title: Ribo-Tre-rep2

description:
Library name: Ribo_Tre2
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: Screen_5_NT_high_biol_rep_1

status: Public on Aug 06 2025

type: SRA

city: Bethesda

first: Derek

last: Narendra

state: MD

address: 35 CONVENT DR RM 2A-215

department: National Institute of Neurological Disorders and Stroke

country: USA

institute: National Institutes of Health

description:
Library name: Sample 2
HeLa_with_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_with_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt

library_source: genomic

data_processing:
First step (R1 and R3) – assign the guide sequence to the gene using Weissman library list (library_1_2_unbalanced.csv) and check for recombinance (hits = both guides for same gene) using parsr swarm file
Assembly: GRCh38 (Weissman library)
Supplementary files format and content: Correctly matched dual guide hit file from r1 were analyzed using MAGeCK-Vispr robust ranked algorithm pipeline (RRA). txt files for gene summary and sgrna summary (counts) provided
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa with Parkin

extract_protocol:
genomic DNA was extracted via the NucleoSpin Blood L, midi kit for DNA from blood from Macherey-Nagel accoding to manufacturor's instructions
gemonic DNA was PCR amplified using custom primers and NEB Next Ultra II Q5 according to manufacturer's instruction

tag: cell line

value: HeLa with Parkin

tag: treatment

value: Non-treated


title: Screen_5_NT_low_biol_rep_1

description:
Library name: Sample 1
HeLa_with_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_with_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Ribo-Con-rep3

city: Nanchang

first: Junyao

last: Jiang

address: 1 Minde Road, Nanchang City, Jiangxi Province

department: Department of Clinical Laboratory

country: China

institute: The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University

description:
Library name: Ribo_Con3
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

library_source: transcriptomic

data_processing:
For ribo-seq, Low quality reads were filtered by fastp. Raw reads without inserted fragment or containing over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 25-36bp were retained for subsequent analysis. Short reads alignment tool Bowtie (v1.3.1) was used for mapping reads to ribosome RNA (rRNA) database. The reads mapped to rRNAs were removed. Raw reads were were aligned to the genome by STAR(v2.7.10b). After that, quantitative analysis of gene expression was performed. Then RFPs were assigned to different genomic features (exon, intron, intergenic) based on the position of the 5’ end of the alignment. Reads uniquely mapped to a gene were remained for downstream analysis, Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene. For RNA-seq, Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality. Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: Ribo-seq

molecule: polyA RNA

source_name: Multiple myeloma

extract_protocol:
For ribo-seq，Sample was treated with specific lysis buffer with cycloheximide to acquire the lysate, cell lysate was treated with unspecific endoribonuclease RNase I. Monosomes were purified from the lysateby fractionation on a linear sucrose gradient. For RNA-seq, total RNA was extracted from cells using RNA isolater Total RNA Extraction Reagent.
For Ribo-seq, following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. The RNA samples were then treated with rRNA depletion kit (Qiagen, Germany) to deplete as much rRNA contamination as possible before PAGE purification of the relatively short (25~36nt) RPFs. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR. Concentration of the cDNA was measured by Qubit® 2.0 Fluorometer. After library construction（Multiplex Small RNA Library Prep Set for ILLumina (Set1)，NEB）, the concentration of library was measured by Qubit® 2.0 Fluorometer. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. The cDNA library products were generated using VAHTS Small RNA Library Prep Kit.; RNA libraries for RNA-seq were prepared using ployA enrichment method following manufacturer's protocol

tag: tissue

value: Multiple myeloma

tag: cell type

value: Multiple myeloma cells

tag: genotype

value: WT

value: No treatment


title: Ribo-Tre-rep1

description:
Library name: Ribo_Tre1
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

value: METTL5 shRNA infection in RPMI-8226 cells

value: METTL5 shRNA infection


title: Sample_376, Prostate adenocarcinoma, biopsy

city: Waltham

first: Ekaterina

last: Postovalova

address: 95 Sawyer Road

institute: BostonGene Corporation

description: Library name: Sample_376

data_processing:
Libraries were sequenced on NovaSeq 6000 as Paired-End Reads (2x150) with a targeted coverage of 50 mln reads per sample
Bulk RNA-seq fastq files were processed by Kallisto version 0.42.4 for Linux. The Kallisto index file was downloaded from the Xena project to be consistent with the TCGA expression data.
The protein-coding transcripts, IGH/K/L- and TCR-related transcripts were retained, while the noncoding RNA, histone- and mitochondria-related transcripts were removed, resulting in 20,062 protein-coding genes. Gene expression was quantified as transcripts per million (TPM).
For the internal cohort samples whose mRNA was captured using target enrichment, the batch effect was eliminated using Procrustes [doi:10.1038/s42003-024-06020-z].
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

molecule: total RNA

source_name: Prostate adenocarcinoma, biopsy

extract_protocol:
To isolate RNA from 313 FFPE samples, 10 μM-thick paraffin slices were trimmed from each FFPE tissue block using a microtome. RNA was extracted from ten paraffin slices with the RNeasy mini kit (Qiagen, Hilden, Germany). RNA from 52 FF tissue samples was extracted with AllPrep DNA/RNA Mini Kit (Qiagen, CA).
For FFPE tissue samples, the library was prepared using target enrichment with theSureSelect XT HS2 RNA kit (Agilent, CA). The SureSelect Human All Exon V7+UTR (Agilent, CA) exome probe set was used for hybridization and capture of RNA. For FF tissue samples, libraries were prepared with Illumina TruSeq® Stranded mRNA Library Prep (Poly-A mRNA; stranded).

tag: diagnosis

value: Prostate adenocarcinoma

tag: tissue preservation

value: FFPE


title: Ribo-Con-rep1

description:
Library name: Ribo_Con1
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: Ribo-Con-rep2

description:
Library name: Ribo_Con2
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: RNA-Tre-rep3

description:
Library name: RNA_Tre3
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

data_processing:
For ribo-seq, Low quality reads were filtered by fastp. Raw reads without inserted fragment or containing over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 25-36bp were retained for subsequent analysis. Short reads alignment tool Bowtie (v1.3.1) was used for mapping reads to ribosome RNA (rRNA) database. The reads mapped to rRNAs were removed. Raw reads were were aligned to the genome by STAR(v2.7.10b). After that, quantitative analysis of gene expression was performed. Then RFPs were assigned to different genomic features (exon, intron, intergenic) based on the position of the 5’ end of the alignment. Reads uniquely mapped to a gene were remained for downstream analysis, Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene. For RNA-seq, Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality. Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: Sample_375, High grade serous carcinoma, biopsy

description: Library name: Sample_375

source_name: High grade serous carcinoma, biopsy

value: High grade serous carcinoma


title: Sample_373, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_373

value: FF


title: Sample_374, High grade serous carcinoma, biopsy

description: Library name: Sample_374


title: RNA-Tre-rep1

description:
Library name: RNA_Tre1
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: Sample_368, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_368

