 2


title: Exon 18, part 7, none, replicate 2


title: Exon 18, part 8, cisplatin, replicate 2


title: Exon 18, part 7, none, replicate 1


title: Exon 18, part 7, olaparib, replicate 1


title: Exon 18, part 7, DMSO, replicate 1


title: Exon 18, part 7, DMSO, replicate 2


title: Exon 18, part 7, cisplatin, replicate 2


title: Exon 18, part 6, olaparib, replicate 2


title: Exon 18, part 6, none, replicate 2


title: Exon 18, part 6, DMSO, replicate 1


title: Exon 18, part 6, none, replicate 1


title: Exon 18, part 6, olaparib, replicate 1


title: Exon 18, part 6, cisplatin, replicate 2


title: Exon 18, part 6, cisplatin, replicate 1


title: Exon 18, parts 4 and 5, none, replicate 2

value: parts 4 and 5


title: Exon 18, parts 4 and 5, olaparib, replicate 2


title: Exon 18, parts 4 and 5, olaparib, replicate 1


title: Exon 18, parts 4 and 5, DMSO, replicate 2


title: Exon 18, parts 4 and 5, DMSO, replicate 1


title: Exon 18, parts 4 and 5, none, replicate 1


title: Exon 18, parts 4 and 5, cisplatin, replicate 2


title: Exon 18, part 8, cisplatin, replicate 1


title: Exon 18, part 3, none, replicate 2


title: Exon 18, part 3, olaparib, replicate 2


title: Exon 18, part 3, none, replicate 1


title: Exon 18, parts 4 and 5, cisplatin, replicate 1


title: Exon 18, part 3, DMSO, replicate 2


title: Exon 18, part 3, DMSO, replicate 1


title: Exon 18, part 3, olaparib, replicate 1


title: Exon 18, part 3, cisplatin, replicate 2


title: Exon 18, part 3, cisplatin, replicate 1


title: Exon 18, part 7, cisplatin, replicate 1


title: Exon 18, part 6, DMSO, replicate 2


title: Exon 18, part 2, none, replicate 1


title: Exon 18, part 2, olaparib, replicate 2


title: Exon 18, part 2, none, replicate 2


title: Exon 18, part 2, DMSO, replicate 1


title: Exon 18, part 1, none, replicate 2


title: Exon 18, part 1, olaparib, replicate 2


title: Exon 18, part 1, cisplatin, replicate 1


title: Exon 18, part 1, cisplatin, replicate 2


title: Exon 18, part 2, olaparib, replicate 1


title: Exon 18, part 2, cisplatin, replicate 1


title: Exon 18, part 1, olaparib, replicate 1


title: Exon 17, part 4, DMSO, replicate 2


title: Exon 17, part 4, DMSO, replicate 1


title: Exon 18, part 1, DMSO, replicate 2


title: Exon 18, part 1, DMSO, replicate 1


title: Exon 17, part 4, none, replicate 2


title: Exon 17, part 3, olaparib, replicate 1


title: Exon 17, part 3, none, replicate 1


title: Exon 17, part 3, DMSO, replicate 2


title: Exon 17, part 4, none, replicate 1


title: Exon 17, part 3, DMSO, replicate 1


title: Exon 17, part 3, cisplatin, replicate 2


title: Exon 17, part 4, olaparib, replicate 2


title: Exon 17, part 4, cisplatin, replicate 2


title: Exon 17, part 4, olaparib, replicate 1


title: Exon 17, part 2, none, replicate 2


title: Exon 17, part 2, none, replicate 1


title: Exon 17, part 3, none, replicate 2


title: Exon 23, part 3, DMSO, replicate 2


title: Exon 17, part 4, cisplatin, replicate 1


title: Exon 17, part 2, DMSO, replicate 2


title: Exon 17, part 2, DMSO, replicate 1


title: Exon 17, part 2, cisplatin, replicate 2


title: Exon 18, part 2, cisplatin, replicate 2


title: Exon 17, part 3, olaparib, replicate 2


title: Exon 18, part 2, DMSO, replicate 2


title: Exon 17, part 1, none, replicate 2


title: Exon 17, part 2, olaparib, replicate 2


title: Exon 18, part 1, none, replicate 1


title: Exon 17, part 1, none, replicate 1


title: Exon 17, part 2, olaparib, replicate 1


title: Exon 17, part 2, cisplatin, replicate 1


title: Exon 16, part 3, none, replicate 2


title: Exon 16, part 3, olaparib, replicate 1


title: Exon 17, part 1, cisplatin, replicate 2


title: Exon 17, part 1, olaparib, replicate 2


title: Exon 17, part 1, olaparib, replicate 1


title: Exon 17, part 1, DMSO, replicate 1


title: Exon 16, part 3, DMSO, replicate 1


title: Exon 16, part 3, none, replicate 1


title: Exon 17, part 1, cisplatin, replicate 1


title: Exon 16, part 3, cisplatin, replicate 2


title: Exon 17, part 3, cisplatin, replicate 1


title: Exon 16, part 2, none, replicate 2


title: Exon 16, part 3, olaparib, replicate 2


title: Exon 16, part 3, DMSO, replicate 2


title: Exon 16, part 2, none, replicate 1


title: Exon 16, part 2, DMSO, replicate 2


title: Exon 16, part 2, cisplatin, replicate 1


title: Exon 15, part 4, none, replicate 2


title: Exon 17, part 1, DMSO, replicate 2


title: Exon 16, part 3, cisplatin, replicate 1


title: Exon 15, part 4, DMSO, replicate 1


title: Exon 16, part 2, cisplatin, replicate 2


title: Exon 15, part 4, none, replicate 1


title: Exon 15, part 4, DMSO, replicate 2


title: Exon 15, part 4, olaparib, replicate 2


title: Exon 16, part 2, DMSO, replicate 1


title: Exon 15, part 4, olaparib, replicate 1


title: Exon 15, part 4, cisplatin, replicate 2


title: Exon 15, part 3, none, replicate 1


title: Exon 15, part 3, olaparib, replicate 2


title: Exon 15, part 3, olaparib, replicate 1


title: Exon 15, part 3, none, replicate 2


title: Exon 15, part 3, DMSO, replicate 2


title: Exon 15, part 4, cisplatin, replicate 1


title: Exon 16, part 2, olaparib, replicate 2


title: Exon 15, part 3, cisplatin, replicate 2


title: Exon 15, part 3, DMSO, replicate 1


title: Exon 15, part 2, none, replicate 1


title: Exon 15, part 2, DMSO, replicate 2


title: Exon 16, part 2, olaparib, replicate 1


title: Exon 15, part 3, cisplatin, replicate 1


title: Exon 15, part 2, olaparib, replicate 2


title: Exon 15, part 2, none, replicate 2


title: Exon 15, part 2, cisplatin, replicate 2


title: Exon 15, part 2, olaparib, replicate 1


title: Exon 15, part 1, none, replicate 2


title: Exon 15, part 2, cisplatin, replicate 1


title: Exon 15, part 1, none, replicate 1


title: Exon 15, part 1, olaparib, replicate 2


title: Exon 15, part 2, DMSO, replicate 1


title: Exon 15, part 1, DMSO, replicate 1


title: Exon 15, part 1, cisplatin, replicate 1


title: Exon 15, part 1, DMSO, replicate 2


title: Exon 15, part 1, cisplatin, replicate 2


title: HN_ChIP_317_Input_Nostim_1h_ILC2_rep1

status: Public on Sep 25 2024

city: Bethesda

first: Hiroyuki

last: Nagashima

state: Maryland

address: 10 Center Dr, Room 13C120

institute: NIH

data_processing:
Sequencing data from ChIP-Seq were mapped onto mouse genome build mm10 using Bowtie 0.12.8. All ChIP-Seq experiments were done in biological duplicates. BigWig tracks were generated from Bam files and converted into bedGraph format using bedtools. These were further reformatted with the UCSC tool bedGraphToBigWig. MACS (version 1.4.2) was used for peak calling using a P value threshold of 1 × 10-5.
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: peak files

source_name: lung

extract_protocol:
Stimulated or unstimulated cells were fixed for 10 min with 1% formaldehyde (ThermoFisher, #28908). Fixation was quenched by adding glycine (Sigma) at a final concentration of 125 mM. The nuclei preparation, chromatin digestion and chromatin immunoprecipitation were performed using SimpleChIP Plus Enzymatic Chromatin IP Kit (#9005, Cell Signaling Technology) with the antibodies against RNA polymerase II (#ab5408, abcam), p300 (#ab14984, abcam), GATA3 (#5852, Cell signaling), NFAT1 (#5861, Cell Signaling Technology), RelA (#8242, Cell Signaling Technology), CTCF (#07-729, Millipore Sigma) and Rad21 (#ab992, abcam).
The immunoprecipitated DNAs were subsequently processed to generate a DNA library using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, # E7645L) and NEBNext® Multiplex Oligos for Illumina (NEB, #E6440S).

