title: TMA2, cap69, PtID13, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap59, PtID12, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0

status: Public on Nov 11 2024

type: SRA

city: Stanford

first: Magdalena

last: Matusiak

state: California

address: 300 Pasteur Dr

department: Pathology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Base calls from the NextSeq were de-multiplexed and converted to FASTQ format with bcl2fastq (NextSeq system suite software, Illumina v2.20.0.422). The five-base unique molecular identifier (UMI) sequence and the G-overhang were extracted from FASTQ data, and A-tails were removed with umi_homopolymer.py (github.com/jwfoley/3SEQtools). Reads were aligned and further processed to remove duplicates using STAR v2.7.3a (github.com/alexdobin/STAR)
Assembly: hg38
Supplementary files format and content: .csv format; provides raw counts for each sequencing library

molecule: total RNA

organism: Homo sapiens

source_name: Merkel cell carcinoma

extract_protocol: Sequencing libraries were prepared according to the Smart-3Seq protocol for LCM HS caps, as previously described with slight modifications (see Foley et al. doi: 10.1101/gr.234807.118)

tag: tissue

value: Merkel cell carcinoma

tag: cell line

value: tissue

tag: cell type

value: tumor

tag: genotype

value: negative

tag: treatment

value: ICB

tag: cpi orr

tag: local disease

tag: progress to_metastatic_disease

tag: pat id

tag: baseline fu_biopsy

value: pre


title: TMA2, cap61, PtID80, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: positive


title: CG612A

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNAs were hybridized to beadchips provided the Illumina Infinium MethylationHM450K BeadChip Kit

data_processing:
Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus
Normalized Beta values

molecule: genomic DNA

source_name: Blood

label_protocol: Sample barcoding and staining were carried out by following the instructions of Illumina provided in the Infinium MethylationHM450K BeadChip Kit

growth_protocol: Monocytes, defined as CD14+, were separated using immune-magnetic capturing methods (Miltenyi AutoMACS)

extract_protocol: DNA was isolated from the purified monocytes using a column-based method and assessed for quality using NanoDrop, bisulfite converted using EZ-96 DNA Methylation kits (Zymo Research, Irvine, CA)

value: Blood

value: Monocytes


title: TMA2, cap57, PtID71, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: bulk antigen-experienced CD8+ T cells, ME patient 982

city: Ithaca

first: David

middle: S

last: Iu

state: NY

address: 427 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

library_source: genomic

data_processing:
fastq files were trimmed to remove low quality and adaptor sequences as described (Martin, 2011). Trimmed reads were then aligned to hg38 using bowtie2 (v2.4.5; Langmead et al., 2019). Mitochondrial reads and blacklisted regions (Amemiya et al., 2019) were removed, and PICARD (v2.26.1) and samtools (v1.18; Danecek et al., 2021) were used to sort and remove duplicate reads.
Peaks were called using MACS3 (v3.0.0b1; Zhang et al., 2008; callpeak –f BAMPE –g hg –B –q 0.01). Consensus peaks from all cell types and biological conditions were then merged by muMerge (v1.1.0; Rubin et al., 2021) to create a unified set of chromatin accessible regions (ChARs). featureCounts under subread (v2.0.3; Liao et al., 2014) was used to calculate raw read counts per ChAR.
Assembly: hg38
Supplementary files format and content: comma-delimited file with consensus chromatin accessible regions and their raw counts per sample

source_name: antigen-experienced CD8+ T cell

extract_protocol:
CD3+ cells were enriched using the CD3+ MicroBeads (Miltenyi Biotech Cat#130-097-043) from PBMCs. After enrichment, cells were incubated with Aqua dead cell stain kit (Thermo) with Human TruStain FcX™ Fc Receptor Blocking Solution (Biolegend) for 10 minutes at room temperature. Fluorescently labeled antibodies (CD4-FITC Cat#357406, CD8a-BV785 Cat#301406, CD45RA-BV650 Cat#304136, CCR7-APC-Cy7 Cat#353212, and CD56-PE-Cy7 Cat#362510 all from BioLegend) were subsequently added to the cells and incubated on ice for 30 minutes. 1 mL of FACS buffer (heat inactivated FBS, 0.5M EDTA pH8.0 1x PBS) was added to the cells, mixed well and centrifuged at 300 rcf for 5 minutes at 4 °C. The supernatant was removed and the cells were washed once more. The final cell pellet was resuspended in 100µl of FACS buffer and kept on ice in the dark. Flow sorting was performed on a FACSARia Fusion at the Cornell BRC Flow Cytometry Facility. Live and CD56 negative cells were selected for CD4 and CD8 expressions. Naïve cells were sorted as CD45RA+CCR7+. Memory cells were sorted as CD45RA-CCR7+/-. Nuclei were prepared from 12,000-50,000 sorted CD8 T cells using a modified Omni-ATAC-seq protocol. Briefly, cells were pelleted at 500 xg for 5 minutes at 4°C, supernatant removed, and cells were permeablized in cold lysis/permeabilization buffer with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin for 3 minutes. Cells were washed three times with fresh 1 x RSB-T (10mM Tris pH 7-8, 10mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Cells were pelleted and supernatant removed. 1x PBS + 10% DMSO  is used to slow freeze the cell pellet and placed in a Mr. Frosty for slow freezing at -80°C for processing.
Nuclei were prepared from 12,000-50,000 CD8+ T cells sorted as described above, using a modified Omni-ATAC-seq protocol (Corces et al., 2017). Briefly, cells were pelleted at 500 xg for 5 minutes at 4C, supernatant removed, and cells were permeablized in 50 ul cold lysis/permeabilization buffer with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice. Lysis was quenched by adding 1mL ice-cold RSB-T (10mM Tris pH 7-8, 10mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Nuclei were pelleted at 500 xg for 10 minutes at 4C and supernatant was replaced with 50 ul 1x PBS + 10% DMSO for slow freezing and storage at -80C. For tagmentation, nuclei were thawed and washed twice with 1x RSB+T before resuspending in 25 ul Tagmentation buffer (1x Cutsmart buffer (NEB), 10% DMF, 0.1% Tween-20, 0.01% digitonin, and 0.1uM Tn5). Nuclei were tagmented for 30 minutes at 37C with 500 rpm shaking on an Eppendorf Thermomixer. Following tagmentation, DNA was purified using a Zymo clean and concentrate-5 column and PCR performed using Nextera primers containing unique dual indices and 2X NEBNext High Fidelity master mix for 11-13 cycles (depending on starting input; 72C for 5min, 98C 30sec, cycles of 98C 10 sec, 63C 30 sec, 72C 1min). PCR products were purified using SparQ beads (Quanta Bio) and resuspended in 0.1X TE. Libraries were checked on a Fragment Analyzer (Agilent) and size selected using a Pippin HT (Sage Sciences).  Libraries were shallow sequenced on a MiSeq at Cornell BRC Genomics to check the balance of the pooled libraries. The pool was adjusted and sent for sequencing on two NovaSeq6000 (Illumina) S4 lanes at URMC to a depth of 50M reads per library.