value: Liver carcinoma and Cholangiocarcinoma


title: Sample_372, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_372


title: Sample_370, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_370


title: Sample_371, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_371


title: Sample_365, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_365

source_name: Gastric Adenocarcinoma, biopsy

value: Gastric Adenocarcinoma


title: Sample_367, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_367


title: Sample_369, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_369


title: Sample_366, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_366

source_name: Colorectal Adenocarcinoma, biopsy

value: Colorectal Adenocarcinoma


title: Sample_364, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_364


title: Sample_363, Breast cancer, biopsy

description: Library name: Sample_363

source_name: Breast cancer, biopsy

value: Breast cancer


title: Sample_359, Breast cancer, biopsy

description: Library name: Sample_359


title: Sample_362, Breast cancer, biopsy

description: Library name: Sample_362


title: Sample_358, Breast cancer, biopsy

description: Library name: Sample_358


title: Sample_356, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_356


title: Sample_354, Prostate adenocarcinoma, biopsy

description: Library name: Sample_354


title: Sample_355, Lung Adenocarcinoma, biopsy

description: Library name: Sample_355

source_name: Lung Adenocarcinoma, biopsy

value: Lung Adenocarcinoma


title: Sample_377, Prostate adenocarcinoma, biopsy

description: Library name: Sample_377


title: Sample_353, Prostate adenocarcinoma, biopsy

description: Library name: Sample_353


title: Sample_352, Prostate adenocarcinoma, biopsy

description: Library name: Sample_352


title: Sample_351, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_351

source_name: Squamous Cell Carcinoma of Lung, biopsy

value: Squamous Cell Carcinoma of Lung


title: Sample_349, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_349


title: Sample_350, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_350


title: Sample_361, Breast cancer, biopsy

description: Library name: Sample_361


title: Sample_347, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_347


title: Sample_345, Renal cell carcinoma, biopsy

description: Library name: Sample_345

source_name: Renal cell carcinoma, biopsy

value: Renal cell carcinoma


title: Sample_348, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_348


title: Sample_342, Renal cell carcinoma, biopsy

description: Library name: Sample_342


title: Sample_341, Renal cell carcinoma, biopsy

description: Library name: Sample_341


title: Sample_344, Renal cell carcinoma, biopsy

description: Library name: Sample_344


title: Sample_346, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_346


title: Sample_343, Renal cell carcinoma, biopsy

description: Library name: Sample_343


title: Sample_339, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_339


title: Sample_338, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_338


title: Sample_340, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_340


title: Sample_336, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_336


title: Sample_337, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_337


title: Sample_360, Breast cancer, biopsy

description: Library name: Sample_360


title: Sample_335, Breast cancer, biopsy

description: Library name: Sample_335


title: Sample_357, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_357


title: Sample_334, Breast cancer, biopsy

description: Library name: Sample_334


title: Sample_330, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_330


title: Sample_331, Breast cancer, biopsy

description: Library name: Sample_331


title: Sample_329, Breast cancer, biopsy

description: Library name: Sample_329


title: Sample_328, Breast cancer, biopsy

description: Library name: Sample_328


title: Sample_327, Breast cancer, biopsy

description: Library name: Sample_327


title: Sample_323, Breast cancer, biopsy

description: Library name: Sample_323


title: Sample_322, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_322


title: Sample_324, Breast cancer, biopsy

description: Library name: Sample_324


title: Sample_333, Breast cancer, biopsy

description: Library name: Sample_333


title: Sample_321, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_321


title: Sample_318, Breast cancer, biopsy

description: Library name: Sample_318


title: Sample_313, Breast cancer, biopsy

description: Library name: Sample_313


title: Sample_317, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_317

source_name: Neuroendocrine neoplasm, biopsy

value: Neuroendocrine neoplasm


title: Sample_314, Breast cancer, biopsy

description: Library name: Sample_314


title: Sample_308, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_308


title: Sample_311, Breast cancer, biopsy

description: Library name: Sample_311


title: Sample_310, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_310


title: Sample_332, Breast cancer, biopsy

description: Library name: Sample_332


title: Sample_304, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_304


title: Sample_309, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_309

source_name: Pancreatic Adenocarcinoma, biopsy

value: Pancreatic Adenocarcinoma


title: Sample_303, Lung Adenocarcinoma, biopsy

description: Library name: Sample_303


title: Sample_307, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_307

source_name: Esophageal Adenocarcinoma, biopsy

value: Esophageal Adenocarcinoma


title: Sample_305, Breast cancer, biopsy

description: Library name: Sample_305


title: Sample_298, Breast cancer, biopsy

description: Library name: Sample_298


title: Sample_302, Lung Adenocarcinoma, biopsy

description: Library name: Sample_302


title: Sample_297, Breast cancer, biopsy

description: Library name: Sample_297


title: Sample_301, Breast cancer, biopsy

description: Library name: Sample_301


title: Sample_290, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_290


title: Sample_300, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_300


title: Sample_288, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_288


title: Sample_319, Breast cancer, biopsy

description: Library name: Sample_319


title: Sample_285, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_285


title: Sample_289, Breast cancer, biopsy

description: Library name: Sample_289


title: Sample_292, Breast cancer, biopsy

description: Library name: Sample_292


title: Sample_291, Breast cancer, biopsy

description: Library name: Sample_291


title: Sample_287, Breast cancer, biopsy

description: Library name: Sample_287


title: Sample_293, Breast cancer, biopsy

description: Library name: Sample_293


title: Sample_283, Breast cancer, biopsy

description: Library name: Sample_283


title: Sample_284, Breast cancer, biopsy

description: Library name: Sample_284


title: Sample_312, Lung Adenocarcinoma, biopsy

description: Library name: Sample_312


title: Sample_281, Breast cancer, biopsy

description: Library name: Sample_281


title: Sample_282, Breast cancer, biopsy

description: Library name: Sample_282


title: Sample_277, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_277


title: Sample_279, Breast cancer, biopsy

description: Library name: Sample_279


title: Sample_275, Breast cancer, biopsy

description: Library name: Sample_275


title: Sample_276, Adrenocortical carcinoma, biopsy

description: Library name: Sample_276

source_name: Adrenocortical carcinoma, biopsy

value: Adrenocortical carcinoma


title: Sample_278, Breast cancer, biopsy

description: Library name: Sample_278


title: Sample_271, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_271


title: Sample_272, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_272


title: Sample_274, Breast cancer, biopsy

description: Library name: Sample_274


title: Sample_273, Breast cancer, biopsy

description: Library name: Sample_273


title: Sample_270, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_270


title: Sample_266, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_266


title: Sample_267, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_267


title: Sample_286, Lung Adenocarcinoma, biopsy

description: Library name: Sample_286


title: Sample_269, Breast cancer, biopsy

description: Library name: Sample_269


title: Sample_264, Breast cancer, biopsy

description: Library name: Sample_264


title: Sample_265, Breast cancer, biopsy

description: Library name: Sample_265


title: Sample_263, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_263


title: Sample_262, Breast cancer, biopsy

description: Library name: Sample_262


title: Sample_260, Breast cancer, biopsy

description: Library name: Sample_260


title: Sample_257, Breast cancer, biopsy

description: Library name: Sample_257


title: Sample_258, Lung Adenocarcinoma, biopsy

description: Library name: Sample_258


title: Sample_259, Breast cancer, biopsy

description: Library name: Sample_259


title: Sample_261, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_261


title: Sample_255, Breast cancer, biopsy

description: Library name: Sample_255


title: Sample_254, Breast cancer, biopsy

description: Library name: Sample_254


title: Sample_280, Breast cancer, biopsy

description: Library name: Sample_280


title: Sample_253, Breast cancer, biopsy

description: Library name: Sample_253


title: Sample_252, Breast cancer, biopsy

description: Library name: Sample_252


title: Sample_249, Lung Adenocarcinoma, biopsy

description: Library name: Sample_249


title: Sample_247, Breast cancer, biopsy

description: Library name: Sample_247


title: Sample_248, Breast cancer, biopsy

description: Library name: Sample_248


title: Sample_246, Breast cancer, biopsy

description: Library name: Sample_246


title: Sample_250, Breast cancer, biopsy

description: Library name: Sample_250


title: Sample_244, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_244


title: Sample_242, Breast cancer, biopsy

description: Library name: Sample_242


title: Sample_245, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_245


title: Sample_241, Breast cancer, biopsy

description: Library name: Sample_241


title: Sample_243, Breast cancer, biopsy

description: Library name: Sample_243


title: Sample_240, Breast cancer, biopsy

description: Library name: Sample_240


title: Sample_236, Breast cancer, biopsy

description: Library name: Sample_236


title: Sample_237, Lung Adenocarcinoma, biopsy

description: Library name: Sample_237


title: Sample_239, Breast cancer, biopsy

description: Library name: Sample_239


title: Sample_256, Endometrial carcinoma, biopsy

description: Library name: Sample_256

source_name: Endometrial carcinoma, biopsy

value: Endometrial carcinoma


title: Sample_235, Breast cancer, biopsy

description: Library name: Sample_235


title: Sample_238, Breast cancer, biopsy

description: Library name: Sample_238


title: Sample_230, Lung Adenocarcinoma, biopsy

description: Library name: Sample_230


title: Sample_234, Breast cancer, biopsy

description: Library name: Sample_234


title: Sample_232, Breast cancer, biopsy

description: Library name: Sample_232


title: Sample_228, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_228


title: Sample_233, Breast cancer, biopsy

description: Library name: Sample_233


title: Sample_226, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_226


title: Sample_224, Breast cancer, biopsy

description: Library name: Sample_224


title: Sample_227, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_227


title: Sample_223, Salivary Adenocarcinoma, biopsy

description: Library name: Sample_223

source_name: Salivary Adenocarcinoma, biopsy

value: Salivary Adenocarcinoma


title: Sample_229, Salivary Adenocarcinoma, biopsy

description: Library name: Sample_229


title: Sample_225, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_225


title: Sample_220, Breast cancer, biopsy

description: Library name: Sample_220


title: Sample_221, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_221


title: Sample_222, Breast cancer, biopsy

description: Library name: Sample_222


title: Sample_219, Breast cancer, biopsy

description: Library name: Sample_219


title: Sample_218, Breast cancer, biopsy

description: Library name: Sample_218


title: Sample_216, Breast cancer, biopsy

description: Library name: Sample_216


title: Sample_251, Breast cancer, biopsy

description: Library name: Sample_251


title: Sample_217, Breast cancer, biopsy

description: Library name: Sample_217


title: Sample_215, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_215