tag: tissue

value: lung

value: WT


title: HN_ChIP_316_Input_CD3_CD28_1h_Th2_rep2

source_name: spleen

value: spleen


title: HN_ChIP_319_Input_33_NMU_1h_ILC2_HN_rep1


title: HN_ChIP_318_Input_Nostim_1h_ILC2_rep2


title: HN_ChIP_309_Rad21_Nostim_1h_ILC2_rep1


title: HN_ChIP_310_Rad21_Nostim_1h_ILC2_rep2


title: HN_ChIP_311_Rad21_33_NMU_1h_ILC2_rep1


title: HN_ChIP_313_Input_Nostim_1h_Th2_rep1


title: HN_ChIP_314_Input_Nostim_1h_Th2_rep2


title: HN_ChIP_308_Rad21_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_306_Rad21_Nostim_1h_Th2_rep2


title: HN_ChIP_307_Rad21_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_183_NFAT1_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_185_CTCF_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_182_p65_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_190_Input_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_305_Rad21_Nostim_1h_Th2_rep1


title: HN_ChIP_180_p300_CD3_CD28_1h_Th2_rep2


title: Exon 15, part 1, olaparib, replicate 1


title: HN_ChIP_181_GATA3_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_320_Input_33_NMU_1h_ILC2_HN_rep2


title: HN_ChIP_171_NFAT1_Nostim_1h_Th2_rep2


title: HN_ChIP_173_CTCF_Nostim_1h_Th2_rep2


title: HN_ChIP_170_p65_Nostim_1h_Th2_rep2


title: HN_ChIP_179_Pol_II_CD3_CD28_1h_Th2_rep2


title: HN_ChIP_169_GATA3_Nostim_1h_Th2_rep2


title: HN_ChIP_312_Rad21_33_NMU_1h_ILC2_rep2


title: HN_ChIP_178_Input_Nostim_1h_Th2_rep2


title: HN_ChIP_161_CTCF_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_159_NFAT1_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_167_Pol_II_Nostim_1h_Th2_rep2


title: HN_ChIP_315_Input_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_149_CTCF_Nostim_1h_Th2_rep1


title: HN_ChIP_157_GATA3_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_155_Pol_II_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_156_p300_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_147_NFAT1_Nostim_1h_Th2_rep1


title: HN_ChIP_096_Input_33_NMU_1h_ILC2_rep2


title: HN_ChIP_146_p65_Nostim_1h_Th2_HN_rep1


title: HN_ChIP_158_p65_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_095_CTCF_33_NMU_1h_ILC2_rep2


title: HN_ChIP_145_GATA3_Nostim_1h_Th2_rep1


title: HN_ChIP_092_p65_33_NMU_1h_ILC2_rep2


title: HN_ChIP_143_Pol_II_Nostim_1h_Th2_rep1


title: HN_ChIP_144_p300_Nostim_1h_Th2_rep1


title: HN_ChIP_091_GATA3_33_NMU_1h_ILC2_rep2


title: HN_ChIP_168_p300_Nostim_1h_Th2_rep2


title: HN_ChIP_089_Pol_II_33_NMU_1h_ILC2_rep2


title: HN_ChIP_079_CTCF_Nostim_1h_ILC2_rep2


title: HN_ChIP_076_p65_Nostim_1h_ILC2_rep2


title: HN_ChIP_090_p300_33_NMU_1h_ILC2_rep2


title: HN_ChIP_077_NFAT1_Nostim_1h_ILC2_rep2


title: HN_ChIP_166_Input_CD3_CD28_1h_Th2_rep1


title: HN_ChIP_073_Pol_II_Nostim_1h_ILC2_rep2


title: HN_ChIP_074_p300_Nostim_1h_ILC2_rep2


title: HN_ChIP_064_Input_33_NMU_1h_ILC2_rep1


title: HN_ChIP_075_GATA3_Nostim_1h_ILC2_rep2


title: HN_ChIP_154_Input_Nostim_1h_Th2_rep1


title: HN_ChIP_061_NFAT1_33_NMU_1h_ILC2_rep1


title: HN_ChIP_060_p65_33_NMU_1h_ILC2_rep1


title: HN_ChIP_057_Pol_II_33_NMU_1h_ILC2_rep1


title: HN_ChIP_048_Input_Nostim_1h_ILC2_rep1


title: HN_ChIP_047_CTCF_Nostim_1h_ILC2_rep1


title: HN_ChIP_043_GATA3_Nostim_1h_ILC2_rep1


title: HN_ChIP_042_p300_Nostim_1h_ILC2_rep1


title: HN_ChIP_045_NFAT1_Nostim_1h_ILC2_rep1


title: HN_ChIP_093_NFAT1_33_NMU_1h_ILC2_rep2


title: HN_ChIP_041_Pol_II_Nostim_1h_ILC2_rep1


title: HN_ChIP_080_Input_Nostim_1h_ILC2_rep2


title: HN_HiC_007_CD3_CD28_1h_Th2_rep1

data_processing:
The initial Hi-C data processing was done with HOMER 4.11.1. The MboI restriction sites used for self ligation (GATC) were trimmed from the FastQ files using “homerTools trim” function. The trimmed reads were mapped onto mm10 using Bowtie 2.4.5. The paired-end tag directories were created using “makeTagDirectory” command, which also generated several quality control analysis files. The .hic files were created using HOMER function “tagDir2hicFile.pl” with Juicer 1.6 and visualized with Juicebox 1.9.8.
Assembly: mm10 or hg38
Supplementary files format and content: .hic files

extract_protocol: A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245


title: HN_HiC_008_CD3_CD28_1h_Th2_rep2


title: HN_HiC_006_Nostim_1h_Th2_rep2


title: HN_HiC_005_Nostim_1h_Th2_rep1


title: HN_HiC_001_33_NMU_1h_ILC2_rep1


title: HN_BL_182_invitroTh2_CD3_CD28_4h_rep2

library_source: transcriptomic

data_processing:
Raw sequencing data were processed with bcl2/2.20.0 to generate FastQ files. Sequence reads were mapped onto mouse genome build mm10 or human genome build hg38 using TopHat 2.1.0. Gene expression values (FPKM; fragments per kilobase exon per million mapped reads) were calculated with Cufflinks 2.2.1.
Assembly: mm10 or hg38
Supplementary files format and content: Excel files include FPKM values for each samples

molecule: total RNA

extract_protocol:
Approximately 20,000–50,000 cells (cell viability >98%) were lysed with TRIzol (Life Technologies) and total RNAs were extracted using Direct-zol™ RNA MicroPrep (Zymo Research).
Total RNAs were subsequently processed to generate an mRNA-seq library using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530S) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S) according to the manufacturer's instructions.

value: Th cells


title: HN_HiC_003_Nostim_1h_ILC2_rep2


title: HN_BL_179_invitroTh2_Nostim_4h_rep1


title: HN_HiC_002_Nostim_1h_ILC2_rep1


title: HN_fHiC_043_33_NMU_1h_WT_ILC2_rep1

data_processing:
The initial Hi-C data processing was done with HOMER 4.11.1. The MboI restriction sites used for self ligation (GATC) were trimmed from the FastQ files using “homerTools trim” function. The trimmed reads were mapped onto mm10 using Bowtie 2.4.5. The paired-end tag directories were created using “makeTagDirectory” command, which also generated several quality control analysis files. The .hic files were created using HOMER function “tagDir2hicFile.pl” with Juicer 1.6 and visualized with Juicebox 1.9.8.
Assembly: mm10
Supplementary files format and content: .hic files

extract_protocol:
A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245. For focused HiC-seq, we designed 1490 probes targeting chr11:53,250,000 – 54,250,000 (length: 1Mb) containing type 2 cytokine locus.
A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245. For focused HiC-seq, we designed 1490 probes targeting chr11:53,250,000 – 54,250,000 (length: 1Mb) containing type 2 cytokine locus.
focused HiC


title: HN_ChIP_063_CTCF_33_NMU_1h_ILC2_rep1


title: HN_fHiC_044_33_NMU_1h_WT_ILC2_rep2


title: HN_ChIP_044_p65_Nostim_1h_ILC2_rep1


title: HN_BL_181_invitroTh2_CD3_CD28_4h_rep1


title: HN_fHiC_042_Nostim_1h_WT_ILC2_rep2


title: HN_fHiC_041_Nostim_1h_WT_ILC2_rep1


title: HN_fHiC_040_33_NMU_1h_6.5kbIl13_ILC2_rep2


title: HN_ChIP_059_GATA3_33_NMU_1h_ILC2_rep1


title: HN_fHiC_038_Nostim_1h_6.5kbIl13_ILC2_rep2


title: HN_fHiC_037_Nostim_1h_6.5kbIl13_ILC2_rep1


title: HN_fHiC_012_33_NMU_1h_5HSIII_ILC2_rep2


title: HN_fHiC_039_33_NMU_1h_6.5kbIl13_ILC2_rep1


title: HN_BL_180_invitroTh2_Nostim_4h_rep2


title: HN_fHiC_008_33_NMU_1h_WT_ILC2_rep2


title: HN_fHiC_009_33_NMU_1h_5HSII_ILC2_rep1


title: HN_HiC_004_33_NMU_1h_ILC2_rep2


title: HN_fHiC_011_33_NMU_1h_5HSIII_ILC2_rep1


title: HN_fHiC_005_Nostim_1h_5HSIII_ILC2_rep1


title: HN_fHiC_010_33_NMU_1h_5HSII_ILC2_rep2


title: HN_ChIP_058_p300_33_NMU_1h_ILC2_rep1


title: HN_fHiC_004_Nostim_1h_5HSII_ILC2_rep2


title: HN_fHiC_001_Nostim_1h_WT_ILC2_rep1


title: HN_fHiC_003_Nostim_1h_5HSII_ILC2_rep1


title: HN_fHiC_002_Nostim_1h_WT_ILC2_rep2


title: HN_ATAC_057_ILC2_6.5kbIl13KO_IL33_NMU_4h_rep3

data_processing:
Reads were mapped to the mouse genome (mm10 assembly) or the human genome (hg38 assembly) using Bowtie 1.1.1. In all cases, redundant reads were removed using FastUniq, and customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. Distributions of fragment sizes were similar to previously published data (data not shown). Reads whose fragment lengths were less than 175 bp were kept and only one mapped read per a unique genomic region was used to call peaks. Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files

extract_protocol:
Ten thousand cells were pelleted and washed with 50 μL 1 × PBS. After lysis, nuclei were pelleted by centrifuging at 500 × g for 10 min, and re-suspended in 50 μL transposase mixture (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, 22 μl of nuclease-free water) (#20034197, Illumina; #G9441, Promega) for incubattion at 37°C with shaking at 300 rpm for 30 min. The tagmentated DNAs were then purified using a QIAGEN MinElute kit and amplified with 10 or 11 cycles of PCR based on the amplification curve
The libraries were purified using a QIAGEN PCR cleanup kit, and sequenced for 50 cycles (paired-end reads) on a HiSeq 3000 or NovaSeq 6000 (Illumina)