value: antigen-experienced CD8+ T cell

tag: phenotype

value: ME patient


title: TMA2, cap56, PtID71, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: bulk naïve CD8+ T cells, ME patient 958

source_name: naive CD8+ T cell

value: naive CD8+ T cell


title: TMA2, cap55, PtID1, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: CG611B

scan_protocol: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus


title: TMA2, cap54, PtID2, virusnegative, response0, treatmentpost, LocalDisease1, Metastasis1, Survival1

value: post


title: CG611A


title: TMA2, cap52, PtID66, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival1

value: FU


title: bulk naïve CD8+ T cells, ME patient 948


title: TMA2, cap51, PtID72, virusnegative, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap50, PtID77, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: CG610B


title: TMA2, cap58, PtID29, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: bulk naïve CD8+ T cells, healthy sedentary control 996

value: Healthy Control


title: bulk antigen-experienced CD8+ T cells, ME patient 948


title: CG610A


title: CG609B


title: bulk antigen-experienced CD8+ T cells, healthy sedentary control 992


title: TMA2, cap49, PtID20, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA2, cap60, PtID9, viruspositive, response0, treatmentpost, LocalDisease1, Metastasis1, Survival1


title: TMA2, cap45, PtID64, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA2, cap44, PtID64, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival1


title: CG609A


title: TMA2, cap43, PtID64, viruspositive, responseNA, treatmentpost, LocalDisease0, Metastasis1, Survival1


title: bulk antigen-experienced CD8+ T cells, healthy sedentary control 986


title: CG608A


title: bulk antigen-experienced CD8+ T cells, ME patient 524


title: TMA2, cap40, PtID31, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis0, Survival0


title: TMA2, cap42, PtID25, viruspositive, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap37, PtID59, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: bulk naïve CD8+ T cells, healthy sedentary control 992


title: TMA2, cap39, PtID32, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: bulk naïve CD8+ T cells, healthy sedentary control 986


title: CG607B


title: CG606B


title: TMA2, cap41, PtID31, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: RASH_sample_154

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Individual lane files were combined into one FASTQ file for each sample
Salmon (v1.5.2 with options gcBias and seqBias) was used to derive read count, gene-length and total read count normalized counts (TPM)
Assembly: GENCODE Release 38 (GrCh38.p13)
Supplementary files format and content: comma-separated file containing Bulk RNAseq gene expression normalized TPM for all samples

source_name: Primary  PDAC

extract_protocol:
Total RNA was extracted from cassettes using the AllPrep DNA/RNA FFPE Kit (Qiagen, 80234). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
For samples below dv200 30%, a 1.1X or a 1.1X and successive 1.0X bead cleanups was completed using RNAClean XP Beads (Beckman Coulter, A63987) cDNA libraries were prepped with the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche, KR1151) if total RNA was >25ng and >24% dv200. If dv200 was below 50%, the low input KAPA Prep protocol was used. 17 cycles were used for the final PCR cycle. The remaining samples were prepped using AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, 20019170, 20019102).16 cycles were used to amplify target regions in the cDNA

value: Primary  PDAC

value: Gemcitabine/Erlotinib


title: TMA2, cap48, PtID23, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: Merkel cell carcinoma


title: TMA2, cap38, PtID39, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0

value: tissue


title: TMA2, cap36, PtID35, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival1

value: tumor


title: bulk naïve CD8+ T cells, ME patient 524


title: TMA2, cap47, PtID62, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: negative


title: bulk antigen-experienced CD8+ T cells, ME patient 424


title: TMA2, cap35, PtID52, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0

value: ICB


title: CG607A


title: TMA2, cap46, PtID63, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: pre


title: CG606A


title: TMA2, cap33, PtID27, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0

value: positive


title: TMA2, cap32, PtID58, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: CG605B

value: Blood


title: TMA2, cap34, PtID78, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: bulk naïve CD8+ T cells, ME patient 424


title: TMA2, cap31, PtID9, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1


title: bulk antigen-experienced CD8+ T cells, ME patient 101


title: CG605A

value: Monocytes


title: bulk naïve CD8+ T cells, ME patient 101


title: TMA2, cap28, PtID15, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap29, PtID10, viruspositive, response1, treatmentFU, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap27, PtID15, virusnegative, response1, treatmentpost, LocalDisease1, Metastasis1, Survival0


title: CG604B


title: CG604A


title: bulk antigen-experienced CD8+ T cells, healthy sedentary control 410

value: antigen-experienced CD8+ T cell


title: TMA2, cap8, PtID56, virusnegative, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: bulk naïve CD8+ T cells, healthy sedentary control 410