title: Sample_214, Breast cancer, biopsy

description: Library name: Sample_214


title: Sample_212, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_212


title: Sample_231, Lung Adenocarcinoma, biopsy

description: Library name: Sample_231


title: Sample_213, Breast cancer, biopsy

description: Library name: Sample_213


title: Sample_211, Breast cancer, biopsy

description: Library name: Sample_211


title: Sample_206, Breast cancer, biopsy

description: Library name: Sample_206


title: Sample_210, Breast cancer, biopsy

description: Library name: Sample_210


title: Sample_208, Breast cancer, biopsy

description: Library name: Sample_208


title: Sample_205, Breast cancer, biopsy

description: Library name: Sample_205


title: Sample_203, Breast cancer, biopsy

description: Library name: Sample_203


title: Sample_207, Breast cancer, biopsy

description: Library name: Sample_207


title: Sample_202, Breast cancer, biopsy

description: Library name: Sample_202


title: Sample_197, Breast cancer, biopsy

description: Library name: Sample_197


title: Sample_196, Breast cancer, biopsy

description: Library name: Sample_196


title: Sample_195, Breast cancer, biopsy

description: Library name: Sample_195


title: Sample_198, Breast cancer, biopsy

description: Library name: Sample_198


title: Sample_201, Breast cancer, biopsy

description: Library name: Sample_201


title: Sample_192, Breast cancer, biopsy

description: Library name: Sample_192


title: Sample_190, Breast cancer, biopsy

description: Library name: Sample_190


title: Sample_194, Breast cancer, biopsy

description: Library name: Sample_194


title: Sample_189, Breast cancer, biopsy

description: Library name: Sample_189


title: Sample_188, Breast cancer, biopsy

description: Library name: Sample_188


title: Sample_191, High grade serous carcinoma, biopsy

description: Library name: Sample_191


title: Sample_193, Breast cancer, biopsy

description: Library name: Sample_193


title: Sample_209, Breast cancer, biopsy

description: Library name: Sample_209


title: Sample_186, Renal cell carcinoma, biopsy

description: Library name: Sample_186


title: Sample_185, Breast cancer, biopsy

description: Library name: Sample_185


title: Sample_204, Breast cancer, biopsy

description: Library name: Sample_204


title: Sample_179, Breast cancer, biopsy

description: Library name: Sample_179


title: Sample_180, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_180


title: Sample_183, Breast cancer, biopsy

description: Library name: Sample_183


title: Sample_184, Breast cancer, biopsy

description: Library name: Sample_184


title: Sample_177, Salivary Adenocarcinoma, biopsy

description: Library name: Sample_177


title: Sample_178, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_178


title: Sample_200, Breast cancer, biopsy

description: Library name: Sample_200


title: Sample_199, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_199


title: Sample_175, Breast cancer, biopsy

description: Library name: Sample_175


title: Sample_174, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_174


title: Sample_172, Breast cancer, biopsy

description: Library name: Sample_172


title: Sample_173, Breast cancer, biopsy

description: Library name: Sample_173


title: Sample_171, Breast cancer, biopsy

description: Library name: Sample_171


title: Sample_169, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_169


title: Sample_168, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_168


title: Sample_167, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_167


title: Sample_163, Breast cancer, biopsy

description: Library name: Sample_163


title: Sample_162, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_162


title: Sample_181, Breast cancer, biopsy

description: Library name: Sample_181


title: Sample_161, Prostate adenocarcinoma, biopsy

description: Library name: Sample_161

value: Prostate adenocarcinoma


title: Sample_160, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_160

value: FFPE


title: Sample_157, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_157


title: Sample_158, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_158


title: Sample_155, Prostate adenocarcinoma, biopsy

description: Library name: Sample_155


title: Sample_154, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_154


title: Sample_153, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_153


title: Sample_156, Breast cancer, biopsy

description: Library name: Sample_156


title: Sample_182, Breast cancer, biopsy

description: Library name: Sample_182


title: Sample_149, Lung Adenocarcinoma, biopsy

description: Library name: Sample_149


title: Sample_150, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_150


title: Sample_148, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_148


title: Sample_152, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_152


title: Sample_170, Breast cancer, biopsy

description: Library name: Sample_170


title: Sample_187, Breast cancer, biopsy

description: Library name: Sample_187


title: Sample_146, Endometrial carcinoma, biopsy

description: Library name: Sample_146


title: Sample_159, Breast cancer, biopsy

description: Library name: Sample_159


title: Sample_147, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_147


title: Sample_145, Breast cancer, biopsy

description: Library name: Sample_145


title: Sample_151, Breast cancer, biopsy

description: Library name: Sample_151


title: Sample_143, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_143


title: Sample_165, Breast cancer, biopsy

description: Library name: Sample_165


title: Sample_164, Breast cancer, biopsy

description: Library name: Sample_164


title: Sample_140, Breast cancer, biopsy

description: Library name: Sample_140


title: Sample_142, Breast cancer, biopsy

description: Library name: Sample_142


title: Sample_141, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_141


title: Sample_144, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_144


title: Sample_136, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_136


title: Sample_137, Breast cancer, biopsy

description: Library name: Sample_137


title: Sample_135, Adrenocortical carcinoma, biopsy

description: Library name: Sample_135


title: Sample_133, Urothelial_cancer, biopsy

description: Library name: Sample_133

source_name: Urothelial_cancer, biopsy


title: Sample_131, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_131


title: Sample_130, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_130


title: Sample_134, Breast cancer, biopsy

description: Library name: Sample_134


title: Sample_132, Breast cancer, biopsy

description: Library name: Sample_132


title: Sample_138, Breast cancer, biopsy

description: Library name: Sample_138


title: Sample_127, Breast cancer, biopsy

description: Library name: Sample_127


title: Sample_128, Breast cancer, biopsy

description: Library name: Sample_128


title: Sample_126, Breast cancer, biopsy

description: Library name: Sample_126


title: Sample_122, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_122


title: Sample_123, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_123


title: Sample_125, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_125


title: Sample_124, Renal cell carcinoma, biopsy

description: Library name: Sample_124


title: Sample_118, Breast cancer, biopsy

description: Library name: Sample_118


title: Sample_121, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_121


title: Sample_117, Lung Adenocarcinoma, biopsy

description: Library name: Sample_117


title: Sample_116, Urothelial_cancer, biopsy

description: Library name: Sample_116


title: Sample_115, Lung Adenocarcinoma, biopsy

description: Library name: Sample_115


title: Sample_114, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_114


title: Sample_113, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_113


title: Sample_139, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_139


title: Sample_176, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_176


title: Sample_112, Lung Adenocarcinoma, biopsy

description: Library name: Sample_112


title: Sample_111, Breast cancer, biopsy

description: Library name: Sample_111


title: Sample_109, Adrenocortical carcinoma, biopsy

description: Library name: Sample_109


title: Sample_129, Pancreatic Adenocarcinoma, biopsy

description: Library name: Sample_129


title: Sample_108, Urothelial_cancer, biopsy

description: Library name: Sample_108


title: Sample_103, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_103


title: Sample_110, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_110


title: Sample_107, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_107


title: Sample_104, Breast cancer, biopsy

description: Library name: Sample_104


title: Sample_106, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_106


title: Sample_100, Breast cancer, biopsy

description: Library name: Sample_100


title: Sample_119, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_119


title: Sample_102, Breast cancer, biopsy

description: Library name: Sample_102


title: Sample_099, Urothelial_cancer, biopsy

description: Library name: Sample_099


title: Sample_095, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_095


title: Sample_097, Renal cell carcinoma, biopsy

description: Library name: Sample_097


title: Sample_101, Breast cancer, biopsy

description: Library name: Sample_101


title: Sample_094, Breast cancer, biopsy

description: Library name: Sample_094


title: Sample_120, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_120


title: Sample_091, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_091


title: Sample_090, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_090


title: Sample_092, Breast cancer, biopsy

description: Library name: Sample_092


title: Sample_089, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_089


title: Sample_096, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_096


title: Sample_087, Lung Adenocarcinoma, biopsy

description: Library name: Sample_087


title: Sample_105, Breast cancer, biopsy

description: Library name: Sample_105


title: Sample_084, Breast cancer, biopsy

description: Library name: Sample_084


title: Sample_085, Squamous Cell Carcinoma of Lung, biopsy

description: Library name: Sample_085


title: Sample_082, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_082


title: Sample_086, Lung Adenocarcinoma, biopsy

description: Library name: Sample_086


title: Sample_083, Lung Adenocarcinoma, biopsy

description: Library name: Sample_083


title: Sample_081, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_081


title: Sample_080, Breast cancer, biopsy

description: Library name: Sample_080


title: Sample_098, Breast cancer, biopsy

description: Library name: Sample_098


title: Sample_074, Breast cancer, biopsy

description: Library name: Sample_074


title: Sample_078, Gastric Adenocarcinoma, biopsy

description: Library name: Sample_078


title: Sample_073, Breast cancer, biopsy

description: Library name: Sample_073


title: Sample_077, Breast cancer, biopsy

description: Library name: Sample_077


title: Sample_093, Breast cancer, biopsy

description: Library name: Sample_093


title: Sample_079, Breast cancer, biopsy

description: Library name: Sample_079


title: Sample_070, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_070


title: Sample_076, Breast cancer, biopsy

description: Library name: Sample_076


title: Sample_071, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_071


title: Sample_075, Breast cancer, biopsy

description: Library name: Sample_075


title: Sample_068, Breast cancer, biopsy

description: Library name: Sample_068


title: Sample_069, Breast cancer, biopsy

description: Library name: Sample_069


title: Sample_067, Breast cancer, biopsy

description: Library name: Sample_067


title: Sample_066, Breast cancer, biopsy

description: Library name: Sample_066


title: Sample_064, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_064


title: Sample_061, Renal cell carcinoma, biopsy

description: Library name: Sample_061


title: Sample_063, Breast cancer, biopsy

description: Library name: Sample_063


title: Sample_065, Breast cancer, biopsy

description: Library name: Sample_065


title: Sample_088, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_088


title: Sample_059, Breast cancer, biopsy

description: Library name: Sample_059


title: Sample_056, Breast cancer, biopsy

description: Library name: Sample_056


title: Sample_057, Urothelial_cancer, biopsy

description: Library name: Sample_057


title: Sample_060, Breast cancer, biopsy

description: Library name: Sample_060


title: Sample_055, Lung Adenocarcinoma, biopsy