title: HN_ATAC_055_ILC2_6.5kbIl13KO_IL33_NMU_4h_rep1


title: HN_fHiC_007_33_NMU_1h_WT_ILC2_rep1


title: HN_ATAC_050_ILC2_6.5kbIl13KO_nostim_4h_rep2


title: HN_ATAC_053_ILC2_WT_IL33_NMU_4h_rep2


title: HN_ATAC_052_ILC2_WT_IL33_NMU_4h_rep1


title: HN_ATAC_054_ILC2_WT_IL33_NMU_4h_rep3


title: HN_ATAC_049_ILC2_6.5kbIl13KO_nostim_4h_rep1


title: HN_ATAC_051_ILC2_6.5kbIl13KO_nostim_4h_rep3


title: HN_ATAC_048_ILC2_WT_nostim_4h_rep3


title: HN_fHiC_006_Nostim_1h_5HSIII_ILC2_rep2


title: HN_HiC_054_human_invitroTh2_PI_4h_donor3

organism: Homo sapiens

source_name: blood

value: blood


title: HN_ATAC_046_ILC2_WT_nostim_4h_rep1


title: HN_HiC_053_human_invitroTh2_PI_4h_donor1


title: HN_BL_189_human_invitroTh2_PI_4h_donor1


title: HN_HiC_051_human_invitroTh2_nostim_donor1


title: HN_BL_188_human_invitroTh2_nostim_donor3


title: HN_BL_190_human_invitroTh2_PI_4h_donor2


title: HN_BL_186_human_invitroTh2_nostim_donor1


title: HN_BL_191_human_invitroTh2_PI_4h_donor3


title: HN_ATAC_047_ILC2_WT_nostim_4h_rep2


title: HN_HiC_052_human_invitroTh2_nostim_donor3


title: HN_BL_185_human_naiveTh_donor3


title: HN_BL_184_human_naiveTh_donor2


title: HN_ATAC_056_ILC2_6.5kbIl13KO_IL33_NMU_4h_rep2


title: HN_ATAC_045_human_invitroTh2_PI_4h_donor3


title: HN_ATAC_044_human_invitroTh2_PI_4h_donor2


title: HN_ATAC_043_human_invitroTh2_PI_4h_donor1


title: HN_BL_183_human_naiveTh_donor1


title: HN_ATAC_042_human_invitroTh2_nostim_donor3


title: HN_ATAC_040_human_invitroTh2_nostim_donor1


title: HN_ATAC_038_human_naiveTh_donor2


title: Gene expression library from human and cynomolgus UGP2 KO, day 7

status: Public on Sep 05 2024

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

country: Germany

institute: University Leiden

library_source: transcriptomic single cell

data_processing:
3’ Gene Expression libraries of each time point (days 0, and 7) were mapped against the human genome GRCh38 (GENCODE v32/Ensembl98), obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0), obtained from Ensembl. Mapping was performed the callranger count function of CellRanger 7.2.0 (10x Genomics).
Assembly: human genome GRCh38 (GENCODE v32/Ensembl98), obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every timepoint (containing counts for both species): matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx

molecule: polyA RNA

organism:
Macaca fascicularis
Homo sapiens

source_name: H9 human embryonic stem cells and 56A1 cynomolgus induced pluripotent stem cells

growth_protocol: PSCs were singularized using Accutase (Sigma Aldrich) and counted on the Countess II FL Automated Cell Counter (Invitrogen). For human ESCs and cynomolgus iPSCs 1.25 x 105 cells/cm2 were seeded onto Matrigel coated plates in UPPS media supplemented with 10 µM Y-27632 (R&D Systems) and incubated overnight, resulting in confluent cultures the following day for each species. For neural induction, media was exchanged to NPC differentiation and maintenance media consisting of 1:1 DMEM/F12 and Neuropan (PAN Biotech) supplemented with 0.5x N2 and B27 supplements, 1x MEM-NEAA, 1x GlutaMAX, 0.1 mM 2-Mercaptoethanol, 5 µg/mL Insulin, human recombinant (all Thermo Fisher Scientific), 10 µM SB431542 and 100 nM LDN193189 (both Peprotech). Cells were washed with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific) before daily media exchange.

extract_protocol:
Equal amounts of cynomolgus and human cells were combined for each time point
Chromium Next GEM Single Cells 3’ Reagent Kits v3.1 (Dual Index) according to the manufacturer's instructions.

treatment_protocol: Neural induction for 7 days

value: NPC differentiation

tag: day


title: MultiPerturb-seq, epigenomic remodeler and NT libraries, BT16 and NIH3T3

status: Public on Sep 22 2024

city: New York

first: Neville

last: Sanjana

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

library_source: other

data_processing:
For alignment and pre-processing, we demultiplexed reads using bcl2fastq (version 2.20) with FASTQs for index reads. Reads were then trimmed with cutadapt (version 4.0) to extract barcode 1 (well barcode), barcode 2 (droplet barcode), ATAC reads, mRNA reads, gRNA reads, and UMIs based on position, then aligned separately. Barcodes and gRNA spacers were aligned with bowtie (version 1.1.2) with the settings -v 2 -m 1 –norc –best –strata. The barcode 1 reference was derived from oligonucleotide sequences and the barcode 2 reference was constructed from the whitelist provided by cellranger-atac (10X Genomics). ATAC reads were aligned with bowtie2 (version 2.5.1) with default parameters to the joint human (hg38) and mouse (mm10) genome reference provided by 10X Genomics. Open chromatin peaks were called using macs2 callpeak (version 2.2.7.1) with the parameters -f BED -g hs -p 0.01 –nomodel –shift 37 –extsize 73 -B –SPMR –keep-dup all –call-summits then reads were assigned to peaks based on loci with bedtools window (version 2.30.0) with a 100 bp window around the start position. mRNA reads were aligned with STAR (version 2.7.3a) using  the settings –quantMode GeneCounts –soloFeatures GeneFull_Ex50pAS, then annotated with subread featureCounts (version 2.0.4) using a joint human (hg38) and mouse (mm10) gtf (10X Genomics, 2020-A) with the settings -t gene -R SAM. Aligned reads were then joined to create a list of cell barcodes (barcode 1 and barcode 2), unique molecular identifiers (UMIs) if applicable, and aligned/annotated reads. These were then deduplicated using awk based on barcode, UMI, and position, then reformatted as a counts matrix using DropletUtils.
For guide RNA assignment, we implemented an algorithm that collapsed highly similar UMIs within the same cell. We did this because, within individual cells, we sometimes identified guide RNA UMIs that differed by only one or two bases. This phenomenon likely arose from sequencing or PCR error, rather than representing genuine biological diversity among UMIs. Consequently, these errors could lead to inflated UMI counts for certain guide-UMI combinations, ultimately skewing the guide assignment and biasing our analysis towards overamplified reads. The algorithm first ranked UMIs based on their read count, assuming that the UMI with the most reads represented the original molecule, that was then mutated during sequencing or PCR. Subsequently, the algorithm recursively removed UMIs that were within a Levenshtein distance of 2 from any remaining UMI with a higher read count or any UMI previously removed. This approach allowed us to account for UMIs that underwent multiple perturbations, such as mutations in both PCR and sequencing stages. Furthermore, we occasionally encountered instances where a single UMI with a high read count was associated with multiple guide RNA, with one association typically dominating in read support. In these cases, we only retained the UMI-guide pairing with the highest read count.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98) and mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: SingleCellExperiment object with counts matrices
Library strategy: Single-nuclei ATAC-seq, single-nuclei RNA-seq, CRISPR guide RNA capture

molecule: other

organism:
Homo sapiens
Mus musculus

source_name: Mixture of BT16 with 20% NIH3T3

growth_protocol: All cell lines were maintained at 37 °C and 5% CO2 in D10 medium: DMEM with high glucose and stabilized L-glutamine (Caisson DML23) supplemented with 10% Serum Plus II (Sigma 14009C).

extract_protocol:
Cells were combined and lysed in 1ml Omni lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40 (ThermoFisher 85124), 0.1% Tween-20 (Sigma P1379), 0.01% digitonin (Promega G9441)) for 10 minutes on ice.
MultiPerturb-seq library preparation: After nuclei isolation and distribution into wells, chromatin was tagmented using barcoded transposomes, then reverse transcription was performed with a mix of poly-dT and CRISPR gRNA-specific primers and barcoded template switch oligonucleotides with matching barcodes. Wells were then pooled and mixed prior to second-round barcoding via droplet microfluidics using 10X Genomics ATAC kit gel beads. Lastly, ATAC, RNA, and CRISPR gRNA libraries were amplified and prepared for sequencing.

treatment_protocol: BT16 and 3T3 cells expressing a second-generation CRISPR repressor were transduced at a low multiplicity-of-infection (~0.05) to achieve one guide per cell and selected using puromycin for cells receiving a CRISPR perturbation, then collected at 7 days post-transduction for MultiPerturb-seq library preparation.

value: Mixture of BT16 with 20% NIH3T3

value: Cells infected with pooled CRISPR library of 344 guide RNAs (BT16) or 50 guide RNAs (NIH3T3)


title: HN_ATAC_037_human_naiveTh_donor1


title: HN_BL_187_human_invitroTh2_nostim_donor2


title: VU1

status: Public on Sep 04 2024

city: Nanjing

first: Dongqing

last: Li

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

country: China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

description:
single cell gene expression sequencing
VU1.zip

data_processing:
The single-cell sequence data were mapped with CellRanger (version 5.0.1) to a manually built human reference genome GRCh38 with annotation file GENCODE version 38. The low-quality cells expressing <500 genes, >20% mitochondrial genes, and <1000 gene counts were filtered out. We excluded mitochondrial and hemoglobin genes, as well as genes expressed in fewer than 10 cells. The Scrublet (v0.2.3) and DoubletFinder (v2.0.3) were further performed on each sample to detect potential doublets. Cell doublets identified by overlaps of two tools or in the same cluster with well-known markers of distinct cell types were also excluded from the analysis.
Data normalization and scaling were performed using the SCTransform package with regressing out the mitochondrial percentage and cell cycle effects. Top 4000 variable genes were used for principal component analysis (PCA). The batch effect of sample-to-sample variation was corrected using top 40 PCs as input of the RunHarmony function when integrating data. Uniform Manifold Approximation and Projection (UMAP) and k-nearest neighbors graph were generated using the RunUMAP and FindNeighbors functions inside Seurat (v4), respectively. The major cell clusters were identified using the Louvain graph-based algorithm with a resolution of 0.8, which resulted in 27 clusters. The differentially expressed genes among clusters were calculated using the FindAllMarkers functions with the MAST method. Genes with adjusted Pvalue<0.05, log fold change>0.25, and detected in at least 25 percent of cells were considered significantly high in the cluster. The clusters were annotated according to the top 20 marker genes of each cluster and documented signature genes of different cell types.
Assembly: GRCh38
Supplementary files format and content: zip files: contain the raw counts of gene expression, cell barcodes, and gene IDs.
Supplementary files format and content: txt file: cell and cluster annotation information