title: CG603B


title: TMA2, cap9, PtID56, virusnegative, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap6, PtID60, viruspositive, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: bulk antigen-experienced CD8+ T cells, healthy sedentary control 145


title: CG603A


title: TMA2, cap5, PtID18, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: bulk naïve CD8+ T cells, healthy sedentary control 145


title: TMA2, cap4, PtID21, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: TMA2, cap2, PtID26, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap30, PtID10, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: CG602A


title: bulk antigen-experienced CD8+ T cells, healthy sedentary control 481


title: TMA2, cap25, PtID2, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1


title: TMA2, cap24, PtID4, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: CG601B


title: bulk naïve CD8+ T cells, healthy sedentary control 481


title: TMA2, cap23, PtID5, viruspositive, response0, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap7, PtID60, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap22, PtID5, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap20, PtID8, viruspositive, response0, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA2, cap21, PtID6, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: EMCD8-P8-ME-HL982

data_processing:
Fastq files were trimmed and aligned to GRCh38 as previously described (TrimGalore v0.6 and STAR v2.7; Vu, Ahmed, and Zhu et al., 2024). A count table of reads per gene (according to Ensembl gene annotations) was output by STAR.
Assembly: hg38
Supplementary files format and content: comma-delimited file which includes raw counts for each sample

source_name: bulk antigen-experienced CD8+ T cells, ME patient 982

extract_protocol:
CD3+ cells were enriched using the CD3+ MicroBeads (Miltenyi Biotech Cat#130-097-043) from PBMCs. After enrichment, cells were incubated with Aqua dead cell stain kit (Thermo) with Human TruStain FcX™ Fc Receptor Blocking Solution (Biolegend) for 10 minutes at room temperature. Fluorescently labeled antibodies (CD4-FITC Cat#357406, CD8a-BV785 Cat#301406, CD45RA-BV650 Cat#304136, CCR7-APC-Cy7 Cat#353212, and CD56-PE-Cy7 Cat#362510 all from BioLegend) were subsequently added to the cells and incubated on ice for 30 minutes. 1 mL of FACS buffer (heat inactivated FBS, 0.5M EDTA pH8.0 1x PBS) was added to the cells, mixed well and centrifuged at 300 rcf for 5 minutes at 4 °C. The supernatant was removed and the cells were washed once more. The final cell pellet was resuspended in 100µl of FACS buffer and kept on ice in the dark. Flow sorting was performed on a FACSARia Fusion at the Cornell BRC Flow Cytometry Facility. Live and CD56 negative cells were selected for CD4 and CD8 expressions. Naïve cells were sorted as CD45RA+CCR7+. Memory cells were sorted as CD45RA-CCR7+/-. Samples were then submitted to the Transcriptional Regulation and Gene Expression Facility (TREx), where RNA extraction and library preparation were performed as previously reported (Vu, Ahmed, and Zhu et al., 2024).
Bulk polyA + RNAseq libraries were generated from 25 ng total RNA with the NEBNext Ultra II Directional RNA kit (New England Biolabs). Libraries were quantified with a Qubit HS DNA assay (Thermo) and sequenced on a NovaSeq6000 (Illumina) at Novogene to a minimum of 30M 2x150bp paired-end reads.

value: ME


title: TMA2, cap1, PtID51, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: TMA2, cap19, PtID8, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival1


title: EMCD8-P7-ME-HL981

source_name: bulk antigen-experienced CD8+ T cells, ME patient 981


title: CG614A


title: CG601A


title: EMCD8-P6-ME-HL958

source_name: bulk antigen-experienced CD8+ T cells, ME patient 958


title: CG602B


title: TMA2, cap17, PtID61, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EUB199

description: ethnicity: African descent

growth_protocol: Monocyte DNA samples were obtained from PBMCs frozen in 90% fetal calf serum (FCS) and 10% dimethyl sulfoxide dimethyl sulfoxid

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions followed by ethanol precipitation

treatment_protocol: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions

value: CD14+ Monocytes, resting cells

value: CD14+ Monocytes


title: TMA2, cap18, PtID60, viruspositive, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0

value: FU


title: EUB176

description: ethnicity: African descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: TMA2, cap26, PtID30, viruspositive, response1, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: TMA2, cap16, PtID65, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA2, cap14, PtID66, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: EMCD8-P4-HC-HL996

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 996

value: HC


title: EMCD8-P5-ME-HL948

source_name: bulk antigen-experienced CD8+ T cells, ME patient 948


title: TMA2, cap13, PtID66, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival1


title: EMCD8-P3-HC-HL992

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 992


title: TMA2, cap15, PtID65, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: CG613A


title: EUB174

description: ethnicity: African descent


title: TMA2, cap12, PtID76, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1


title: TMA2, cap11, PtID57, virusnegative, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: EMCD8-P2-HC-HL986