description: Library name: Sample_055


title: Sample_052, Breast cancer, biopsy

description: Library name: Sample_052


title: Sample_054, Breast cancer, biopsy

description: Library name: Sample_054


title: Sample_049, Breast cancer, biopsy

description: Library name: Sample_049


title: Sample_050, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_050


title: Sample_053, Esophageal Adenocarcinoma, biopsy

description: Library name: Sample_053


title: Sample_047, Breast cancer, biopsy

description: Library name: Sample_047


title: Sample_046, Breast cancer, biopsy

description: Library name: Sample_046


title: Sample_072, Liver carcinoma and Cholangiocarcinoma, biopsy

description: Library name: Sample_072


title: Sample_044, Breast cancer, biopsy

description: Library name: Sample_044


title: Sample_042, Breast cancer, biopsy

description: Library name: Sample_042


title: Sample_043, Breast cancer, biopsy

description: Library name: Sample_043


title: Sample_039, Breast cancer, biopsy

description: Library name: Sample_039


title: Sample_040, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_040


title: Sample_051, Breast cancer, biopsy

description: Library name: Sample_051


title: Sample_062, Breast cancer, biopsy

description: Library name: Sample_062


title: Sample_038, Lung Adenocarcinoma, biopsy

description: Library name: Sample_038


title: Sample_045, Breast cancer, biopsy

description: Library name: Sample_045


title: Sample_048, Breast cancer, biopsy

description: Library name: Sample_048


title: Sample_041, Breast cancer, biopsy

description: Library name: Sample_041


title: Sample_037, Breast cancer, biopsy

description: Library name: Sample_037


title: Sample_036, Breast cancer, biopsy

description: Library name: Sample_036


title: Sample_058, Breast cancer, biopsy

description: Library name: Sample_058


title: Sample_033, Salivary Adenocarcinoma, biopsy

description: Library name: Sample_033


title: Sample_034, Lung Adenocarcinoma, biopsy

description: Library name: Sample_034


title: Sample_032, Breast cancer, biopsy

description: Library name: Sample_032


title: Sample_029, Breast cancer, biopsy

description: Library name: Sample_029


title: Sample_030, Squamous Cell Carcinoma (other than Lung), biopsy

description: Library name: Sample_030


title: Sample_031, Breast cancer, biopsy

description: Library name: Sample_031


title: Sample_028, Breast cancer, biopsy

description: Library name: Sample_028


title: Sample_027, Breast cancer, biopsy

description: Library name: Sample_027


title: Sample_026, Breast cancer, biopsy

description: Library name: Sample_026


title: Sample_024, Breast cancer, biopsy

description: Library name: Sample_024


title: Sample_023, Breast cancer, biopsy

description: Library name: Sample_023


title: Sample_022, Breast cancer, biopsy

description: Library name: Sample_022


title: Sample_020, Breast cancer, biopsy

description: Library name: Sample_020


title: Sample_025, Breast cancer, biopsy

description: Library name: Sample_025


title: Sample_018, Breast cancer, biopsy

description: Library name: Sample_018


title: Sample_021, Breast cancer, biopsy

description: Library name: Sample_021


title: Sample_017, Breast cancer, biopsy

description: Library name: Sample_017


title: Sample_015, Breast cancer, biopsy

description: Library name: Sample_015


title: Sample_013, Breast cancer, biopsy

description: Library name: Sample_013


title: Sample_012, Breast cancer, biopsy

description: Library name: Sample_012


title: Sample_011, Breast cancer, biopsy

description: Library name: Sample_011


title: Sample_014, Neuroendocrine neoplasm, biopsy

description: Library name: Sample_014


title: Sample_016, Breast cancer, biopsy

description: Library name: Sample_016


title: Sample_035, Breast cancer, biopsy

description: Library name: Sample_035


title: Sample_009, Breast cancer, biopsy

description: Library name: Sample_009


title: Sample_005, Breast cancer, biopsy

description: Library name: Sample_005


title: Sample_008, Colorectal Adenocarcinoma, biopsy

description: Library name: Sample_008


title: Sample_003, Breast cancer, biopsy

description: Library name: Sample_003


title: Sample_006, Breast cancer, biopsy

description: Library name: Sample_006


title: Sample_007, Breast cancer, biopsy

description: Library name: Sample_007


title: Sample_002, Breast cancer, biopsy

description: Library name: Sample_002


title: Sample_004, Breast cancer, biopsy

description: Library name: Sample_004


title: HeLa-W146-rep3

city: Hangzhou

first: Wang

last: Hui

state: Zhejiang

address: First of Xueshi road

department: Department of Gynecological Oncology

institute: Women’s Hospital, School of Medicine, Zhejiang University

description: Library name: sample6

data_processing:
Initially, raw data (Raw Reads) underwent stringent quality control filtering to yield high-quality sequences (Clean Reads). All subsequent analyses, including reference genome alignment, gene expression quantification, differential expression analysis, enrichment analysis, novel transcript prediction, protein interaction network construction, and gene structure annotation, were conducted based on these Clean Reads.
Assembly: Homo_sapiens.GRCh38.91.chr
Supplementary files format and content: W146-HeLa.anno.xls

source_name: Epithelium

extract_protocol:
Total RNA was extracted with Total RNA Kit I (OMEGA; R6834).
After the total RNA passed quality control, mRNA was selectively enriched using Oligo(dT)-conjugated magnetic beads. The mRNA was then fragmented by adding Fragmentation Buffer. Subsequently, first-strand and second-strand cDNA synthesis was performed from the fragmented mRNA, followed by purification of the double-stranded cDNA. The purified cDNA underwent end repair, adenylation at 3' ends, and ligation of sequencing adapters. cDNA fragments approximately 350 bp in length were selected. PCR amplification was conducted to enrich the cDNA library. Finally, the double-stranded cDNA was denatured into single-stranded DNA at high temperature, and looping primers were added to generate a single-stranded circular DNA library.

value: Epithelium

value: HeLa

value: adenocarcinoma

value: WT

value: 10μmol W146


title: Sample_001, Breast cancer, biopsy

description: Library name: Sample_001

value: Breast cancer

value: FF


title: HeLa-W146-rep1

description: Library name: sample4


title: HeLa-control-rep2

description: Library name: sample2

value: control


title: Sample_019, Breast cancer, biopsy

description: Library name: Sample_019


title: HeLa-control-rep3

description: Library name: sample3


title: Sample_010, Breast cancer, biopsy

description: Library name: Sample_010


title: HeLa-control-rep1

description: Library name: sample1


title: JTE013-rep2

description:
Library name: sample23
JTE013-rep2

data_processing:
Initially, raw data (Raw Reads) underwent stringent quality control filtering to yield high-quality sequences (Clean Reads). All subsequent analyses, including reference genome alignment, gene expression quantification, differential expression analysis, enrichment analysis, novel transcript prediction, protein interaction network construction, and gene structure annotation, were conducted based on these Clean Reads.
Assembly: Homo_sapiens.GRCh38.91.chr
Supplementary files format and content: 2-DG-HPV-KI.anno.xlsx
Supplementary files format and content: FSG67-HPV-KI.anno.xlsx
Supplementary files format and content: W146-HPV-KI.anno.xlsx
Supplementary files format and content: JTE013-HPV-KI.anno.xlsx

value: HaCaT

value: keratinocyte

value: HPV18 knock-in

value: 25μmol JTE013


title: JTE013-rep3

description:
Library name: sample24
JTE013-rep3


title: JTE013-control-rep3

description:
Library name: sample21
JTE013-control-rep3


title: JTE013-control-rep1

description:
Library name: sample19
JTE013-control-rep1


title: JTE013-control-rep2

description:
Library name: sample20
JTE013-control-rep2


title: JTE013-rep1

description:
Library name: sample22
JTE013-rep1


title: W146-rep2

description:
Library name: sample17
W146-rep2


title: W146-control-rep2

description:
Library name: sample14
W146-control-rep2


title: W146-control-rep1

description:
Library name: sample13
W146-control-rep1


title: W146-control-rep3

description:
Library name: sample15
W146-control-rep3


title: W146-rep3

description:
Library name: sample18
W146-rep3


title: W146-rep1

description:
Library name: sample16
W146-rep1


title: FSG67-rep3

description:
Library name: sample12
FSG67-rep3

value: 25μmol FSG67


title: HeLa-W146-rep2

description: Library name: sample5


title: FSG67-control-rep1

description:
Library name: sample7
FSG67-control-rep1


title: FSG67-control-rep2

description:
Library name: sample8
FSG67-control-rep2


title: 2-DG-control-rep2

description:
Library name: sample5
2-DG-control-rep2


title: FSG67-rep2

description:
Library name: sample11
FSG67-rep2


title: FSG67-rep1

description:
Library name: sample10
FSG67-rep1


title: 2-DG-control-rep1

description:
Library name: sample4
2-DG-control-rep1


title: Kasumi-1 sgNT#3

city: changchun

first: yongwei

last: su

address: 2699 qianjin street

institute: Jilin university

description:
Library name: Sample 3
kasu_3

data_processing:
FPKM (Fragments Per Kilobase Million Reads) values were used for normalization, and differential expression analysis was carried out with DESeq2 software.
Assembly: High-quality reads were aligned to the human genome build hg38 using Hisat2.
Supplementary files format and content: csv

growth_protocol: Kasumi-1 were cultured in Roswell Park Memorial Institute 1640 medium with 10% fetal bovine serum, supplemented with streptomycin (100 μg/mL) and penicillin (50 U/mL).

extract_protocol:
Total RNA was extracted using Invitrogen TRIzol reagent, and mRNA was enriched with poly-T oligo-attached magnetic beads.
mRNA libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit (NEB) according to the manufacturer's instructions.

treatment_protocol: SETD8 knockout with CRISPR/Cas9

value: acute myeloid leukemia cell lins


title: 2-DG-control-rep3

description:
Library name: sample6
2-DG-control-rep3


title: Kasumi-1 sgSETD8#1

description:
Library name: Sample 4
kasu19_1

value: SETD8 knockout


title: Kasumi-1 sgNT#2

description:
Library name: Sample 2
kasu_2


title: 2-DG-rep2

description:
Library name: sample2
2-DG-rep2

value: 2mmol 2-DG


title: Kasumi-1 sgNT#1

description:
Library name: Sample 1
kasu_1


title: Kasumi-1 sgSETD8#2

description:
Library name: Sample 5
kasu19_2


title: Kasumi-1 sgNT H4K20me1 CUT&Tag

description: Library name: Sample 1

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 × 150 paired-end sequencing. Adapter trimming and sequence filtering were performed using Cutadapt.
Assembly: high-quality reads were aligned to the human genome build hg38 using Bowtie 2.
Supplementary files format and content: treatedvscontrol_deseq_all_PeakAnno.txt
Library strategy: CUT&Tag

extract_protocol:
1 × 10^5 cells were used for library construction using the Epi™ CUT&Tag Library Fast Kit (D202203, Epibiotek) according to the manufacturer’s instructions. Epi™ DNA Clean Beads (R1809, Epibiotek) were used to purify the DNA product.
Quantification and quality control of the libraries were performed using the Bioptic Qsep100 Analyzer.

tag: cut&tag antibody


title: Kasumi-1 sgSETD8 H3K27ac CUT&Tag

description: Library name: Sample 2

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 × 150 paired-end sequencing. Adapter trimming and sequence filtering were performed using Cutadapt.
Assembly: high-quality reads were aligned to the human genome build hg38 using Bowtie 2.
Supplementary files format and content: kasu-DsgS8_peaks_Gateway_Enhancers.txt
Supplementary files format and content: kasumi-1_peaks_Gateway_Enhancers.txt
Library strategy: CUT&Tag


title: Kasumi-1 sgSETD8 ATAC-seq

description: Library name: Sample 2

data_processing:
Unique mapping paired reads were extracted and sorted using SAMtools. Peak calling was performed using MACS2 (v2.1.2). Viewable bigwig files were generated using DeepTools software. Genomic annotation was conducted using the ChIPseeker R package.
Assembly: Adapters were removed using Cutadapt, and high-quality reads were aligned to the human genome build hg38 using Bowtie 2.
Supplementary files format and content: csv

extract_protocol:
5 × 10^4 cells were used for library construction using the Epi™ One-Step ATAC-seq Kit (D231102, Epibiotek) according to the manufacturer’s instructions. Epi™ DNA Clean Beads (R1809, Epibiotek) were employed for DNA product purification.
Quantification and quality control of the libraries were performed using the Bioptic Qsep100 Analyzer (Bioptic Inc.). Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 × 150 paired-end sequencing.