source_name: Skin

extract_protocol:
Venous ulcer and age- and body-location-matched healthy control samples from nine donors were collected at the Dermatology Hospital of Chinese Academy of Medical Sciences, Nanjing, China. Patients with apparent soft tissue infection and need of systemic antibiotics treatment were excluded. After written informed consent was obtained from patients, chronic wound edge tissue samples were collected using a 4 mm biopsy punch after local lidocaine injection.
Wound skin tissues were incubated with 5U/ml Dispase II at 4°C overnight. The epidermis was separated from dermis by tweezers gently and incubated in 0.025% Trypsin/ EDTA (Thermo Fisher) for 10-15 minutes at 37 ℃. The dermal cell suspension was prepared using the whole skin dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions. To capture as many cell types as possible, equal amounts of epidermal and dermal cells were mixed. The red blood cells and dead cells were depleted by Red Blood Cell Removal Solution (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec), respectively. After cleaning, viable cells were loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics). The libraries were subsequently sequenced on an Illumina Novaseq6000 platform to achieve an average of approximately 50K read-pairs per cell.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 used for  venous ulcer (VU) patients (n=4) and matched healthy controls (n=5)

tag: Sex

value: Female

tag: age

value: Skin


title: HN_ATAC_039_human_naiveTh_donor3


title: VU4

description:
single cell gene expression sequencing
VU6.zip

value: Male


title: VU2

description:
single cell gene expression sequencing
VU4.zip


title: Skin6

description:
single cell gene expression sequencing
NS23.zip


title: Skin7

description:
single cell gene expression sequencing
NS24.zip


title: Skin8

description:
single cell gene expression sequencing
NS36.zip


title: Skin9

description:
single cell gene expression sequencing
NS62E.zip


title: J-Lat 10.6, NSC, rep2

status: Public on Aug 31 2024

city: Los Angeles

first: Oliver

middle: I.

last: Fregoso

state: CA

address: 615 Charles E Young

department: MIMG

institute: University of California Los Angeles

data_processing:
Sequencing was performed on Illumina NovaSeq 6000 for PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Data was further checked with through FastQC and MultiQC.
A custom reference genome was generated by combining the Genome Reference Consortium Human build 38 (GRCh38/hg38) and the HIV-1 genome specific to J-Lat 10.6 before aligning the reads to the genome through STAR.
Aligned reads were then normalized through the DESeq2 package in R.
Assembly: GRCh38/hg38 (human); MN989412.1 (HIV)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: J-Lat 10.6 cells were maintained in RPMI 1640 growth medium (L-glutamine, Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from 4x106 J-Lat 10.6 cells according to the W.M. Keck Foundation Biotechnology Resource Laboratory at Yale University TRIzol RNA Isolation protocol
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit (Cat.KK8420).

treatment_protocol: J-Lat 10.6 or 5A8 cells were plated in 6-well tissue culture-treated plates (Greiner Bio-one) 24 hours. They were untreated or treated with 10.0 ng/mL PMA, 25.0 uM SAHA, or 2.5 uM NSC95397 for 24 hrs

value: T lymphocyte


title: J-Lat 10.6, NSC, rep3


title: J-Lat 10.6, NSC, rep1


title: Gene expression library from human and cynomolgus UGP2 KO, day 0

value: H9 human embryonic stem cells and 56A1 cynomolgus induced pluripotent stem cells

value: pluripotent

value: UPPS


title: J-Lat 10.6, SAHA, rep3

value: SAHA


title: VU3

description:
single cell gene expression sequencing
VU5.zip


title: J-Lat 10.6, SAHA, rep2


title: J-Lat 10.6, PMA, rep4


title: J-Lat 10.6, PMA, rep3


title: J-Lat 10.6, SAHA, rep1


title: HN_ATAC_041_human_invitroTh2_nostim_donor2


title: J-Lat 10.6, PMA, rep2

value: PMA


title: J-Lat 10.6, untreated, rep4


title: J-Lat 10.6, untreated, rep3

value: untreated


title: J-Lat 10.6, untreated, rep1

value: WT


title: Skin10

description:
single cell gene expression sequencing
NS63D.zip


title: Synovial cells, mRNA-derived cDNA [BRI1355]

status: Public on Aug 08 2024

city: Boston

first: Heather

last: Faust

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

description:
Meta_data_healthy_synovium_12212024.csv
Normalized_count_matrix_healthy_synovium_12212024.csv

data_processing:
Reads were processed with Cell Ranger v3.1, which demultiplexed cells from different samples and quantified transcript counts per putative cell. Quantification was performed using the STAR aligner against the GRCh38-3.0.0 transcriptome.
Further processing was done with Seurat v 4.0.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38-3.0.0
Supplementary files format and content: Meta_data_healthy_synovium_12212024.csv, contains donor ID, sex, age, BMI, and steroid use status
Supplementary files format and content: Normalized_count_matrix_healthy_synovium_12212024.csv, contains count data for all 16 donors from 3 pooled 10x runs with hashing

source_name: Synovium

extract_protocol:
Cryo-preserved synovial tissue was thawed and rinsed in RPMI with 5% FBS. Samples were transferred to a gentleMACS tube containing digest media (0.2mg/mL Liberase TL, 0.1mg/mL DNase1 in RPMI). Tissue was macerated with gentleMACS followed by shaking at 37 degrees for 30 minutes. The tissue was then filtered through a 70µm cell strainer and spun down. Live cells were sorted on an Aria cell sorter for loading on the 10x chip.
Library generation was performed according to the manufacturer’s protocol (Chromium Single Cell 3ʹ kit (10x Genomics).
HASH-seq library: amplification was performed at 98°C for 2’ followed by 13 cycles 98°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 4°C hold.

value: Synovium

value: live cells

tag: library type

value: mRNA


title: J-Lat 10.6, untreated, rep2


title: Synovial cells, mRNA-derived cDNA [BRI1351]


title: Synovial cells, HTO-derived cDNA [BRI1352 ]

molecule: protein

value: HTO

value: Totalseq


title: J-Lat 10.6, NSC, rep4


title: Synovial cells, HTO-derived cDNA [BRI719 ]


title: Arabidopsis, WT_3, rep3

status: Public on Jul 08 2024

city: Tianjin

first: Ce

last: Song

address: Weijin road NO.94

institute: Nankai University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: TAIR10.1
Supplementary files format and content: FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis grown best under 16/8 hours light / dark cycle at room temperature (18-22 ° C), with light intensity of 120-150 µ mol / m2 (normal conditions).

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (DNBSEQ-T7) and 125bp/150bp paired-end reads were generated.

treatment_protocol: treat under normal conditions

value: seedling

value: normal conditions


title: Arabidopsis, lon1-2_1, rep1

value: LON1 knockout


title: Arabidopsis, lon1-2_3, rep3


title: Arabidopsis, WT_1, rep1


title: JURKAT, oxamate, H3K27ac

status: Public on May 31 2024

city: Shanghai

first: Wu

last: Wenyan

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children's Medical Center

data_processing:
Upon removal of low-quality reads and adapters, quality control was executed using FastQ Screen (version 0.13.0) and FastQC (version 0.11.9)
The Burrows-Wheeler Aligner (version 0.7.17-r1188) was then employed to align the data to the human hg19 genome reference, with non-uniquely mapping reads being discarded.
Duplicate reads were marked with the MarkDuplicates feature in Picard (version 2.22.9, http://broadinstitute.github.io/picard).
BigWig files standardized by spike-in were generated using the bamCoverage tool of deepTools (version 3.4.3)
Assembly: hg19
Supplementary files format and content: bigWig

source_name: JURKAT

growth_protocol: RPMI 1640 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
Cell pellets were resuspended in 50μl nuclear isolation buffer (Sigma NUC-10) with added protease inhibitors. Chromatin digestion was performed using MNase (4-5U, NEB M0247) for 9-20 minutes
Library construction was performed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer's protocol.

treatment_protocol: For the sodium oxamate inhibition experiment, Jurkat cells were cultured for 48 hours in standard medium, medium containing 50mM sodium oxamate, and medium supplemented with both 50mM sodium oxamate and 10mM L-sodium lactate. For the 2DG treatment, JURKAT cells were cultured for 24 hours in standard medium or medium containing 5 mM 2DG.

value: JURKAT

tag: antibody

value: oxamate


title: Arabidopsis, WT_2, rep2


title: JURKAT, oxamate and lactate, H3K27ac

value: oxamate and lactate


title: JURKAT, oxamate, H3K18la


title: Synovial cells, mRNA-derived cDNA [BRI718]


title: JURKAT, oxamate and lactate, H3K18la


title: JURKAT, control, H3K27ac

value: control


title: J-Lat 10.6, SAHA, rep4

value: T lymphocyte


title: DND41, rep2, H3K18la


title: J-Lat 10.6, PMA, rep1


title: Synovial cells, HTO-derived cDNA [BRI1356 ]


title: Arabidopsis, lon1-2_2, rep2


title: DND41, rep1, H3K18la


title: ChIP-seq, H3K27me3, 2205 in vitro, AG120+IFNg, Replicate 2

status: Public on May 06 2024

city: Cambridge

first: Robert

middle: T

last: Manguso

address: 75 Ames Street, Rm 7053

institute: Broad Institute of MIT & Harvard

data_processing:
Fastq files were preprocessed using fastp.
Reads were mapped to mm10 using bowtie2
Duplicates were removed using Picard MarkDuplicates.
For sharp histone modification peaks seen in H3K4me3, we used MACS2 for peak-calling over input control with a parameter of -q 0.01.
For H3K9me3 and H3K27me3, peaks were first called using SICER2 with parameters of -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 (default settings).
To better represent the characteristics of broad histone modification of these markers, we removed peaks of less than 5 kb in length, and then merged neighboring peaks separated by less than 20 kb into one domain
For visualization, bam files were merged by replicates, normalized using scaling factor from trimmed mean of M (TMM) values from edgeR, and smoothed by 150-bp sliding windows with 20-bp bin size using bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig files for samples merged by replicates

source_name: cholangiocarcinoma

growth_protocol: Murine IDH1R132C ICC cell line (2205) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.

extract_protocol:
20 million cells per replicate for each condition (DMSO, AG120, IFNγ, AG120 + IFNγ) were cross-linked using 1% formaldehyde for 10 minutes at room temperature and quenched using glycine for 5 minutes. ChIP experiments were performed using SimpleChIP Enzymatic Chromatin IP Kit based on manufacturer's protocol.
Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit (New England Biolabs)