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 986


title: EUB196

description: ethnicity: African descent


title: TMA2, cap10, PtID25, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EUB173

description: ethnicity: African descent


title: TMA1, cap72, PtID79, virusnegative, response1, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: NVCD8-J8-ME-HL982

source_name: bulk naive CD8+ T cells, ME patient 982


title: EUB172

description: ethnicity: African descent


title: TMA1, cap73, PtID80, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis0, Survival0


title: NVCD8-J7-ME-HL981

source_name: bulk naive CD8+ T cells, ME patient 981


title: TMA1, cap70, PtID54, viruspositive, response1, treatmentFU, LocalDisease0, Metastasis1, Survival0


title: TMA1, cap71, PtID19, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EUB166

description: ethnicity: African descent


title: TMA1, cap69, PtID68, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA1, cap68, PtID69, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival1


title: NVCD8-J5-ME-HL948

source_name: bulk naive CD8+ T cells, ME patient 948


title: EUB175

description: ethnicity: African descent


title: NVCD8-J6-ME-HL958

source_name: bulk naive CD8+ T cells, ME patient 958


title: TMA1, cap67, PtID17, virusnegative, response1, treatmentFU, LocalDisease0, Metastasis1, Survival0


title: EUB162

description: ethnicity: African descent


title: NVCD8-J4-HC-HL996

source_name: bulk naive CD8+ T cells, healthy sedentary control 996


title: TMA1, cap65, PtID22, virusnegative, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0

source_name: Merkel cell carcinoma


title: TMA1, cap64, PtID13, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: NVCD8-J3-HC-HL992

source_name: bulk naive CD8+ T cells, healthy sedentary control 992


title: EUB161

description: ethnicity: African descent

source_name: Blood


title: TMA1, cap63, PtID17, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: EUB160

description: ethnicity: African descent


title: TMA1, cap61, PtID33, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: NVCD8-J2-HC-HL986

source_name: bulk naive CD8+ T cells, healthy sedentary control 986


title: EUB157

description: ethnicity: African descent


title: TMA1, cap59, PtID40, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival0

value: post


title: EMCD8-P17-ME-D1-EN524

source_name: bulk antigen-experienced CD8+ T cells, ME patient 524


title: EMCD8-P15-ME-D1-EN424

source_name: bulk antigen-experienced CD8+ T cells, ME patient 424


title: TMA1, cap60, PtID25, viruspositive, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0

value: Merkel cell carcinoma


title: EUB164

description: ethnicity: African descent


title: TMA1, cap58, PtID6, viruspositive, response0, treatmentpost, LocalDisease1, Metastasis0, Survival0

value: tissue


title: EUB156

description: ethnicity: African descent


title: EUB155

description: ethnicity: African descent


title: EMCD8-P14-ME-D1-EN101

source_name: bulk antigen-experienced CD8+ T cells, ME patient 101


title: TMA1, cap57, PtID80, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: tumor


title: TMA1, cap54, PtID12, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0

value: negative


title: EUB153

description: ethnicity: African descent


title: TMA1, cap56, PtID7, virusnegative, response0, treatmentpost, LocalDisease0, Metastasis1, Survival1

value: ICB


title: EMCD8-P13-HC-D1-EN410

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 410


title: TMA1, cap66, PtID72, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival0

value: pre


title: TMA1, cap53, PtID29, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: positive


title: TMA1, cap52, PtID71, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap62, PtID79, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA1, cap51, PtID22, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EUB143

description: ethnicity: African descent

value: Blood


title: TMA1, cap9, PtID56, virusnegative, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EMCD8-P12-HC-D1-EN759

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 759


title: TMA1, cap8, PtID56, virusnegative, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: EMCD8-P11-HC-D1-EN145

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 145


title: TMA1, cap7, PtID60, viruspositive, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: EUB141

description: ethnicity: African descent


title: TMA1, cap55, PtID9, viruspositive, response0, treatmentpost, LocalDisease1, Metastasis1, Survival1


title: TMA1, cap6, PtID60, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EMCD8-P10-HC-D1-EN481

source_name: bulk antigen-experienced CD8+ T cells, healthy sedentary control 481


title: NVCD8-J17-ME-D1-EN524

source_name: bulk naive CD8+ T cells, ME patient 524


title: NVCD8-J15-ME-D1-EN424

source_name: bulk naive CD8+ T cells, ME patient 424


title: TMA1, cap48, PtID72, virusnegative, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival0


title: TMA1, cap49, PtID2, virusnegative, response0, treatmentpost, LocalDisease1, Metastasis1, Survival1


title: TMA1, cap5, PtID60, viruspositive, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: EUB146

description: ethnicity: African descent


title: NVCD8-J13-HC-D1-EN410

source_name: bulk naive CD8+ T cells, healthy sedentary control 410


title: EUB140

description: ethnicity: African descent


title: TMA1, cap50, PtID2, virusnegative, response0, treatmentpost, LocalDisease1, Metastasis1, Survival1


title: TMA1, cap4, PtID18, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: EUB139

description: ethnicity: African descent


title: EUB138

description: ethnicity: African descent


title: NVCD8-J12-HC-D1-EN759

source_name: bulk naive CD8+ T cells, healthy sedentary control 759


title: TMA1, cap47, PtID77, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap42, PtID64, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: NVCD8-J14-ME-D1-EN101

source_name: bulk naive CD8+ T cells, ME patient 101


title: TMA1, cap45, PtID23, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap44, PtID62, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap38, PtID31, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap43, PtID63, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap35, PtID59, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: H460 cells, trametinib, D10, biol rep2

city: Shanghai

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

country: China

institute: Shanghai Chest Hospital

data_processing:
FastQC-11.8
Sequence reads were trimmed for adaptor sequence/low-qcccccuality sequence using TrimGalore-0.5.0 (parameter:  -q 25 --phred33 --length 36 -e 0.1 --stringency 3)
Trimmed sequence reads were mapped to GRCh38 using hisat2-2.1.0
Read count extraction and normalization were performed using stringtie
Assembly: GRCh38
Supplementary files format and content: The csv file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values and TPM values for each Sample

growth_protocol: Cells were maintained in a humidified incubator at 37 °C with 5% CO2, grown in RPMI 1640 or DMEM supplemented with 10% FBS and penicillin (100 U/ml)/streptomycin(100μg/ml) (Gibco/Thermo Fisher).