title: FSG67-control-rep3

description:
Library name: sample9
FSG67-control-rep3


title: 2-DG-rep1

description:
Library name: sample1
2-DG-rep1


title: Kasumi-1 sgSETD8 H4K20me1 CUT&Tag

description: Library name: Sample 2


title: PC9-OR, DAC+OSI3

city: Guangzhou

first: 碧莹

last: 门

address: 广东省广州市白云区广州大道北1838号南方医科大学

institute: 南方医科大学

data_processing:
Raw image Data files obtained by high-throughput sequencing are analyzed by CASAVA Base Calling and converted into original Sequenced Reads, which are called Raw Data or Raw Reads. The results were stored in FASTQ (fq for short) file format, which contained sequence information of sequencing sequence reads and their corresponding sequencing quality information.
1. Comparison and analysis with reference genome: HISAT2 is a second-generation sequencing sequence comparison software, which can compare the whole genome, transcriptome and exome data with the reference genome. Using the improved BWT algorithm, sequencing Reads can be efficiently compared to the reference genome. In this project, the HISAT2 software was used to sequence Clean Reads with a specified genome to obtain information about their location on the reference genome. The HISAT2 algorithm is mainly divided into three parts: (1) The whole sequencing sequence is compared to the single exon of the genome; (2) segmented alignment of the sequencing sequence to two exons of the genome; (3) Segmenting the sequencing sequence to more than three (including three) exons of the genome.
Second, gene expression level calculation: the direct reflection of gene expression level is the abundance information of its transcript, the higher the abundance of transcript, the higher the gene expression level. The FPKM value of FragmentsPer Kilobase of transcript sequence per Millions was calculated by using featureCounts software. expected number of FragmentsPer Kilobase of transcript sequence per Millions base pairs sequenced. FPKM represents the number of bases per thousand of the transcript per million of the alignment fragment, which can eliminate the influence of differences in gene length and sequencing volume on calculated gene expression, and the calculated gene expression quantity can be directly used to compare gene expression differences between different samples.
Assembly: human NCBI genome build 36
Supplementary files format and content: Excel file includes raw counts for each Sample

extract_protocol:
Trizol法
After the samples were qualified, the eukaryotic mRNA was enriched with magnetic beads with Oligo dT. mRNA was then randomly interrupted by fragmentation buffer. Using mRNA as template, the first strand of cDNA was synthesized with six-base random hexamers, and then the second strand of cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I. AMPure XP beads were then used to purify double-stranded cDNA. The purified double-stranded cDNA was then end-repaired, A tail was added and sequencing joints were connected. Then AMPure XP beads were used for fragment size selection, and finally PCR enrichment was performed to obtain the final cDNA library.

value: NSCLC

value: DAC+OSI


title: Kasumi-1 sgNT ATAC-seq

description: Library name: Sample 1


title: PC9-OR, DAC2

address: 广东省广州市白云区广州大道北1838号南方医科大学

value: DAC


title: PC9-OR, DAC3

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: PC9-OR, DAC+OSI2

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: PC9-OR, DAC+OSI1

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: PC9-OR, DAC1

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: PC9-OR, OSI3

address: 广东省广州市白云区广州大道北1838号南方医科大学

value: OSI


title: PC9-OR, OSI2

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: 2-DG-rep3

description:
Library name: sample3
2-DG-rep3

value: Epithelium


title: Kasumi-1 sgSETD8#3

description:
Library name: Sample 6
kasu19_3


title: PC9-OR, Control3

address: 广东省广州市白云区广州大道北1838号南方医科大学

value: Control


title: PC9-OR, Control2

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: PC9-OR, Control1

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: RBPJ_WT_Rep2

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Raw sequencing reads were quality and adapter trimmed using TrimGalore.
Trimmed reads were aligned against hg19 using HISAT2.
Peaks were called using MACS2.
Coverage tracks were generated using deepTools.
Assembly: hg19
Supplementary files format and content: Normalized coverage tracks as .bigwig file.
Supplementary files format and content: MACS2 peaks as .narrowPeak file.

growth_protocol: Human HG3 cells were grown at 37°C with 5% CO2 in RPMI-1640 medium (Gibco 61870-010) supplemented with 10% FCS, and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907). CUT&TAG was performed using a kit (Active Motif 53160).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v3 (C05010001). Lybrary-prep kit for CUT&TAG: CUT&TAG kit (Active Motif 53160).

value: chronic B cell leukemia


title: RBPJ_WT_Input


title: Kasumi-1 sgNT H3K27ac CUT&Tag

description: Library name: Sample 1

value: WT


title: RBPJ_WT_Rep1


title: CT_WT_K27ac_Rep1

data_processing:
Raw sequencing reads were quality and adapter trimmed using TrimGalore.
Trimmed reads were aligned against hg19 using HISAT2.
Peaks were called using MACS2.
Coverage tracks were generated using deepTools.
Assembly: hg19
Supplementary files format and content: Normalized coverage tracks as .bigwig file.
Supplementary files format and content: MACS2 peaks as .narrowPeak file.
Library strategy: CUT&TAG


title: MAF-811, Normoxia, 72 hours, rep3

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

data_processing:
FASTQ files were processed using the nf-core-rnaseq pipeline (v3.7) (forward strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR and quantified to gene counts using RSEM.
Assembly: GRCh38
Supplementary files format and content: Comma-separated text file includes raw counts for each Sample

growth_protocol: EPN cell lines were grown in normoxia (5%O2) or hypoxia (2% O2) for 72hrs.

extract_protocol:
RNA was extracted using Qiagen All DNA/RNA mini prep kit. Quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Aligent Technologies) to ensure sufficient quality for library preparation.
Following quality assessment, cDNA libraries were generated using the Universal Plus mRNA-Seq Sample Prep Kit (Nugen). Libraries were then sequenced using the Illumina NovaSeq6000 platform with paired-end reads (2×151). On average 70 million reads were collected for each sample.

tag: condition

value: Normoxia

tag: time point

value: 72 hours


title: MAF-928, Normoxia, 72 hours, rep3


title: MAF-811, Normoxia, 72 hours, rep4


title: CT_WT_K27ac_Rep2


title: MAF-928, Normoxia, 72 hours, rep1


title: MAF-811, Normoxia, 72 hours, rep2


title: MAF-928, Hypoxia, 72 hours, rep3

value: Hypoxia


title: MAF-928, Normoxia, 72 hours, rep2


title: MAF-811, Hypoxia, 72 hours, rep3


title: MAF-811, Normoxia, 72 hours, rep1


title: MAF-811, Hypoxia, 72 hours, rep4


title: MAF-811, Hypoxia, 72 hours, rep2


title: MAF-928, Normoxia, 72 hours, H3K27me3, rep2

data_processing:
FASTQ files were processed using the nf-core-cutandrun pipeline (v3.0).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCh38 (NCBI, p.14, release 110) and duplicates were removed for only control samples using picard.
Peaks were called with macs2 (normalization mode: CPM), and were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Comma-separated text file includes consensus peak counts for each Sample
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
A total of 500,000 cells per reaction were harvested and captured using 10µL of pre-activated ConA beads (EpiCypher). Beads with attached cells were incubated at room temperature for 10 min to ensure complete adsorption. Subsequently, 50µL of antibody buffer (wash buffer supplemented with 0.1% digitonin and 2mM EDTA) was added:  H3K27me3 (MA5-11198, Thermo Fisher), and a negative control, IgG (EpiCypher, 13-0042K). Cells were incubated overnight on a nutator at 4°C and permeabilized using a 5% digitonin buffer. Next, 2.5µL/reaction pAG-MNase (Epicypher) was added and beads were gently resuspended by pipetting. The mixture was incubated for 10min at room temperature. Calcium Chloride, CaCl2 (100mM, 1µL/reaction) was added, followed by a 2-hour incubation at 4°C. After incubation, 34µL of Stop Master Mix was added, followed by a 10-minute incubation at 37°C. Tubes were quick-spun and placed on a magnet for slurry separation. Clear supernatants were transferred to 8-strip tubes for DNA purification. DNA was quantified using dsDNA High Sensitivity Assay kit (Thermo Fisher).
Libraries were prepared with the NEBNext Ultra II DNA kit, according to the manufacturer’s instructions (New England Biolabs). Final libraries were size-selected (200-600 bp) and analyzed on Bioanalyzer High Sensitivity DNA chips (Agilent) to confirm 200 to 400 bp fragment size range. Paired-end 150 bp sequencing of pooled barcoded libraries was carried out on the Illumina Novaseq 6000 platform by the Novogene (CA,USA) facility or functional genomics core (CU Anschutz)

tag: cut&run antibody

value: H3K27me3 (MA5-11198, Thermo Fisher)


title: MAF-928, Hypoxia, 72 hours, rep2


title: PC9-OR, OSI1

address: 广东省广州市白云区广州大道北1838号南方医科大学


title: MAF-928, Hypoxia, 72 hours, H3K27me3, rep2


title: MAF-928, Normoxia, 72 hours, H3K27me3, rep1


title: MAF-811, Hypoxia, 72 hours, rep1


title: MAF-928, Normoxia, 72 hours, IgG, rep2

value: IgG (EpiCypher, 13-0042K)


title: MAF-928, Hypoxia, 72 hours, H3K27me3, rep1


title: MAF-928, Hypoxia, 72 hours, rep1


title: MAF-928, Hypoxia, 72 hours, IgG, rep2


title: MAF-928, Normoxia, 72 hours, IgG, rep1


title: MAF-811, Normoxia, 72 hours, H3K27me3, rep2


title: MAF-811, Hypoxia, 72 hours, H3K27me3, rep2


title: MAF-811, Normoxia, 72 hours, IgG, rep1


title: MAF-811, Hypoxia, 72 hours, H3K27me3, rep1


title: MAF-811, Hypoxia, 72 hours, IgG, rep2


title: 3 groups: Control, pump+NS, pump+AZD

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

library_source: transcriptomic single cell

data_processing:
The alignment of cells to the mouse mm10 transcriptome was carried out using CellRanger version 8.0.1 software (10x Genomics), following the manufacturer’s instructions.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Left ventricle

extract_protocol:
The harvested LV tissues were minced into small pieces in a glass petri dish. Following this, the tissues were incubated in a fixation buffer containing 4% formaldehyde for 16 hours at 4°C. The fixed tissues were dissociated using the gentleMACS Dissociator (Miltenyi Biotec) as per the manufacturer's instructions.
The cells were subsequently processed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit from 10x Genomics. For each sample, 10,000 cells were loaded into a Chip Q for GEM generation. Reverse transcription, barcoding, complementary DNA amplification, and library preparation were executed according to the protocol outlined in CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_E.