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine ICC (2205) cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.

value: cholangiocarcinoma

value: tumor cells

value: Albumin-Cre; KrasG12D; IDH1R132C

value: AG120 + IFNgamma


title: ChIP-seq, H3K9me3, 2205 in vitro, AG120+IFNg, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, AG120+IFNg, Replicate 2


title: ChIP-seq, H3K4me3, 2205 in vitro, AG120+IFNg, Replicate 2


title: ChIP-seq, H3K27me3, 2205 in vitro, AG120+IFNg, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, AG120+IFNg, Replicate 1


title: 72h after injure, caudal 0.5mm from epicenter

status: Public on Jun 19 2024

city: Guangzhou

first: Guangdun

last: Peng

address: Kaiyuan Ave 190

department: Guangzhou Institute of Biomedicine and Health

institute: Chinese Academy of Sciences

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
The raw Visium spatial RNA-seq data and histological H&E images were processed using the Space Ranger pipeline (v.1.0.0, 10x Genomics) to align and summarize unique molecular identifier (UMI) counts according to the reference genome “Mouse Genome mm10”.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count of each tissue spot in Hierarchical Data Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tiisue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: spinal cord

growth_protocol: Adult female mice of 8-9 weeks old were used in the SCI.

extract_protocol:
Four consecutive spinal cord cryosections were cut at 20-μm thickness each and attached to one of the four capture areas of the Visium Spatial Gene Expression slides (10x Genomics, 1000184).
The spatial transcriptomics library was constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics, CG000239 Rev D).

treatment_protocol: a complete transection of the spinal cord of C57BL/6J mice at the tenth thoracic vertebra was performed.

value: spinal cord

value: transection


title: ChIP-seq, H3K4me3, 2205 in vitro, AG120+IFNg, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, AG120, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, AG120+IFNg, Replicate 1


title: ChIP-seq, H3K27me3, 2205 in vitro, AG120, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, AG120, Replicate 2


title: ChIP-seq, H3K4me3, 2205 in vitro, AG120, Replicate 2


title: ChIP-seq, H3K27me3, 2205 in vitro, AG120, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, AG120, Replicate 1


title: ChIP-seq, H3K4me3, 2205 in vitro, AG120, Replicate 1


title: JURKAT, control, H3K18la


title: ChIP-seq, H3K27me3, 2205 in vitro, IFNg, Replicate 2

value: IFNγ


title: ChIP-seq, H3K4me3, 2205 in vitro, IFNg, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, AG120, Replicate 1


title: ChIP-seq, H3K27me3, 2205 in vitro, IFNg, Replicate 1


title: ChIP-seq, Input, 2205 in vitro, IFNg, Replicate 2


title: ChIP-seq, H3K4me3, 2205 in vitro, IFNg, Replicate 1


title: ChIP-seq, Input, 2205 in vitro, IFNg, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, IFNg, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, DMSO, Replicate 2

value: DMSO


title: ChIP-seq, H3K27me3, 2205 in vitro, DMSO, Replicate 1


title: ChIP-seq, H3K27me3, 2205 in vitro, DMSO, Replicate 2


title: ChIP-seq, H3K9me3, 2205 in vitro, DMSO, Replicate 1


title: ChIP-seq, H3K4me3, 2205 in vitro, DMSO, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, DMSO, Replicate 2


title: ChIP-seq, Input, 2205 in vitro, DMSO, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day AG120, Replicate 3

status: Public on Apr 30 2024

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
For protein coding gene transcripts, trimmed reads were quantified by pseudoalignment to mm10 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample

growth_protocol: Immunocompetent mice harboring subcutaneous allograft tumors generated with murine CKIR132C ICC cells (2205-sgCtrl, -sgCgas, -sgRT) .

extract_protocol:
Tumors were harvested at serial time points (Vehcle, AG120-Day3 and AG120-Day 6). sgCtrl, sgCgas and sgRT CKIR132C ICC cells were isolated by magnetic bead–mediated depletion of stromal populations from tumors treated with vehicle or AG120 for 3 or 6 days. Single-cell suspensions from cells cultured in a monolayer were homogenized in 300 to 600 μL of TRIzol. RNA was extracted from homogenized samples using the Direct-zol RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
NEBNext Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: Tumor-bearing mice were treated (~100 mm^3 starting volume) with vehicle or AG120 (150 mg/kg; twice daily)


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day AG120, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 3-day AG120, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 3-day AG120, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day Vehicle, Replicate 1

value: Vehicle


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 3-day AG120, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 6-day AG120, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day Vehicle, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 3-day AG120, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 6-day AG120, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day Vehicle, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 3-day AG120, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 3-day AG120, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 6-day Vehicle, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 1


title: ChIP-seq, H3K9me3, 2205 in vitro, IFNg, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas 6-day Vehicle, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 6-day Vehicle, Replicate 3


title: ChIP-seq, H3K4me3, 2205 in vitro, DMSO, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 3


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day AG120, Replicate 2

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
For protein coding gene transcripts, trimmed reads were quantified by pseudoalignment to mm10 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
For transposable elements, trimmed reads were mapped to mm10 and quantified using SQuIRE (v0.9.9.9a)
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample
Supplementary files format and content: comma-separated text file includes raw counts for transposable elements in each sample

growth_protocol: Immunocompetent mice harboring subcutaneous allograft tumors generated with murine CKIR132C ICC cells (2205-sgCtrl, -sgTet2) .

extract_protocol:
Tumors were harvested at serial time points (Vehcle, AG120-Day3 and AG120-Day 6). sgCtrl, sgTet2 CKIR132C ICC cells were isolated by magnetic bead–mediated depletion of stromal populations from tumors treated with vehicle or AG120 for 3 or 6 days. Single-cell suspensions from cells cultured in a monolayer were homogenized in 300 to 600 μL of TRIzol. RNA was extracted from homogenized samples using the Direct-zol RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by rRNA depletion by Ribo-ZeroTM & NEB directional library


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 3


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day AG120, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCgas, 6-day AG120, Replicate 1


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 3-day AG120, Replicate 3


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day AG120, Replicate 3


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 3-day AG120, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 3-day AG120, Replicate 1


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day Vehicle, Replicate 2


title: RNA-seq, polyA RNA, 2205 in vivo, sgRT, 6-day AG120, Replicate 1


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day Vehicle, Replicate 3


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgTet2, 6-day Vehicle, Replicate 1


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 1


title: RNA-seq, polyA RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120+IFNg, Replicate 3

status: Public on Apr 28 2024

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.20.0)
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
For protein coding gene transcripts, trimmed reads were quantified by pseudoalignment to hg38 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
Assembly: hg38
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample

growth_protocol: Human IDH1R132C ICC cell line (SNU1079 sgControl or sgcGAS) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.

extract_protocol:
Single-cell suspensions from cells cultured in a monolayer were homogenized in 300 to 600 μL of TRIzol. RNA was extracted from homogenized samples using the Direct-zol RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by NEB RNA Ultra™ II Directional kit

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Human ICC cells (SNU1079 sgControl or sgcGAS) were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120) with or without Zidovudine/AZT. Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.

value: SNU1079 sgCtrl

value: Known:IDH1R132C; CDKN2A.del; PBRM1.fs

value: AG120 + IFNγ + AZT


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day Vehicle, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120, Replicate 1

value: AG120 + AZT


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120+IFNg, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120+IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+IFNg, Replicate 1

value: IFNγ + AZT


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+DMSO, Replicate 3

value: DMSO + AZT


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+IFNg, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+DMSO, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+DMSO, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AZT+AG120, Replicate 3


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 6-day AG120, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCGAS, IFNg, Replicate 3

value: SNU1079 sgCGAS


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120+IFNg, Replicate 1

value: AG120 + IFNγ


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120, Replicate 1

value: cholangiocarcinoma


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120, Replicate 3

value: tumor cells


title: RNA-seq, SNU1079 in vitro, sgCGAS, DMSO, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCGAS, IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCGAS, DMSO, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCGAS, DMSO, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120+IFNg, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120, Replicate 2


title: RNA-seq, total RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 2

value: Albumin-Cre; KrasG12D; IDH1R132C


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120+IFNg, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCtrl, DMSO, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, IFNg, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120, Replicate 3


title: RNA-seq, SNU1079 in vitro, sgCtrl, AG120+IFNg, Replicate 2


title: RRBS, MNNK1 in vitro

data_processing:
Sequencing reads were assessed for QC with FastQC (Babraham Bioinformatics)
Reads were trimmed using Trim Galore (Babraham Bioinformatics, wrapper around Cutadapt for RRBS libraries), using the parameters “--paired -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC.”
Diversity adapters were trimmed using the trimRRBSdiversityAdaptCustomers Python script available from Tecan Genomics.
Bismark aligner (Babraham Bioinformatics, wrapper around Bowtie2) was used to align sequencing reads to the hg38 human genome with default parameters.
The bismark_methylation_extractor function was used to quantify methylated sites with the parameters “-p --comprehensive –bedgraph."
Assembly: hg38
Supplementary files format and content: COV files outputted by bismark which has percent methylation and methylated and total read counts for each CpG

growth_protocol: Human ICC cell lines included the patient-derived models established in Bardeesy lab and cholangiocarcinoma cell lines from other academic labs. The detail culture conditions are listed in the Materials and Methods section.

extract_protocol:
Genomic DNA was extracted from frozen cell pellets using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s instructions and quantified using a NanoDrop.
RRBS libraries were prepared using the Ovation RRBS Methyl-Seq kit (Tecan Genomics, formerly Nugen Technologies) according to the v7 user guide following the True Methyl Module.