extract_protocol:
Total RNA isolation were performed using TRIzol reagent (Life Technologies, Inc., USA) and RNA isolation Kit (Qiagen, Germany).
mRNA isolation and residual genomic DNA degradation were performed, and then, 100 ng mRNA from each sample was reverse-transcribed into cDNA and fragmented into 100-300-bp pieces. End-repair and adapter-ligation were performed via the NEBNext Ultra Directional RNA Library Prep Kit (NEB, USA). Amplification and sequencing were performed using PCR and Illumina Next500 (Illumina, USA).

treatment_protocol: NSCLC cells were treated with trametinib (10nM) for 2, 5, and 10 days in 6-well plates, respectively.

value: non-small cell lung cancer

value: WT

value: trametinib (10nM)

tag: time

value: Day 10


title: TMA1, cap46, PtID20, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0


title: TMA1, cap33, PtID52, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: H460 cells, trametinib, D10, biol rep1


title: TMA1, cap36, PtID39, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: H460 cells, trametinib, D5, biol rep3

value: Day 5


title: TMA1, cap41, PtID64, viruspositive, responseNA, treatmentFU, LocalDisease0, Metastasis1, Survival1

value: FU


title: NVCD8-J11-HC-D1-EN145

source_name: bulk naive CD8+ T cells, healthy sedentary control 145


title: TMA1, cap31, PtID27, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0

source_name: Merkel cell carcinoma


title: TMA1, cap3, PtID21, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: EUB131

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: EUB126

description: ethnicity: African descent


title: EUB124

description: ethnicity: African descent


title: EUB134

description: ethnicity: African descent


title: EUB136

description: ethnicity: African descent


title: EUB137

description: ethnicity: African descent


title: EUB137_R

description: ethnicity: African descent


title: EUB122

description: ethnicity: African descent


title: TMA1, cap40, PtID64, viruspositive, responseNA, treatmentpost, LocalDisease0, Metastasis1, Survival1

value: Merkel cell carcinoma

value: post


title: TMA1, cap39, PtID25, viruspositive, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0

value: tissue

value: tumor


title: TMA1, cap30, PtID58, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0


title: NVCD8-J10-HC-D1-EN481

source_name: bulk naive CD8+ T cells, healthy sedentary control 481

value: HC


title: TMA1, cap37, PtID32, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival0

value: negative

value: pre


title: H460 cells, trametinib, D10, biol rep3


title: TMA1, cap29, PtID9, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1

value: ICB


title: TMA1, cap2, PtID26, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0

value: positive


title: EUB128

description: ethnicity: African descent

source_name: Blood

value: Blood


title: TMA1, cap34, PtID35, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival1


title: TMA1, cap32, PtID78, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: H460 cells, trametinib, D5, biol rep2

value: non-small cell lung cancer

value: WT

value: trametinib (10nM)


title: EUB119

description: ethnicity: African descent


title: TMA1, cap25, PtID15, virusnegative, response1, treatmentpost, LocalDisease1, Metastasis1, Survival0


title: TMA1, cap28, PtID9, virusnegative, response0, treatmentFU, LocalDisease1, Metastasis1, Survival1

value: FU


title: EUB115

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells


title: TMA1, cap21, PtID5, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival0


title: EUB110

description: ethnicity: African descent

value: CD14+ Monocytes


title: EUB120

description: ethnicity: African descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: EUB117

description: ethnicity: African descent


title: H460 cells, D0, biol rep2

value: Day 0


title: H460 cells, D0, biol rep3


title: TMA1, cap26, PtID15, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0

value: Merkel cell carcinoma


title: EUB121

description: ethnicity: African descent


title: H460 cells, trametinib, D5, biol rep1

value: Day 5


title: TMA1, cap27, PtID10, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0

value: tissue

value: tumor


title: H460 cells, trametinib, D2, biol rep3

value: Day 2


title: H460 cells, trametinib, D2, biol rep2


title: H460 cells, D0, biol rep1


title: EUB107

description: ethnicity: African descent


title: TMA1, cap15, PtID65, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1

value: negative

value: pre


title: TMA1, cap1, PtID51, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0

value: positive


title: TMA1, cap18, PtID8, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival1

value: ICB

value: post


title: TMA1, cap17, PtID60, viruspositive, responseNA, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: H460 cells, trametinib, D2, biol rep1

value: non-small cell lung cancer

value: WT


title: EUB118

description: ethnicity: African descent

value: Blood


title: TMA1, cap24, PtID2, virusnegative, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1


title: TMA1, cap19, PtID8, viruspositive, response0, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA1, cap22, PtID5, viruspositive, response0, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: EUB106

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells


title: TMA1, cap16, PtID61, viruspositive, responseNA, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: H23 cells, trametinib, D10, biol rep2

value: trametinib (10nM)

value: Day 10


title: TMA1, cap14, PtID65, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA1, cap13, PtID66, viruspositive, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA1, cap23, PtID4, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival1


title: TMA1, cap10, PtID25, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: EUB103

description: ethnicity: African descent

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: EUB100

description: ethnicity: African descent


title: TMA1, cap12, PtID76, viruspositive, response0, treatmentpre, LocalDisease1, Metastasis1, Survival1

value: Merkel cell carcinoma


title: H23 cells, trametinib, D10, biol rep1


title: TAS129 V10 [103697-001-079]

city: Leiden

first: Abilash

last: Ravi

address: Albinusdreef 2

department: Department of Pulmonology

country: Netherlands

institute: Leiden University Medical Center

description: in vivo bronchial epithelium

data_processing:
The reference of ‘Homo_sapiens.GRCh37.75’ was used to align the reads. The mapping to the reference sequence was done using a short reader aligner based on Burrows-Wheeler transform.
Clustering and RNA sequencing was performed according to the manufacture’s protocol using the Illumina NextSeq 500
The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment
The read counts were loaded into the DESeq2 package, a statistical package within the R/BioConductor platform to determine the differentially expressed genes (paired)
Image analysis, base calling and quality check was performed with Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Genome_build: hg19
Supplementary_files_format_and_content: count files: curated counts of genes in each sample