value: Left ventricle

tag: strain

value: C57BL/6 mice

tag: age

value: 8-10 weeks old

value: none, normal saline, AZD4547


title: MAF-811, Normoxia, 72 hours, H3K27me3, rep1


title: RNA-seq on ESC-derived NPCs treated with 1uM EPZ-6438 for one week (biol rep2)

city: San Francisco

first: Mitchel

last: Cole

state: CA

address: 35 Medical Center Way

department: Neurological Surgery

institute: UCSF

data_processing:
All fastq files were aligned to the reference genome (GENCODE GRCh38) by STAR 2.7.11b after adaptor trimming. Reads that passed QC and with read length greater than 50 bp were carried over for downstream counting after mapping to a gene transfer format (GTF) file. Read counts were calculated using featureCounts. All differential expression analysis was performed by DESeq2 (v1.4) using raw counts across all conditions or cell types. Genes with read count > 50 in at least one sample of a comparison were kept for further analysis. A given gene was considered significantly changing if the false-discovery-rate (FDR) is < 0.05, P value is < 0.05, and Log1p fold-change is ≥ 0.05. Transcripts Per Million (TPM) were calculated to estimate the absolute expression level for each gene.  RNA-seq data obtained in this study from GW20 RG, IPC and EN and GW17 RG, IPC and EN from published datasets 45 were integrated together into the analysis.
Assembly: hg38
Supplementary files format and content: tab-deliminated txt file include TPM values for each file

source_name: ESC-derived NPCs

growth_protocol: Human pluripotent stem cells (WTC11-iPSC and H1-ESC) were cultured in Matrigel-coated 6-well plates in StemFlex media (Gibco). Media was supplemented with 10 µM ROCK inhibitor Y-27632 (ROCKi) for the first 16-20 hours of culture and was subsequently removed. Cells were fed fresh media every day until they reached 80-90% confluency at which point they were passaged as clumps using ReLeSR (Stemcell Technologies). WTC11-iPSCs were differentiated into NPCs and neurons as described in Ciceri et al. 2024  HEK293T cells were cultured in DMEM (Gibco) supplemented with 10% FBS and 1X antibiotic/antimycotic mixture (Gibco).

extract_protocol:
NPCs and neurons were harvested using Accutase. The cell pellet was resuspended in 1 mL ice cold PBS (Gibco). The cells were centrifuged at 500g for 3 min at 4 °C and the cell pellet was resuspended in 1 ml of nuclei isolation buffer (NIB: 10 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% NP40, 0.5 mM spermidine and 1× Halt protease inhibitor cocktail) and incubated for 10 min on ice. Nuclear pellet was collected by centrifuging at 600g for 3 min at 4°C and again resuspended in 1 ml of NIB to wash. Nuclei were fixed in 0.1% formaldehyde for 2 minutes and washed in NIB. Fixed nuclei were bound to concanavalin A beads  and ~50,000 nuclei were subjected to GO-CaRT/CUT&RUN and CUT&Tag. For GO-CaRT.ChIP-reChIP, LaminB1 GO-CaRT was performed on native (unfixed) nuclei and the LaminB1-enriched chromatin from the supernatant was used for subsequent sequential (2-step) ChIP. For Fab blocking experiments, HEK293T cells were harvested by trypsinization. Cells were fixed in 0.1% formaldehyde for 2 minutes at room temperature, followed by quenching in 0.1M Glycine (prepared in wash buffer). Cells were resuspended in 1 ml wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM spermidine (sigma) and 1× Halt protease inhibitor cocktail)) and centrifuged at 300g for 5 min. This step was repeated for a total of two washes. Cells were then bound to concanavalin A beads  and ~100,000 cells were subjected to CUT&RUN/GO-CaRT with or without Fab fragments. For all experiments, DNA was extracted using Phenol: Chloroform extraction method. Purified DNA fragments were analyzed by Tapestation High Sensitivity D1000 (Agilent), before proceeding to sequencing library construction.
Total RNA from NPCs was extracted using Direct-Zol RNA Miniprep kit (Zymo Research, R2052). Samples were depleted of ribosomal RNA (rRNA) using the NEBNext rRNA Depletion kit v2 (NEB, E7400L). Libraries for sequencing were prepared using the NEBNext Ultra II directional library kit (NEB, E7760) following the manufacturer’s protocol. Libraries were quantified by Tapestation D1000 (Agilent) and Qubit high sensitivity dsDNA (Invitrogen) assays, pooled, and sequenced on NovaSeq 6000 or NovaSeq X Plus systems (Illumina).

treatment_protocol: Human H1-ESCs were differentiated into NPCs using the StemXVivo Neural differentiation kit (R&D systems) following manufacturer instructions. At day 8, ESC-derived NPCs were treated with DMSO or EPZ-6438 (0.5uM and 1uM) for one week. Cells were fed fresh media containing the inhibitor (or DMSO) every day for one week at which point they were harvested for downstream experimental analyses.

value: ESC-derived NPCs


title: RNA-seq on ESC-derived NPCs treated with 1uM EPZ-6438 for one week (biol rep1)


title: RNA-seq on induced neurons (one week) derived from WTC11-NPCs (biol rep1)

source_name: iPSC-derived neurons

value: iPSC-derived neurons


title: RNA-seq on ESC-derived NPCs treated with DMSO for one week (biol rep1)

value: DMSO


title: RNA-seq on induced neurons (one week) derived from WTC11-NPCs (biol rep2)


title: MAF-811, Normoxia, 72 hours, IgG, rep2


title: RNA-seq on ESC-derived NPCs treated with DMSO for one week (biol rep2)


title: RNA-seq on NPCs derived from WTC11-iPSCs (biol rep2)

source_name: iPSC-derived NPCs

value: iPSC-derived NPCs


title: LaminB1 GO-CaRT after Fab blocking of H3K27me3 antibodies

data_processing:
Paired-end fastq data was first processed through a quality control assessment using the FastQC software package (v0.11.9) to evaluate the sequencing quality. The high-quality reads were aligned to the human reference genome hg38 utilizing Bowtie2 (v2.3.5.1), a widely used aligner known for its speed and accuracy. Post-alignment reads with a Mapping Quality score of less than 30 were filtered out using samtools (v1.12) and only non-duplicated mapped reads were retained. For the detection of enriched narrow peaks, indicating regions of significant read accumulation, the MACS2 (Model-based Analysis of ChIP-Seq) (v2.1.2) was employed with its default parameters with IgG as a control. For the detection of enriched broad peaks, the MACS2 (Model-based Analysis of ChIP-Seq) (v2.1.2) was employed with IgG as a control using option “–broad −q 0.05” in addition to default parameters.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
NPCs and neurons were harvested using Accutase. The cell pellet was resuspended in 1 mL ice cold PBS (Gibco). The cells were centrifuged at 500g for 3 min at 4 °C and the cell pellet was resuspended in 1 ml of nuclei isolation buffer (NIB: 10 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% NP40, 0.5 mM spermidine and 1× Halt protease inhibitor cocktail) and incubated for 10 min on ice. Nuclear pellet was collected by centrifuging at 600g for 3 min at 4°C and again resuspended in 1 ml of NIB to wash. Nuclei were fixed in 0.1% formaldehyde for 2 minutes and washed in NIB. Fixed nuclei were bound to concanavalin A beads  and ~50,000 nuclei were subjected to GO-CaRT/CUT&RUN and CUT&Tag. For GO-CaRT.ChIP-reChIP, LaminB1 GO-CaRT was performed on native (unfixed) nuclei and the LaminB1-enriched chromatin from the supernatant was used for subsequent sequential (2-step) ChIP. For Fab blocking experiments, HEK293T cells were harvested by trypsinization. Cells were fixed in 0.1% formaldehyde for 2 minutes at room temperature, followed by quenching in 0.1M Glycine (prepared in wash buffer). Cells were resuspended in 1 ml wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM spermidine (sigma) and 1× Halt protease inhibitor cocktail)) and centrifuged at 300g for 5 min. This step was repeated for a total of two washes. Cells were then bound to concanavalin A beads  and ~100,000 cells were subjected to CUT&RUN/GO-CaRT with or without Fab fragments. For all experiments, DNA was extracted using Phenol: Chloroform extraction method. Purified DNA fragments were analyzed by Tapestation High Sensitivity D1000 (Agilent), before proceeding to sequencing library construction.
Sequencing libraries for GO-CaRT, CUT&RUN and LaminB1-GO-CaRT.ChIP-reChIP were generated using KAPA HyperPrep Kit (KAPA, KK8504) following the manufacturer’s instructions. The libraries were amplified for 12–14 PCR cycles. DNA fragments were quantified by Tapestation D1000 (Agilent) and Qubit high sensitivity dsDNA (Invitrogen) assays, pooled, and sequenced by 150-bp paired-end sequencing on NovaSeq 6000 or NovaSeq X Plus systems (Illumina).
CUT&RUN, CUT&Tag, GO-CaRT and  GO-CaRT followed by sequential ChIP (GO-CaRT.ChIP-reChIP).

value: Human Embryonic Kidney


title: IgG control for GO-CaRT/CUT&RUN


title: LaminB1 GO-CaRT


title: RNA-seq on NPCs derived from WTC11-iPSCs (biol rep1)


title: CUT&RUN for H3K27me3 after Fab blocking (biol rep2)


title: IgG control for CUT&RUN


title: MAF-928, Hypoxia, 72 hours, IgG, rep1


title: CUT&RUN for H3K27me3 (biol rep1)


title: CUT&RUN for H3K27me3 (biol rep2)


title: CUT&RUN for H3K4me3 on ESC-derived NPCs treated with 1uM EPZ-6438 for one week


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep2)


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep2)


title: CUT&RUN for H3K27me3 after Fab blocking (biol rep1)


title: IgG control for ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep2)


title: MAF-811, Hypoxia, 72 hours, IgG, rep1


title: CUT&RUN for H3K4me3 on ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week


title: IgG control for ESC-derived NPCs treated with DMSO for one week(biol rep2)


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep2)


title: IgG control for ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep2)


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with DMSO for one week(biol rep2)


title: CUT&RUN for H3K4me3 on ESC-derived NPCs treated with DMSO for one week


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep2)


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep1)


title: IgG control for ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep1)


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with 1uM EPZ-6438 for one week(biol rep1)


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep1)


title: IgG control for ESC-derived NPCs treated with DMSO for one week(biol rep1)


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep1)


title: IgG control for CUT&Tag on induced neurons (one week) derived from WTC11-NPCs


title: CUT&Tag for H3K4me3 on induced neurons (one week) derived from WTC11-NPCs


title: CUT&RUN for H3K27me3 on ESC-derived NPCs treated with DMSO for one week(biol rep1)