treatment_protocol: No treatment

value: Known:IDH1 wildtype


title: RNA-seq, SNU1079 in vitro, sgCtrl, DMSO, Replicate 1


title: RRBS, ICC25 in vitro


title: RNA-seq, SNU1079 in vitro, sgCtrl, IFNg, Replicate 1


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120+IFNg, Replicate 3


title: RRBS, KKU100 in vitro


title: RNA-seq, SNU1079 in vitro, sgCtrl, DMSO, Replicate 2


title: RRBS, SNU1079 in vitro


title: RRBS, ICC21 in vitro


title: RRBS, YSCCC in vitro

value: YSCCC


title: RRBS, ICC11 in vitro


title: RRBS, ICC23 in vitro


title: RRBS, RBE in vitro

value: RBE

value: Known:IDH1R132S, KRASG12V


title: RRBS, ICC3 in vitro


title: RRBS, SNU308 in vitro


title: RNA-seq, SNU1079 in vitro, sgCGAS, IFNg, Replicate 1

value: IFNγ


title: RRBS, ICC10 in vitro


title: RRBS, HuH28 in vitro


title: WGBS, SNU1079 in vitro, AG120+IFNg, Replicate 3

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36).
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Bismark (v0.24.0, Babraham Bioinformatics, wrapper around Bowtie2) was used to align reads to the hg38 genomes with default parameters.
The Bismark function deduplicate_bismark was used to remove read duplicates from alignment files.
The bismark_methylation_extractor function was used to quantify methylated sites with the parameters “-p --comprehensive --no_overlap –bedgraph”.
Assembly: hg38
Supplementary files format and content: COV files outputted by bismark which has percent methylation and methylated and total read counts for each CpG

growth_protocol: Human IDH1R132C ICC cell line (SNU1079) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.

extract_protocol:
Genomic DNAs from single-cell suspensions from cells cultured in a monolayer were extracted from homogenized samples using the QIAamp DNA Mini Kit in accordance with the manufacturer’s suggested protocol.
EZ DNA Methylation Gold Kit (Zymo Research) for DNA bisulfite conversion and Accel-NGS® Methyl-Seq DNA Library Kit for lib prep

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Human ICC (SNU1079) cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.

value: AG120 + IFNg


title: WGBS, SNU1079 in vitro, AG120+IFNg, Replicate 2


title: WGBS, SNU1079 in vitro, AG120, Replicate 3


title: RRBS, SG231 in vitro


title: RNA-seq, SNU1079 in vitro, sgCGAS, AG120+IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, sgCtrl, IFNg, Replicate 2

value: SNU1079 sgCtrl


title: WGBS, SNU1079 in vitro, IFNg, Replicate 2

value: Known:IDH1R132C; CDKN2A.del; PBRM1.fs

value: IFNg


title: WGBS, SNU1079 in vitro, AG120, Replicate 1


title: WGBS, SNU1079 in vitro, IFNg, Replicate 3


title: WGBS, SNU1079 in vitro, AG120+IFNg, Replicate 1


title: WGBS, SNU1079 in vitro, IFNg, Replicate 1


title: RRBS, ICC5 in vitro


title: RNA-seq, MGG152 in vitro, AG120+IFNg, Replicate 2

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
For protein coding gene transcripts, trimmed reads were quantified by pseudoalignment to hg38 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
For transposable elements, trimmed reads were mapped to hg38 and quantified using SQuIRE (v0.9.9.9a)
Assembly: hg38
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample
Supplementary files format and content: tab-delimited text file includes raw counts for transposable elements in each sample

source_name: Brain

growth_protocol: MGG152 glioma spheroid cells were cultured in NeuroCult NS-A Basal Medium (Human) with human Proliferation Supplement (StemCell Technologies 05750) supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 1% penicillin/streptomycin, amphotericin B (250 ng/mL), and Plasmocin (2.5 μg/mL).

extract_protocol:
Single-cell suspensions from cells cultured in a monolayer were homogenized in 300 to 600 μL of TRIzol. RNA was extracted from homogenized samples using the Direct-zol RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by rRNA depletion by Ribo-ZeroTM & NEB directional library

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Human glioma (MGG152) spheroids were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.

value: Brain

value: Glioma

value: IDH1R132H; TP53.mut; ATRX.mut

value: AG120 + IFNgamma


title: RNA-seq, MGG152 in vitro, IFNg, Replicate 3

value: IFNgamma


title: WGBS, SNU1079 in vitro, DMSO, Replicate 2

value: cholangiocarcinoma

value: DMSO


title: WGBS, SNU1079 in vitro, DMSO, Replicate 1

value: tumor cells


title: RNA-seq, MGG152 in vitro, AG120+IFNg, Replicate 3


title: WGBS, SNU1079 in vitro, AG120, Replicate 2


title: RNA-seq, MGG152 in vitro, DMSO, Replicate 1


title: RNA-seq, MGG152 in vitro, AG120, Replicate 2


title: RNA-seq, MGG152 in vitro, AG120+IFNg, Replicate 1


title: RNA-seq, MGG152 in vitro, IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, AG120+IFNg, Replicate 1


title: RNA-seq, MGG152 in vitro, AG120, Replicate 3


title: RNA-seq, SNU1079 in vitro, AG120, Replicate 3


title: RNA-seq, MGG152 in vitro, IFNg, Replicate 1


title: RNA-seq, MGG152 in vitro, AG120, Replicate 1


title: RNA-seq, SNU1079 in vitro, AG120, Replicate 2


title: RNA-seq, SNU1079 in vitro, AG120, Replicate 1


title: WGBS, SNU1079 in vitro, DMSO, Replicate 3


title: RNA-seq, SNU1079 in vitro, IFNg, Replicate 1


title: RNA-seq, SNU1079 in vitro, IFNg, Replicate 3


title: RNA-seq, MGG152 in vitro, DMSO, Replicate 3


title: RNA-seq, SNU1079 in vitro, DMSO, Replicate 1


title: RNA-seq, SNU1079 in vitro, IFNg, Replicate 2


title: RNA-seq, SNU1079 in vitro, DMSO, Replicate 3


title: WGBS, normal liver, AG120, Replicate 2

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36).
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Bismark (v0.24.0, Babraham Bioinformatics, wrapper around Bowtie2) was used to align reads to the mm10 genome with default parameters.
The Bismark function deduplicate_bismark was used to remove read duplicates from alignment files.
The bismark_methylation_extractor function was used to quantify methylated sites with the parameters “-p --comprehensive --no_overlap –bedgraph”.
Assembly: mm10
Supplementary files format and content: COV files outputted by bismark which has percent methylation and methylated and total read counts for each CpG

source_name: liver

extract_protocol:
Genomic DNAs from single-cell suspensions from cells cultured in a monolayer or liver tissues were extracted from homogenized samples using the QIAamp DNA Mini Kit in accordance with the manufacturer’s suggested protocol.
EZ DNA Methylation Gold Kit (Zymo Research) for DNA bisulfite conversion and Accel-NGS® Methyl-Seq DNA Library Kit for lib prep

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine ICC (2205) cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing. The normal livers were from vehicle- or AG120-treated mice for 6 days.

value: liver

value: liver cells

value: Wildtype


title: RNA-seq, SNU1079 in vitro, DMSO, Replicate 2


title: WGBS, normal liver, AG120, Replicate 1


title: WGBS, normal liver, Vehicle, Replicate 2

value: Vehicle


title: WGBS, 2205 in vitro, AG120+IFNg, Replicate 3

value: Albumin-Cre; KrasG12D; IDH1R132C

value: AG120 + IFNγ


title: WGBS, normal liver, Vehicle, Replicate 1


title: RNA-seq, SNU1079 in vitro, AG120+IFNg, Replicate 2

value: AG120 + IFNg


title: RNA-seq, MGG152 in vitro, DMSO, Replicate 2


title: RNA-seq, SNU1079 in vitro, AG120+IFNg, Replicate 3

value: Known:IDH1R132C; CDKN2A.del; PBRM1.fs


title: WGBS, 2205 in vitro, AG120+IFNg, Replicate 2


title: WGBS, 2205 in vitro, AG120+IFNg, Replicate 1


title: WGBS, 2205 in vitro, IFNg, Replicate 3

value: IFNγ


title: WGBS, 2205 in vitro, AG120, Replicate 2


title: WGBS, 2205 in vitro, DMSO, Replicate 2


title: WGBS, 2205 in vitro, DMSO, Replicate 3


title: WGBS, 2205 in vitro, AG120, Replicate 1


title: WGBS, 2205 in vitro, DMSO, Replicate 1


title: WGBS, 2205 in vitro, IFNg, Replicate 2


title: WGBS, 2205 in vitro, AG120, Replicate 3


title: WGBS, 2205 in vitro, IFNg, Replicate 1


title: RNA-seq, 2205 in vitro, AG120+IFNg, Replicate 2


title: RNA-seq, 2205 in vitro, AG120, Replicate 2


title: RNA-seq, 2205 in vitro, AG120, Replicate 3


title: RNA-seq, 2205 in vitro, AG120+IFNg, Replicate 1


title: RNA-seq, 2205 in vitro, AG120+IFNg, Replicate 3


title: RNA-seq, 2205 in vitro, IFNg, Replicate 1


title: RNA-seq, 2205 in vitro, DMSO, Replicate 2


title: RNA-seq, 2205 in vitro, AG120, Replicate 1


title: RNA-seq, 2205 in vitro, DMSO, Replicate 3


title: RNA-seq, PIC496-3 in vitro, AG120+IFNg, Replicate 3

source_name: brain

growth_protocol: Murine glioma spheroid cells were cultured in NeuroCult NS-A Basal Medium (Mouse) with Proliferation Supplement (StemCell Technologies 05701) supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 1% penicillin/streptomycin, amphotericin B (250 ng/mL), and Plasmocin (2.5 μg/mL).

treatment_protocol: This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine glioma (PIC496-3) spheroid cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing. Cells were collected for RNAseq on the fifth day.

value: brain

value: glioma

value: Cas9; Pik3ca-H1047R; Idh1-R132H; Trp53KO; AtrxKO


title: RNA-seq, 2205 in vitro, DMSO, Replicate 1


title: RNA-seq, PIC496-3 in vitro, AG120+IFNg, Replicate 1

value: AG120 + IFNgamma


title: RNA-seq, PIC496-3 in vitro, AG120, Replicate 3


title: RNA-seq, PIC496-3 in vitro, AG120, Replicate 2


title: RNA-seq, PIC496-3 in vitro, AG120, Replicate 1


title: RNA-seq, PIC496-3 in vitro, IFNg, Replicate 3

value: IFNgamma


title: RNA-seq, PIC496-3 in vitro, AG120+IFNg, Replicate 2


title: RNA-seq, PIC496-3 in vitro, IFNg, Replicate 2


title: RNA-seq, PIC496-3 in vitro, DMSO, Replicate 3


title: RNA-seq, PIC496-3 in vitro, DMSO, Replicate 2


title: RNA-seq, PIC496-3 in vitro, DMSO, Replicate 1


title: RNA-seq, PIC496-3 in vitro, IFNg, Replicate 1


title: s6-iPIC extended culture-2

status: Public on Apr 22 2024

city: Fujisawa

first: Hideyuki

last: Hiyoshi

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Sequenced reads were aligned to the human GRCh38 reference and count UMIs using Cell Ranger v2.0.1 software.
Gene barcode matrices were generated from Cell Ranger software.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv,genes.tsv, matrix.mtx)

source_name: pancreatic endocrine like cells

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics ChromiumTM controller and Chromium Single Cell 3' kits v2 (10x Genomics) according to the manufacturer’s instructions.