source_name: primary bronchial epithelial cells

growth_protocol: The bronchial brushes were obtained from bronchoscopy

extract_protocol:
The pellet was dissolved in 1 ml of TRIzol™ and stored at -80°C until RNA was isolated. After all samples were obtained, they were thawed at room temperature and, after 200 µl of chloroform was added, shaken vigorously for 30 seconds. The samples were kept at RT for 10 mins and centrifuged at 16,000g for 15 mins at 4°C. The aqueous phase was cleaned up and concentrated with protocol 5.3 using the Nucleospin® RNA XS extraction kit (Macherey-Nagel). No carrier RNA was added as it would interfere with RNA sequencing.
The NEBNext Ultra Directional RNA library prep kit for Illumina was used to process the samples. The samples preparation was performed according to the protocol “NEBNext Ultra Directional RNA Library Prep Kit for Illumina” (NEB #7420S/L). Briefly, oligo-dT magnetic beads were used to isolate mRNA from total RNA. cDNA synthesis was performed after fragmentation of this mRNA. This was used for ligation with sequencing adapters followed by PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the fragment analyser. The size of the resulting products was consistent with the expected size distribution between 300-500 base pairs. To evaluate the quality of the library preparation and kits used, the raw data was sampled and mapped to annotated genomic references. Mapping positions were classified as intragenic, exonic, intergenic, intronic and rRNA. Clustering and DNA sequencing was performed according to the manufacture’s protocol using the Illumina NextSeq 500. A concentration of 1.6pM was used as input. The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12.

treatment_protocol: The brushes which consisted predominantly (>95%) of PBECs, were pooled (2 brushes for each sample) and centrifuged at 1240 rpm (Rotanta 460S) for 10 minutes at 4°C.

tag: donor

value: Severe asthma patients

tag: collection method

value: direct bronchoscopy

tag: type

value: untreated lobe


title: EUB101

description: ethnicity: African descent


title: EUB094

description: ethnicity: African descent


title: H23 cells, trametinib, D5, biol rep3

value: Day 5


title: H23 cells, trametinib, D10, biol rep3


title: TAS131 V10 [103697-001-077]

description: in vivo bronchial epithelium

value: treated lobe


title: H23 cells, trametinib, D5, biol rep2


title: TAS130 V10 [103697-001-073]

description: in vivo bronchial epithelium


title: EUB093

description: ethnicity: African descent


title: TAS125 V10 [103697-001-071]

description: in vivo bronchial epithelium


title: TAS125 V10 [103697-001-070]

description: in vivo bronchial epithelium


title: EUB091

description: ethnicity: African descent


title: TAS204 V10 [103697-001-067]

description: in vivo bronchial epithelium


title: H23 cells, trametinib, D2, biol rep2

value: Day 2


title: EUB090

description: ethnicity: African descent


title: TAS130 V10 [103697-001-074]

description: in vivo bronchial epithelium


title: TAS203 V10 [103697-001-063]

description: in vivo bronchial epithelium


title: H23 cells, trametinib, D5, biol rep1


title: TAS203 V10 [103697-001-062]

description: in vivo bronchial epithelium


title: TAS201 V10 [103697-001-060]

description: in vivo bronchial epithelium


title: TMA1, cap11, PtID57, virusnegative, responseNA, treatmentpre, LocalDisease1, Metastasis0, Survival0

value: tissue

value: tumor

value: negative

value: pre


title: H23 cells, trametinib, D2, biol rep3

value: non-small cell lung cancer

value: WT


title: TAS129 V10 [103697-001-080]

description: in vivo bronchial epithelium


title: EUB088

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells

value: Blood


title: EUB084_R

description: ethnicity: African descent

value: CD14+ Monocytes


title: EUB085

description: ethnicity: African descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: TAS131 V10 [103697-001-076]

description: in vivo bronchial epithelium


title: H23 cells, D0, biol rep3

value: Day 0


title: TAS128 V10 [103697-001-056]

description: in vivo bronchial epithelium

value: Severe asthma patients


title: H23 cells, D0, biol rep2


title: TAS201 V10 [103697-001-059]

description: in vivo bronchial epithelium

value: direct bronchoscopy


title: H23 cells, D0, biol rep1


title: TAS128 V10 [103697-001-055]

description: in vivo bronchial epithelium

value: untreated lobe


title: TAS204 V10 [103697-001-066]

description: in vivo bronchial epithelium


title: TAS126 V10 [103697-001-052]

description: in vivo bronchial epithelium


title: TAS126 V10 [103697-001-053]

description: in vivo bronchial epithelium


title: H23 cells, trametinib, D2, biol rep1

value: trametinib (10nM)


title: TAS124 V10 [103697-001-051]

description: in vivo bronchial epithelium

value: treated lobe


title: EUB083

description: ethnicity: African descent


title: TAS124 V10 [103697-001-050]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D10, biol rep3

value: Day 10


title: Calu1 cells, trametinib, D10, biol rep2


title: TAS121 V10 [103697-001-047]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D10, biol rep1


title: TAS121 V10 [103697-001-046]

description: in vivo bronchial epithelium


title: TAS120 V10 [103697-001-043]

description: in vivo bronchial epithelium


title: EUB081

description: ethnicity: African descent


title: EUB084

description: ethnicity: African descent


title: TAS119 V10 [103697-001-040]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D5, biol rep3

value: Day 5


title: EUB080

description: ethnicity: African descent


title: TAS119 V10 [103697-001-039]

description: in vivo bronchial epithelium


title: TAS118 V10 [103697-001-035]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D5, biol rep2


title: TAS118 V10 [103697-001-036]

description: in vivo bronchial epithelium


title: EUB078

description: ethnicity: African descent


title: TAS117 V10 [103697-001-033]