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with DMSO for one week (biol rep1)


title: LaminB1 CUT&Tag on induced neurons (one week) derived from WTC11-NPCs


title: CUT&Tag for H3K27me3 on NPCs derived from WTC11-iPSCs


title: CUT&Tag for H3K27me3 on induced neurons (one week) derived from WTC11-NPCs


title: Parallel CUT&RUN for H3K27me3


title: Parallel CUT&RUN for H3427me3


title: H3K27me3 reChIP on LaminB1 GO-CaRT-H3K4me3 ChIP

description: GOCaRT_ChIPreChIP_WTCNPC_LMNB_K4me3_K27me3


title: IgG control for CUT&Tag on NPCs derived from WTC11-iPSCs


title: H3K4me3 reChIP on LaminB1 GO-CaRT-H3K27me3 ChIP

description: GOCaRT_ChIPreChIP_WTCNPC_LMNB_K27me3_K4me3


title: CUT&Tag for H3K4me3 on NPCs derived from WTC11-iPSCs


title: IgG ChIP on LaminB1 GO-CaRT input


title: LaminB1 GO-CaRT on ESC-derived NPCs treated with DMSO for one week(biol rep2)


title: LaminB1 ChIP on LaminB1 GO-CaRT input


title: IgG control for ESC-derived NPCs treated with 0.5uM EPZ-6438 for one week(biol rep1)


title: H3K27me3 ChIP on LaminB1 GO-CaRT input


title: H3K4me3 ChIP on LaminB1 GO-CaRT input


title: LaminB1 GO-CaRT input used for ChIPreChIP


title: Negative_Control.c9

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Duodenum

extract_protocol:
RNeasy FFPE Kit (QIAGEN; #73504)
Sigma Seqplex

value: Duodenum

value: Negative control (negative TTG antibody, normal histology)


title: CeD.c14

value: CeD


title: Negative_Control.c11


title: Negative_Control.c15


title: Negative_Control.c10


title: IgG control for GO-CaRT


title: CeD_precursor.33

value: CeD precursor


title: LaminB1 CUT&Tag on NPCs derived from WTC11-iPSCs


title: CeD_precursor.35


title: CeD.22


title: CeD_precursor.31


title: Pt046

city: Tokyo

first: Kotoko

last: Yamatani

address: Building A 6F, Hongo Bunkyo-ku 2-1-1

institute: Juntendo University

data_processing:
After cluster generation, the libraries were sequenced on an NovaSeq 6000 sequencer (Illumina) and 50-base paired-ends were generated. Fastq files were aligned to the GRCh38/hg38 genome by STAR aligner. Gene read counts were quantified by STAR quantMode GeneCounts function.
Assembly: GRCh38/hg38 genome
Supplementary files format and content: text files include raw counts

source_name: PB

extract_protocol:
Peripheral blood or bone marrow were obtained from AML patients and ficol-hypaque density gradient centrifugation was used to separetae mononuclear cells.Then RNA was extracted from cells
OP-illumina-TruSeq-RiboZero-RNA-seq-v1.0 :Sequencing libraries were generated using TruSeq Stranded Total RNA Ribo-Zero Gold Kit for Illumina

value: PB

value: leukemia cells

value: pretreatment

tag: group

value: R/R, nonresponder


title: CeD.19


title: Pt039

source_name: BM

value: BM

value: ND,nonresponder


title: Pt042

value: ND, nonresponder


title: Pt040

value: R/R,responder


title: Pt038

value: ND,responder


title: Pt044


title: Pt045


title: Pt033

value: R/R,nonresponder


title: Pt032


title: Pt029

value: VEN/DECposttreatment


title: Pt031


title: Negative_Control.c13


title: CeD.c12


title: Pt025


title: Pt023


title: Pt027


title: CeD_precursor.34


title: CeD.23


title: Pt020


title: Pt018


title: Pt014


title: Pt016


title: Pt013


title: Pt011


title: Pt008


title: Pt009


title: Pt004

value: R/R, responder


title: Pt005


title: Pt002


title: Pt003


title: SEM_MIChid3

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Resulting bam files were analyzed with Bioconductor package metaseqR and subjected to differential expression analysis
Sequenced reads were mapped to hg19 whole genome using, for RNA-Seq reads, tophat2 with default settings. The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against hg19 with the --local and --very-sensitive options.
Reads overlapping the hg19 human exons were counted and filtered for several artifacts. The final gene counts were calculated as the sums of their exonic reads. The counts table was normalized using DESeq normalization and analyzed for differential expression using DESeq and the Bioconductor package metaseqR. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05 and an absolute log2 fold change greater than 1.5.
Assembly: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary files format and content: Genes with DESeq p-value less than 0.05 and fold change (for each contrast) greater than 0.58 or less than -0.58 in log2 scale, corresponding to 1.5 times up and down, respectively, on a natural scale, were considered differentially expressed.

source_name: SEM-K2 established cell line

growth_protocol: Cells were grown in RPMI complete medium (+10% FBS, +1% Penicllin Streptomycin)

extract_protocol:
Total RNA was extracted and purified with RN-easy mini column kit, following manufacturer's instructions
Paired-end mode with 75bp read length. 40 milion paired-end reads were generated per each sample

treatment_protocol: Where indicated, cells were treated with 1uM MI-538 for 6 days (re-treating after 4 days) and 1uM Chidamide for 48h

value: SEM-K2 established cell line

value: pro-B acute lymphoblastic leukemia

value: t(4;11) rearranged

value: MI-538 + Chidamide


title: SEM_MIChid2


title: SEM_DMSO3

value: DMSO (vehicle)


title: SEM_DMSO1


title: SS.PDX, RNA-seq, treated_3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX6

data_processing:
The SSPDX RNA-seq data were analyzed by Novogene with us performing differential gene expression analysis. Differentially expressed genes were detected using edgeR v.4.0.16.
Assembly: hg38
Supplementary files format and content: Tab-delimited text, gene counts for each sample

source_name: cell line, PDX

growth_protocol: DMEM with 10% FBS and 1 µg/mL penicillin and streptomycin

extract_protocol:
Library preparation and sequencing was pervormed by Novogene. Briefly, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: cell line, PDX

value: human synovial sarcoma cell line


title: SEM_MIChid1


title: SS.PDX, RNA-seq, treated_1

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX4


title: SS.PDX, RNA-seq, treated_2

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX5


title: SEM_DMSO2


title: Macrophages, vWAT infiltrating, obese individual 7

type: RNA

first: Lauro

last: Sumoy

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

hyb_protocol: Labeled cDNAs were hybridized onto Clariom D Human Assay Microarrays, which include probe sets enabling transcriptome-wide gene- and exon-level expression profiling (Affymetrix, ThermoFisher Scientific).

scan_protocol: The arrays were scanned using the GeneChip 3000 system (Affymetrix).

data_processing: Transcript Analysis Console (TAC v4.0; Affymetrix, ThermoFisher) software was used for initial hybridization quality assessment and data inspection. All statistical analyses of microarray data were performed using R-based software environment. Quality control was done with the array QualityMetrics package. Background correction, probe set summarization and normalization were performed with the oligo package using the most up to date annotation in Bioconductor. Subsequent differential expression analysis was performed using the Limma package at the gene level taking the average of all probe sets for a particular gene and focusing on known genes (with assigned gene symbols).

label: biotin

source_name: macrophages from white adipose tissue

label_protocol: CD11b+ cell extracted RNA was reverse transcribed into cDNA and amplified and biotinylated by in vitro transcription (MultiScribe TaqMan Reverse Transcription Reagents; ThermoFisher Scientific, Waltham, MA, USA).

growth_protocol: The study was approved by the Ethical Committee of the Hospital Germans Trias i Pujol (Badalona, Spain) and follow the guidelines of Helsinki convention. Participants of both Cohorts 1 and 2 gave their written informed consent before clinical data collection.Two different cohorts of patients were enrolled in this study. All patients were evaluated by the same endocrinologist (S.P.) following the institutional protocol for bariatric surgery between October 2015 and September 2021, according to criteria for bariatric surgery formulated in Spanish Position Statement between Obesity, Endocrinology, Diabetes and Surgery Societies. For Cohort 1, 11 patients with obesity (BMI>35 kg/m2) and different metabolic status were enrolled, and vWAT and sWAT from the same patient were collected on occasion of bariatric surgery. For Cohort 2, 27 patients with or without severe obesity (BMI>35 kg/m2 or BMI<27 kg/m2, respectively) were enrolled; for individuals with obesity, they attended to bariatric surgery, while for normal-weight individuals on occasion of consultation/minor surgery. Then, vWAT and sWAT were collected during the surgical procedures. The inclusion criterion for individuals with obesity was exhibiting a BMI higher than 35 kg/m2. Exclusion criteria for all cohorts were having active infectious or inflammatory pathologies other than those related to obesity and treatment with immunosuppressant drugs, since these conditions could alter the results of the study.

extract_protocol: Total RNA was then extracted using affinity column-based methodology suitable for small amounts of biological material (NucleoSpin RNA XS; Mecherey-Nagel, Duren, Germany). RNA yield and purity were determined by spectrophotometry and RNA integrities were assessed with the Nano 6000 assay on Agilent's 2100 Bioanalyzer. Samples with RNA integrity number (RIN) values mostly above 6.7 were used as input for subsequent microarray gene expression profiling assays.

treatment_protocol: vWAT and sWAT samples (n = 36 in total) were obtained from these 11 patients from Cohort 1 during bariatric surgery. Fresh WAT collected during surgeries was transferred into two 50 mL tubes containing a 2% fetal bovine serum (FBS) in phosphate saline buffer (PBS) solution and placed on separate multiwell plate wells submerged in collagenase and Hank's Balanced Salt Solution (pH=7.1). The tissue was then minced into small pieces followed by several centrifugation and supernatant removal steps as previously published (19,20). CD11b+ cells were then labeled with anti-CD11b+ MicroBeads and magnetically separated from the unlabeled cells by a magnetic-activated cell sorting (MACS) Column supplied by Miltenyi Biotec (Miltenyi Biotec S.L Madrid). Briefly, the cell suspension was centrifuged at 300 x g for 10 min and the supernatant was completely discarded. Second, the pellet was resuspended in 82 µL of MACS buffer and 2 µL were diluted by adding 18 µl of MACS buffer and reserved at 4º C to evaluate percentage of CD11b+ cells. Then, 20 µL of CD11b+ MicroBeads were added to 80 µL of cell suspension, mixed and incubated for 15 min in ice. Next, the cells were washed by adding 2 mL of MACS buffer and centrifugated at 300 g for 10 minutes at 4ºC. Then the pellet was resuspended in 500 µL of MACS buffer and maintained in ice. Meanwhile, the separation column was prepared. For this, the LS column was placed in the magnetic field, on the MidiMACS™ Separator and rinsed with 3 mL of MACS buffer. Once the column reservoir was empty, the cell suspension was added into the column. When all the suspension passed, the column was washed by adding 3 mL of MACS buffer, twice. After that, the column was removed from the magnetic field, and placed onto a new 15 mL conical tube (collection tube). Then, 5 mL of MACS buffer was added and the fraction with the magnetically labeled cells was immediately flushed out applying the plunger supplied with the column. 20 µL of the eluted fraction was reserved in ice. Next, the CD11b+ fraction of cells was centrifuged at 300 g for 7 min at 4º C, 4 mL of the supernatant was discarded, and the pellet was resuspended in the remaining volume, which was transferred into 1.5 mL conical tube and centrifuged at 11000g for 5 min, the resulting pellet was used to perform RNA extraction. The reserved aliquots from sWAT and vWAT were labeled to quantify the viability and the number of infiltrated CD11b+ cells, respectively. For this purpose, 10 µL of cell sample were mixed with 48 µL of MACS Buffer, 2 µL of 7-AAD and 0.5 µL of CD11b+, the prepared mix was incubated in darkness for 10 min and then 10 µL of Counting beads were added. Isolated macrophages were detected by the flow cytometer FACSCanto II by BD Biosciences. The optic consists of an excitation source and a three-laser system: blue (488 nm, air-cooled, 20-mV solid state), red (633 nm, 17-mV HeNe) and violet (405 nm, 30-mV solid state) allowing measurement of 8 parameters (FSC, SSC and 6 fluorescence detectors) with carrousel acquisition option for tubes. For quantification analysis the FACSDiva software were used, and FlowJo Software (Tree Star Inc.) was used for the graphs and the gating strategy. Cells are being separated based on their size and fluorescence. Viability, percent, and concentration (cells/μL) of macrophage cells (CD11b+) in each tissue (vWAT and sWAT) was measured at the flow cytometer.