tag: cell origin

value: induced pluripotent stem cells

value: iPIC

value: s6-iPIC extended culture


title: Br2743

status: Public on Apr 27 2024

city: Baltimore

first: Keri

last: Martinowich

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: brain (hippocampus)

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (hippocampus)


title: Vivo s6-iPIC 6 months

value: Vivo s6-iPIC 6 months


title: RNA-seq, 2205 in vitro, IFNg, Replicate 3

value: cholangiocarcinoma

value: tumor cells


title: RNA-seq, 2205 in vitro, IFNg, Replicate 2

value: Albumin-Cre; KrasG12D; IDH1R132C


title: Vivo s6-iPIC 2 months

value: Vivo s6-iPIC 2 months


title: Vitro s6-iPIC without PD-166866

value: Vitro s6-iPIC without PD-166866


title: MuscleB_Goat

status: Public on Feb 07 2024

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
The adapter sequences and low-quality bases were filtered using Trimmomatic v0.39
The trimmed reads were mapped to the Ensembl 103 version of reference genomes with annotated genes using STAR aligner v 2.7.6 with the following options: “--outFilterMismatchNmax 3 –outFilterType BySJout –quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 –outSAMtype SAM SortedByCoordinate”.
Gene expression levels were quantified as counts using featureCounts
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

organism: Capra hircus

source_name: Muscle

extract_protocol:
Total RNA were extracted using TRIzol method from frozen Brain samples
mRNA were enriched using magnetic beads with Oligo(dT) and sheared. The cDNA was synthesized using random hexamers, end-repaired, and ligated to A base and sequencing adapters.

value: Muscle

tag: development stage

value: adult


title: Human islet tissue

source_name: pancreatic islet

value: pancreatic islet

value: cadaveric human tissue

value: pancreatic islet cell

value: Human islet


title: BrainC_Goat

value: Brain


title: MuscleB_Sheep

organism: Ovis aries


title: MuscleA_Sheep


title: MuscleC_Sheep


title: BrainC_Sheep


title: BrainB_Sheep


title: BrainA_Sheep


title: MuscleC_Cattle

organism: Bos taurus


title: s6-iPIC extended culture-1

value: induced pluripotent stem cells


title: BrainC_Cattle


title: MuscleB_Cattle


title: BrainB_Cattle


title: MuscleA_Cattle


title: CTC93

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: Oregon Health & Science University

data_processing:
The paired, gzipped raw reads were trimmed using TrimGalore (v. 0.6.2). Initial quality control metrics were calculated using the FASTQC package in addition to the program Fastqscreen (with the Bowtie2 aligner specified). Hisat2 (version 2.0.4) mapped the reads to the hg38/GRCh.38 genome. The Hisat2 options required longer anchor lengths for the de novo discovery of splice sites and ignoring reads that do not align with their paired-end mates (–dta, –no-mixed, –no-discordant). The program featureCounts (part of the subread Anaconda package, version 1.6.4) was used to count reads mapped to individual features. A custom R script filtered this count matrix by mitochondrial contamination and feature biotype.
Assembly: hg38
Supplementary files format and content: Tab-separated file is the output of featureCounts and contains raw gene read counts for each sample.

extract_protocol:
Healthy control PBMCs were isolated using Ficoll-Paque Density Gradient Separation. CTCs were enriched using the StemCell Technologies EasySep Direct Human CTC Enrichment Kit.
Single-cell RNA-seq libraries were prepared following the Smart-seq2 protocol from Picelli et al. 2014. Some subtle differences in library prep thermocycler conditions were required to optimize the preps for patient-derived CTCs when compared to A375s or the “mini-bulk” positive control reactions, as per Smart-seq2’s recommendations. For single A375s, patient-derived CTCs, and PBMCs, samples were preamplified (Smart-seq2 step 14) for 18 cycles, corresponding to the expected 10 pg of input RNA from the initial cell lysis. “Mini-bulk” positive control preps were preamplified for 16 cycles, corresponding to the 100 pg of input RNA. After bead purification, library concentration was determined with a Qubit dsDNA HS Assay Kit (Thermofisher cat. no. Q32851, Waltham, MA, USA) and an Agilent Bioanalyzer High Sensitivity DNA kit (cat. no. 5067-4626, Santa Clara, CA, USA). Next, 1 ng of bead-purified, preamplified dsDNA library was loaded into the tagmentation reaction at step 28 of the Smart-seq2 protocol. The final amplification reaction at step 33 was carried out for 12 cycles. All steps not discussed here were carried out as described in Picelli et al. 2014.

value: circulating tumor cells (CTCs)

tag: patient id

tag: day (relative to treatment start date)


title: CTC95

tag: cell line

tag: cell type


title: CTC94


title: MuscleC_Goat


title: CTC96


title: CTC91


title: Vitro s6-iPIC

value: iPIC

tag: treatment

value: Vitro s6-iPIC


title: CTC92


title: BrainA_Cattle


title: MuscleA_Goat


title: CTC87


title: CTC89


title: CTC88


title: CTC90


title: BrainA_Goat


title: CTC86


title: BrainB_Goat


title: CTC85


title: CTC84


title: CTC82


title: CTC81


title: CTC79


title: CTC80


title: CTC77


title: CTC76


title: CTC75


title: CTC71


title: CTC68


title: CTC70


title: CTC72


title: CTC78


title: CTC74


title: CTC67


title: CTC66


title: CTC63


title: CTC62


title: CTC69


title: CTC61


title: CTC57


title: CTC60


title: CTC55


title: CTC83


title: CTC59


title: CTC58


title: CTC64


title: CTC56


title: CTC54


title: CTC51


title: CTC53


title: CTC49


title: CTC73


title: CTC50


title: CTC47


title: CTC65


title: CTC44


title: CTC41


title: CTC45


title: CTC42


title: CTC40


title: CTC37


title: CTC39


title: CTC31


title: CTC30


title: CTC29


title: CTC38


title: CTC36


title: CTC33


title: CTC52


title: CTC32


title: CTC35


title: CTC28


title: CTC25


title: CTC26


title: CTC23


title: CTC27


title: CTC46


title: CTC21

value: healthy control peripheral blood mononuclear cells


title: CTC19


title: CTC22


title: CTC20


title: CTC18


title: CTC48


title: CTC14

value: melanoma


title: CTC16


title: CTC15


title: CTC13


title: CTC34


title: CTC11


title: CTC12


title: CTC10


title: CTC7


title: CTC8


title: CTC4


title: CTC5


title: CTC24


title: CTC9


title: CTC3


title: CTC6


title: CTC1


title: Ultracentrifugation Isolated, Tumor Patient 4 978T_S35

status: Public on Jan 31 2024

city: Gainesville

first: Mei

last: He

state: FL

address: 2033 Mowry Rd, Cancer and Genetics Research Complex

department: Pharmaceutics

institute: University of Florida

data_processing:
FREYA
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic
Trimmed sequence reads were mapped to hg38 using HiSat2
Read count extraction and processing was performed using dexcount
Assembly: GRCh38.109
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: plasma

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen). 100 ng RNA was used for sequencing
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina with poly-A enrichment per manufacturer's instructions

value: plasma

value: Male

tag: race

value: White

tag: pathologgamma-

tag: histology


title: ExoEasy Isolated, Tumor Patient 4 978T_S21

description: ExoEasy Isolated, Tumor Patient 4


title: Fujifilm Isolated, Tumor Patient 4 978T_S28

description: Fujifilm Isolated, Tumor Patient 4


title: CTC2


title: ExCy Isolated, Tumor Patient 4 978T_S14

description: ExCy Isolated, Tumor Patient 4


title: CTC17


title: Fujifilm Isolated, Healthy Patient 3 958-H_S27

description: Fujifilm Isolated, Healthy Patient 3

value: not determined

value: Unknown


title: Ultracentrifugation Isolated, Healthy Patient 3 958-H_S34


title: ExoEasy Isolated, Healthy Patient 3 958-H_S20

description: ExoEasy Isolated, Healthy Patient 3


title: ExCy Isolated, Healthy Patient 3 958-H_S13

description: ExCy Isolated, Healthy Patient 3


title: Ultracentrifugation Isolated, Tumor Patient 3 781-T_S36

value: Female


title: Fujifilm Isolated, Tumor Patient 3 781-T_S29

description: Fujifilm Isolated, Tumor Patient 3


title: ExoEasy Isolated, Tumor Patient 3 781-T_S22

description: ExoEasy Isolated, Tumor Patient 3


title: Ultracentrifugation Isolated, Tumor Patient 2 585T_S37

value: African American


title: ExCy Isolated, Tumor Patient 3 781-T_S15

description: ExCy Isolated, Tumor Patient 3


title: ExoEasy Isolated, Tumor Patient 2 585T_S23

description: ExoEasy Isolated, Tumor Patient 2


title: Fujifilm Isolated, Tumor Patient 2 585T_S30

description: Fujifilm Isolated, Tumor Patient 2


title: ExCy Isolated, Tumor Patient 2 585T_S16

description: ExCy Isolated, Tumor Patient 2


title: Ultracentrifugation Isolated, Healthy Patient 3 542-H_S33


title: Fujifilm Isolated, Healthy Patient 3 542-H_S26

description: Fujifilm Isolated, Healthy Patient 3


title: ExoEasy Isolated, Healthy Patient 3 542-H_S19

description: ExoEasy Isolated, Healthy Patient 3


title: ExCy Isolated, Healthy Patient 3 542-H_S12

description: ExCy Isolated, Healthy Patient 3


title: Fujifilm Isolated, Healthy Patient 1  479-H_S25

description: Fujifilm Isolated, Healthy Patient 1


title: Ultracentrifugation Isolated, Healthy Patient 1  479-H_S32


title: Ultracentrifugation Isolated, Tumor Patient 1  247T_S38


title: ExCy Isolated, Healthy Patient 1  479-H_S11

description: ExCy Isolated, Healthy Patient 1


title: ExoEasy Isolated, Healthy Patient 1  479-H_S18

description: ExoEasy Isolated, Healthy Patient 1


title: ExoEasy Isolated, Tumor Patient 1  247T_S24

description: ExoEasy Isolated, Tumor Patient 1


title: ExCy Isolated, Tumor Patient 1  247T_S17

description: ExCy Isolated, Tumor Patient 1


title: NFATc1 deficient CD8 T cells isolated from the lymph nodes and treated with Tc17 polarizing cytokines and antibodies

status: Public on Nov 27 2023

city: Wuerzburg

first: Muhammad

last: Azeem

state: Bavaria

address: Josef-Schneider Str. 2

department: Dermatology, Allergology, and Venereology

institute: University Hospital Wuerzburg

description: 10x Genomics

data_processing:
Raw BCL files were de-multiplexed and corresponding FASTQ files for GEX and CellPlex libraries were processed with Cellranger version 7.0 using the multi option with default parameters and mouse assembly 10 (mm10).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lymph node

extract_protocol:
Mesenteric lymph nodes were crushed to prepare single cell suspension using 0.70µm cell strainer and then CD8+ T cells were isolated using affininty beads from Miltenyi. The cells were cultured in RPMI media.
The libraries were prepared using 10X Genomics Chromium Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) according to the manufacturer’s instructions.