description: in vivo bronchial epithelium


title: TAS116 V10 [103697-001-030]

description: in vivo bronchial epithelium


title: TAS116 V10 [103697-001-029]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D5, biol rep1


title: EUB082

description: ethnicity: African descent


title: TAS120 V10 [103697-001-044]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D2, biol rep3

value: Day 2


title: EUB075

description: ethnicity: African descent


title: TAS115 V10 [103697-001-027]

description: in vivo bronchial epithelium


title: TAS114 V10 [103697-001-024]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D2, biol rep2


title: TAS115 V10 [103697-001-026]

description: in vivo bronchial epithelium


title: Calu1 cells, trametinib, D2, biol rep1


title: Calu1 cells, D0, biol rep3


title: EUB076

description: ethnicity: African descent


title: TAS113 V10 [103697-001-020]

description: in vivo bronchial epithelium


title: Calu1 cells, D0, biol rep2


title: TAS108 V10 [103697-001-015]

description: in vivo bronchial epithelium


title: TAS114 V10 [103697-001-023]

description: in vivo bronchial epithelium


title: EUB072

description: ethnicity: African descent


title: EUB077

description: ethnicity: African descent


title: TAS107 V10 [103697-001-012]

description: in vivo bronchial epithelium


title: TAS108 V10 [103697-001-014]

description: in vivo bronchial epithelium


title: Calu1 cells, D0, biol rep1


title: TAS117 V10 [103697-001-032]

description: in vivo bronchial epithelium


title: TAS104 V10 [103697-001-007]

description: in vivo bronchial epithelium


title: EUB070

description: ethnicity: African descent


title: TAS102 V10 [103697-001-003]

description: in vivo bronchial epithelium


title: A549 cells, trametinib, D10, biol rep2


title: A549 cells, trametinib, D10, biol rep1


title: TAS102 V10 [103697-001-002]

description: in vivo bronchial epithelium


title: A549 cells, trametinib, D5, biol rep3


title: A549 cells, trametinib, D10, biol rep3


title: EUB074

description: ethnicity: African descent


title: RAL2A 04 V2

value: Moderate asthma patients

value: in vivo

value: Moderate asthmatic bronchial epithelium


title: TAS104 V10 [103697-001-006]

description: in vivo bronchial epithelium


title: TAS107 V10 [103697-001-011]

description: in vivo bronchial epithelium


title: A549 cells, trametinib, D5, biol rep2

value: non-small cell lung cancer

value: WT


title: RAL2A 10 V2


title: EUB061

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells

value: Blood


title: EUB073

description: ethnicity: African descent

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: RAL2A 05 V2


title: TAS113 V10 [103697-001-021]

description: in vivo bronchial epithelium

value: Severe asthma patients


title: RAL2A 06 V2

value: direct bronchoscopy


title: EUB067

description: ethnicity: African descent


title: EUB065

description: ethnicity: African descent


title: TAS112 V3A

value: Severe asthmatic bronchial epithelium


title: EUB060

description: ethnicity: African descent


title: EUB058

description: ethnicity: African descent


title: A549 cells, trametinib, D5, biol rep1

value: trametinib (10nM)


title: TAS121 V3A


title: TAS203 V3A


title: TAS104 V3 H


title: RILC5 01 V2


title: EUB062

description: ethnicity: African descent


title: A549 cells, trametinib, D2, biol rep3


title: TAS201 V3B H


title: EUB052

description: ethnicity: African descent


title: TAS113 V3A


title: EUB051

description: ethnicity: African descent


title: TAS120 V3B H


title: A549 cells, trametinib, D2, biol rep2


title: TAS204 V3A


title: A549 cells, trametinib, D2, biol rep1


title: EUB049

description: ethnicity: African descent


title: TAS118 V3A H


title: CCI+BZ-2

city: Beijing

first: Wu

last: Dan

address: Dongzhimennei south steet 16

institute: Institute of Chinese Materia Medica，China Academy of Chinese Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations  were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads  were generated.
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 removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All  the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two groups (four biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: rn4
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Lumbar spinal cord(L4-L6)

growth_protocol: Adult male Sprague-Dawley rats (180-200 g)  were housed with a fixed light/dark cycle (12/12 h), a room temperature of 21–22 ℃, and ad libitum access to food and water. CCI rat model was established as previously described. Briefly, the left common sciatic nerve in each rat was exposed at the mid-thigh level. The area proximal to the sciatic nerve’s trifurcation was freed of adhering tissue, and four ligatures were tied loosely around it with approximately 1 mm between each ligature. The sciatic nerve was exposed but not ligated in sham group animals.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sequencing libraries were generated using NEBNextUltra RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations.

treatment_protocol: The CCI rats were randomly assigned to four groups: the CCI group, the CCI+YZP group, the CCI+YH group, and the CCI+BZ group, with 7 rats in each group. YZP (10.8 g crude drug/kg), YH (7.2 g crude drug/kg,) and BZ (3.6 g crude drug/kg) were administered respectively and continuously for 5 days from the postoperative day (POD) 6 to 10. The ipsilateral L4-L6 SC of rats were collected on POD 10, immersed in TRIzol (Invitrogen, CA, USA), and immediately frozen in liquid nitrogen for the RNA-seq.