tag: gender

value: female

value: visceral white adipose tissue (vWAT)

value: macrophages (CD11b+)

tag: health status

value: Obese

tag: individual

tag: batch


title: Macrophages, vWAT infiltrating, obese individual 8


title: Macrophages, vWAT infiltrating, obese individual 9

value: male


title: Macrophages, vWAT infiltrating, obese individual 10


title: Macrophages, vWAT infiltrating, obese individual 5


title: SS.PDX, RNA-seq, untreated_3

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX3

tag: cell line

tag: treatment

value: untreated


title: Macrophages, vWAT infiltrating, obese individual 13

tag: tissue

tag: cell type


title: SS.PDX, RNA-seq, untreated_1

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX1


title: Macrophages, vWAT infiltrating, obese individual 17


title: Macrophages, vWAT infiltrating, obese individual 18


title: Macrophages, vWAT infiltrating, obese individual 2


title: Macrophages, vWAT infiltrating, obese individual 6


title: SYO.1, RNA-seq, Treated, Rep 3

description: Illumina NovaSeq 6000 or NextSeq 2000 platform

data_processing:
The SYO.1 data were aligned to the GRCh38 human genome assembly using bwa v. 0.7.17-r1188 [PMID: 19451168] and gene expression was quantified using featureCounts v. 2.0.1 [PMID: 24227677].
Assembly: hg38
Supplementary files format and content: Tab-delimited text, gene counts for each sample

extract_protocol:
Total RNA was extracted from the SYO-1 untreated and treated cells (with 100 nM TAK-981 for 36h) using the Isolate IIRNA Mini kit #BIO-52072, Bioline)
Stranded mRNA-seq library preparation and next generation sequencing: Approximately 500ng Total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA). The first step in the workflow involved purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-seq library


title: Macrophages, sWAT infiltrating, obese individual 13

value: subcutaneous white adipose tissue (sWAT)


title: Macrophages, vWAT infiltrating, obese individual 16


title: Macrophages, sWAT infiltrating, obese individual 16


title: SS.PDX, RNA-seq, untreated_2

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
SSPDX2


title: Macrophages, vWAT infiltrating, obese individual 12


title: Macrophages, sWAT infiltrating, obese individual 14


title: SYO.1, RNA-seq, Treated, Rep 2


title: Macrophages, vWAT infiltrating, obese individual 3


title: Macrophages, vWAT infiltrating, obese individual 15


title: SYO.1, RNA-seq, Untreated, Rep 3

value: Untreated


title: Macrophages, vWAT infiltrating, obese individual 4


title: Macrophages, vWAT infiltrating, obese individual 1


title: Macrophages, sWAT infiltrating, obese individual 18


title: Macrophages, vWAT infiltrating, obese individual 14


title: Macrophages, sWAT infiltrating, obese individual 15


title: SYO.1, RNA-seq, Treated, Rep 1


title: Macrophages, sWAT infiltrating, obese individual 12


title: Macrophages, vWAT infiltrating, obese individual 11


title: Macrophages, sWAT infiltrating, obese individual 17


title: SYO.1, RNA-seq, Untreated, Rep 1


title: Macrophages, sWAT infiltrating, obese individual 11


title: HS-SY-II, RNA-seq, Untreated, Rep 2

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAun2

data_processing:
The HS-SY-II data were processed with the Nextflow RNA-seq pipeline (https://nf-co.re/rnaseq/3.14.0). Gene expression was quantified using the STAR-RSEM strategy.
Assembly: hg38
Supplementary files format and content: Tab-delimited text, gene counts for each sample

source_name: HS-SY-II

extract_protocol:
Total RNA was extracted from the HS-SY-II untreated and treated cells (with 100 nM TAK-981 for 36h) using the Isolate IIRNA Mini kit #BIO-52072, Bioline)
Stranded mRNA-seq library preparation and next generation sequencing: Approximately 500ng Total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA). The first step in the workflow involved purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-seq library

value: HS-SY-II


title: IFN_gamma_MAB_rep4

city: shanghai

first: Xianwei

last: Wu

address: No.725 South Wanping Road

department: Institute of Respiratory Diseases

institute: Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

description: Library name: SAMPLES 16

data_processing:
Quality-filtered RNA-seq reads were aligned to the mouse genome (GCF_000001635. 27_GRCm39) by Bowtie2 software
Each gene expression was obtained and normalized by software.
Differentially expressed genes (DEGs) were filtered with 2.0-fold cut-off and p < 0.05.
Assembly: The mouse genome, GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text files include gene count values for each Sample

organism: Mus musculus

source_name: BMDMs

extract_protocol:
Total RNA was extracted by Trizol Reagent and the RNA quality was assessed using Qubit®3.0 Fluorometer (Life Technologies, CA, USA).
The mRNA polyA-based enrichment method was performed to establish RNA library. To establish an RNA library, the mRNA polyA-based enrichment method was performed.  RNA sequencing was performed by Illumina NovaSeq 6000 to generate 150-bp paired-end reads with about 40 million reads per sample (Sinotech Genomics).  Quality-filtered RNA-seq reads were aligned to the mouse genome (GCF_000001635.27_GRCm39) by using Hisat2 software.

treatment_protocol: Female C57BL/6J mice (6-8 weeks old) were infected  via intratracheal delivery with M. abscessus at 5 × 10^7 CFU in 40 mL of sterile PBS once. For infected WT mice on 7dpi and 35dpi, lung tissue was harvested, immediately frozen in liquid nitrogen and stored at -80°C.Per condition, four biological replicates were performed.  Three uninfected WT mice served as blank controls.

value: BMDMs

value: Following the 2-hour phagocytosis period, media was changed and IFN-γ was added again


title: IFN_gamma_MAB_rep2

description: Library name: SAMPLES 14


title: HS-SY-II, RNA-seq, Treated, Rep 1

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAtr1


title: SYO-1, H3K27ac, ChIP, untreated 2

data_processing:
SYO-1 H3K27ac ChIP-seq data were quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS23 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using the Bioruptor sonicator from Diagenode.
Approximately 0.1ng to 20ng ChIP DNA was fragmented to size range around 200bps using Covaris (shearing parameter 2 minutes in LV tubes using 15ul microTUBE-15 AFA Beads Screw-cap, Cat: #520145), and used for ChIP-seq library preparation by following the NEBNext Ultra II DNA library preparation Kit for Illumina (Cat. No: E7645L, New England Biolabs Inc, Ipswich, MA, USA). This kit utilizes a proprietary adapter attachment chemistry which minimizes bias and supports very low amount of input sample.


title: HS-SY-II, RNA-seq, Treated, Rep 2

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAtr2


title: Macrophages, sWAT infiltrating, obese individual 10


title: MAB_rep4

description: Library name: SAMPLES 12

value: MAB infection


title: SYO.1, RNA-seq, Untreated, Rep 2


title: HS-SY-II, RNA-seq, Untreated, Rep 1

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAun1


title: HS-SY-II, RNA-seq, Untreated, Rep 3

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAun3


title: Macrophages, sWAT infiltrating, obese individual 5


title: HS-SY-II, RNA-seq, Untreated, Rep 4

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAun4


title: Macrophages, sWAT infiltrating, obese individual 1


title: SYO-1, H3K27ac, ChIP, untreated 3


title: Macrophages, sWAT infiltrating, obese individual 3


title: Macrophages, sWAT infiltrating, obese individual 6


title: Macrophages, sWAT infiltrating, obese individual 8


title: Macrophages, sWAT infiltrating, obese individual 7


title: IFN_gamma_MAB_rep5

description: Library name: SAMPLES 17


title: IFN_gamma_rep3

description: Library name: SAMPLES 7

value: overnight IFN-γ pretreatment


title: SYO-1, H3K27ac, ChIP, input


title: MAB_rep1

description: Library name: SAMPLES 9


title: IFN_gamma_rep1

description: Library name: SAMPLES 5


title: HS-SY-II, RNA-seq, Treated, Rep 4

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAtr4


title: IFN_gamma_rep2

description: Library name: SAMPLES 6


title: Macrophages, sWAT infiltrating, obese individual 4


title: Uninfected_rep4

description: Library name: SAMPLES 4

value: uninfected


title: IFN_gamma_MAB_rep1

description: Library name: SAMPLES 13


title: IFN_gamma_MAB_rep3

description: Library name: SAMPLES 15


title: IFN_gamma_rep4

description: Library name: SAMPLES 8


title: Macrophages, sWAT infiltrating, obese individual 2


title: SYO-1, H3K27ac, ChIP, untreated 1


title: MAB_rep2

description: Library name: SAMPLES 10


title: SYO-1, H3K27ac, ChIP, treated 3


title: MAB_rep3

description: Library name: SAMPLES 11


title: HS-SY-II, RNA-seq, Treated, Rep 3

description:
Illumina NovaSeq 6000 or NextSeq 2000 platform
HSRNAtr3