treatment_protocol: The WT and Nfatc1-/- CD8+ T cells were isolated from mouse lymph nodes and polarized into Tc17 cells using mouse CytoBox Th17 (130-107-758, Miltenyi) kit and stimulated for 3 hours with PMA (100ng/ml)  & Ionomycin (10μg/ml). After that, the polarized Tc17 cells were harvested and tagged with barcodes.

value: Lymph node

tag: strain

value: CD8 T cells

tag: genotype

value: NFATc1 Knock out in T cells


title: CTC43


title: Wild type CD8 T cells isolated from the lymph nodes and treated with Tc17 polarizing cytokines and antibodies

description: 10x Genomics

tag: tissue

value: Wild type


title: BHT injury repeat-1

status: Public on Nov 02 2023

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38.p4 (mm10)

source_name: Lung

extract_protocol:
lungs were inflated with an enzyme dissociation solution (450U/mL Collagenase I (Worthington, LS004197), 5U/mL Dispase (Corning, 354235), and 0.33U/mL DNase I (Roche, 10104159001), in DMEM). Separated lung lobes were minced and incubated in enzyme solution at 37°C for 25-35 minutes. Dissociation was quenched with equivalent volume 10% FBS/DMEM and strained through a 100 µm strainer. Cell pellet was resuspended in red blood cell lysis buffer (100 µm EDTA, 10 mM KHCO3, 155 mM NH4Cl) for 2 minutes, followed by quenching with 10% FBS/DMEM and filtration through a 40 µm strainer. Cell pellet was resuspended in 500µL 2%FBS/DMEM. For MACS, cells were incubated for 30 minutes with the following antibodies: CD45 (MiltenyiBiotech, 130-052-301) and CD31 (MiltenyiBiotech, 130-097-418). MACS depletion was performed as per manufacturer protocol using LD columns (MiltenyiBiotech, 130-042-901). Lung cell suspensions were enriched for epithelial and mesenchymal cell populations and resuspended in PBS supplemented with 0.01% BSA.
We used 10X genomics, 3'-GEX scRNA-seq (V3.1) protocol to capture cells and prepare libraries.
3'-GEX v3.1 (10X genomics)

treatment_protocol: Sftpc-creER;Rosa26-lsl-tdTomato (Ai9); Ctgf-GFP mice were treated with Tamoxifen followed by BHT administration

value: Lung

value: Lung cells

value: Tamoxifen and BHT


title: BHT injury repeat-2

description: 10X genomics


title: scRNA-seq PMBC, PostTx ATL-DC+PolyICLC 21

status: Public on Oct 11 2023

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

data_processing:
The data was demultiplexed, barcode processed and aligned to the Genome Reference Consortium Human Build 38 (GRCh38)  with Cell Ranger (version 3.1.0).
Data was imported into R (version 4.2.1) and analyzed with the Seurat package (version 4.2.0)63. For quality assurance, cells with greater than 20% mitochondrial features were excluded from further analysis. Sample S27-06-2-Day29 (group: Poly-ICLC) was excluded because of poor sequencing quality.
We analyzed a total of 99,590 cells after the QC step. The Seurat data object from each sample were then integrated and scaled, regressing out the percent mitochondrial features and cell cycle score difference, as described(https://satijalab.org/seurat/index.html).
We manually identified each cluster using the genes that were differentially expressed as determined by FindAllMarker function; they are visualized using R’s ggplot2 and pheatmap packages.
Differentially expressed genes (DEGs) corresponding to each treatment group (Placebo vs. Poly-ICLC vs. resiquimod) were computed by computing DEGs between each group against the pre-treatment (Day 0) samples and we visualized recurrent DEGs using pheatmap.
Assembly: GRCh38
Supplementary files format and content: RDS file of Seurat object containing the QC-ed, integrated, scaled and manually annotated clusters of cells.
Supplementary files format and content: Matrix market-formatted raw gene-level count file
Supplementary files format and content: The list of gene names in the raw gene-level count file
Supplementary files format and content: The list of cell barcodes in the raw gene-level count file

source_name: PBMC

extract_protocol:
Viably frozen PBMC were thawed, washed with PBS to remove dead cell debris and resuspended to 1,000 cells/µl. The cells were loaded to the Chromium controller for GEM generation 10x Genomics' protocol. We targeted 10,000 sequenced cells. We only selected representative patients from each treatment group whose PBMC cell quality and quantity were sufficient for single cell RNAseq processing.
Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq)

value: PBMC

value: PolyICLC


title: scRNA-seq PMBC, PostTx ATL-DC+Placebo 12

value: Placebo


title: scRNA-seq PMBC, PreTx 12

value: PreTx


title: scRNA-seq PMBC, PostTx ATL-DC+Placebo 2


title: scRNA-seq PMBC, PreTx 8


title: scRNA-seq PMBC, PreTx 21


title: scRNA-seq PMBC, PostTx ATL-DC+PolyICLC 1


title: scRNA-seq PMBC, PreTx 26


title: scRNA-seq PMBC, PostTx ATL-DC+Resiquimod 8

value: Resiquimod


title: scRNA-seq PMBC, PreTx 1


title: scRNA-seq PMBC, PreTx 27


title: Fujifilm Isolated, Tumor Patient 1  247T_S31

description: Fujifilm Isolated, Tumor Patient 1

value: plasma

tag: Sex

value: White


title: Bulk RNA-seq PMBC, PreTx 27

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads generated using Illumina NovaSeq S4 were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6).
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
Normalized gene-level counts were computed using DESeq2 R package (version 1.24.0). DESeq2 normalized gene expression was log2 transformed after adding a pseudo count of 1
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)
Supplementary files format and content: Gene level normalized counts of each sample as computed by DESeq2 (log2 transformed after adding a pseudo count of 1)

extract_protocol:
Total RNA was isolated from frozen PBMC using Zymo’s Quick-RNA Miniprep Kit
TruSeq RNA exome kit is used to construct the RNA sequencing libraries


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 27


title: scRNA-seq PMBC, healthy donor 7


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 26


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Mixed 24

value: Mixed


title: scRNA-seq PMBC, PostTx ATL-DC+PolyICLC 27

description: not included in analysis because of bad quality


title: scRNA-seq PMBC, healthy donor 6


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 23


title: Bulk RNA-seq PMBC, PreTx 24


title: Bulk RNA-seq PMBC, PreTx 23


title: scRNA-seq PMBC, PostTx ATL-DC+Resiquimod 26


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 21


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Placebo 22


title: Bulk RNA-seq PMBC, PreTx 22


title: Bulk RNA-seq PMBC, PreTx 21


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 20


title: scRNA-seq PMBC, PreTx 2


title: Bulk RNA-seq PMBC, PreTx 20


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 18


title: Bulk RNA-seq PMBC, PreTx 18


title: Bulk RNA-seq PMBC, PreTx 16


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 17


title: Bulk RNA-seq PMBC, PreTx 26


title: Bulk RNA-seq PMBC, PreTx 15


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 13


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Placebo 12


title: Bulk RNA-seq PMBC, PreTx 13


title: Bulk RNA-seq PMBC, PreTx 12


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 11


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 15


title: Bulk RNA-seq PMBC, PreTx 10


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 8


title: Bulk RNA-seq PMBC, PreTx 11


title: Bulk RNA-seq PMBC, PreTx 9


title: Bulk RNA-seq PMBC, PreTx 8


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 7


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 10


title: Bulk RNA-seq PMBC, PreTx 6


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 5


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Placebo 6


title: Bulk RNA-seq PMBC, PreTx 5


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Placebo 9


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Resiquimod 4


title: Bulk RNA-seq PMBC, PreTx 7


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 16


title: Bulk RNA-seq PMBC, PreTx 4


title: Bulk RNA-seq PMBC, PreTx 17


title: Bulk RNA-seq PMBC, PreTx 2


title: Bulk RNA-seq PMBC, PostTx ATL-DC+Placebo 2


title: Bulk RNA-seq PMBC, PreTx 1


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 1


title: Bulk RNA-seq PMBC, PreTx 3


title: Bulk RNA-seq PMBC, PostTx ATL-DC+PolyICLC 3


title: P5 rep1

status: Public on Aug 28 2023

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

data_processing:
Sequence reads were mapped to the mm10 genome and transcriptome by Hisat2 and transcripts quantified using the Cufflinks/cuffdiff pipeline
Reads mapping to the loci for Rpl7 and Rpl7a were extracted in BAM file format using SamTool 1.9
Assembly: mm10
Supplementary files format and content: csv file include FPKM values for Rpl7 from Cuffdiff for all samples

source_name: RGCs

extract_protocol:
Embryonic day18, postnatal day 5 and 8 weeks adult RGCs were purified by immunopanning for Thy1 (after immunopanning depletion of macrophages and amacrine cells)
cDNA libraries prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), paired reads sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

tag: developmental stage

value: RGCs

value: WT


title: Adult rep2

value: Adult