value: Lumbar spinal cord(L4-L6)

tag: gender

value: male

tag: age

value: adult

tag: strain

value: Sprague-Dawley rat

value: BZ (3.6 g crude drug/kg)


title: CCI+BZ-3

tag: tissue


title: TAS119 V3A N

value: in vivo


title: A549 cells, D0, biol rep3

tag: cell line

tag: cell type

value: Day 0


title: CCI+BZ-1

tag: treatment


title: A549 cells, D0, biol rep1

value: non-small cell lung cancer

tag: genotype


title: EUB047

description: ethnicity: African descent


title: EUB046

description: ethnicity: African descent


title: TAS117 V3A H


title: K562_dtagknockin_DMSO_12hr_CTCF_HiChIP_rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

description:
K562_dtagknockin_DMSO_12hr_rep1_CTCF_hichip.allvalidpairs
K562_dtagknockin_DMSO_12hr_rep1_CTCF_hichip.interactions.all.mango

data_processing:
HiChIP reads for each sample were aligned to hg38 and processed with HiC Pro (v 3.0.0) using the default settings with a DPNii digested genome generated with the digest_genome script. This produced .allvalidpairs files.
Hichipper (v 0.7.7) with default parameters was used to produce unfiltered loop lists(.mango files)
Assembly: hg38
Supplementary files format and content: .allvalidpairs files contain all pairs output by HiC-Pro for a given sample.
Supplementary files format and content: .mango files contains a list of all loops identified by hichipper for a given sample along with the associated P value and PET number.
Library strategy: HiChIP

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin. HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Nuclei were isolated and chromatin was subjected to DPNII digestion, biotin fill-in, and in situ ligation. Chromatin was then sheared with a Covaris sonicator and CTCF-bound chromatin was immunoprecipitated overnight.
DNA was tagmented with Tn5 and amplified by PCR.

treatment_protocol: For DNMT1i experiments, cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. For dTAG-13 experiments, cells were treated at 500nMM dTAG-13 or 0.1% DMSO for 6 or 12 hours. All treatments were in duplicate separate cultures.

value: chronic myeloid leukemia


title: TAS115 V3A H


title: CCI+YH-3

value: YH (7.2 g crude drug/kg)


title: EUB043

description: ethnicity: African descent

value: CD14+ Monocytes, resting cells

value: Blood


title: K562_dtagknockin_DMSO_12hr_CTCF_HiChIP_rep1


title: TAS114 V3A N


title: CCI+YH-1


title: TAS106 V3B H


title: EUB041

description: ethnicity: African descent

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: K562_dtagknockin_dtag13_12hr_CTCF_HiChIP_rep2

description:
K562_dtagknockin_dtag13_12hr_rep1_CTCF_hichip.allvalidpairs
K562_dtagknockin_dtag13_12hr_rep1_CTCF_hichip.interactions.all.mango


title: CCI+YZP-3

value: YZP (10.8 g crude drug/kg)


title: EUB040

description: ethnicity: African descent


title: TAS108 V3B H

value: Severe asthma patients

value: direct bronchoscopy

value: Severe asthmatic bronchial epithelium


title: A549 cells, D0, biol rep2

value: WT


title: EUB048

description: ethnicity: African descent


title: CCI+YZP-2

value: Lumbar spinal cord(L4-L6)

value: male

value: adult


title: K562_dtagknockin_dtag13_12hr_CTCF_HiChIP_rep1


title: EUB039

description: ethnicity: African descent


title: TAS102 V3 H

value: in vivo


title: EUB038

description: ethnicity: African descent


title: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_minus_DNMT1i_SON_CutTag_rep2

description: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_minus_DNMT1i_SON_CutTag.bigwig

data_processing:
Reads were aligned to hg38 using Burrow-Wheeler Aligner (BWA-mem, v  0.7.15)
Sam files were converted to bam files and sorted using Samtools view and sort (v 1.5)
Identical equence reads were collapsed to avoid PCR duplicates using Picard Tools MarkDuplicates(v 2.18.5) with Java (v 1.8.0) with parameters VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
Bigwig files averaging replicates were constructed from deduplicated bam files using Deeptools (v 3.4.3) bamCoverage with -normalizeUsing RPKM --operation mean
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files are provided for each Cut&Tag condition with replicates averaged.
Library strategy: Cut&Tag

extract_protocol:
Cells were harvested and nuclei were isolated and lightly fixed with 0.1% formaldehyde for 2 minutes. Nuclei were bound to Concavalin A beads and anti-SON antibody was added at 4C overnight. Following addition of secondary antibody and subsequent washes, pA-Tn5 was added.
Chromatin was tagmented with PA-Tn5 and DNA was extracted and amplified by PCR.

treatment_protocol: Cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. Cells were treated with 330nM HaloPROTAC3 for 32 hours (8 hours before adding DNMT1i  or DMSO for 24 hours more).

value: colorectal carcinoma


title: CCI+YH-2

value: Sprague-Dawley rat


title: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_minus_DNMT1i_SON_CutTag_rep1


title: TAS101 V3 N


title: EUB036

description: ethnicity: European descent


title: CCI+YZP-1


title: CCI-3

value: CCI


title: A007 V1

value: Mild asthma patients

value: Mild asthmatic bronchial epithelium


title: EUB035

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells

value: Blood


title: EUB034

description: ethnicity: European descent

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: CCI-1


title: EUB033

description: ethnicity: European descent


title: A055 V1


title: Sham-3

value: Sham


title: HCT116_HaloTag_CTCF_32hr_HaloPROTAC3_24hr_DNMT1i_SON_CutTag_rep2

description: HCT116_HaloTag_CTCF_32hr_HaloPROTAC3_24hr_DNMT1i_SON_CutTag.bigwig

value: HaloPROTAC3 330nM 32hr, DNMT1i 10uM 24hr


title: Sham-2


title: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_24hr_DNMT1i_SON_CutTag_rep2

description: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_24hr_DNMT1i_SON_CutTag.bigwig

value: DNMT1i 10uM 24hr


title: HCT116_HaloTag_CTCF_32hr_HaloPROTAC3_24hr_DNMT1i_SON_CutTag_rep1


title: A062 V1

value: direct bronchoscopy


title: EUB032

description: ethnicity: European descent


title: CCI-2

value: Lumbar spinal cord(L4-L6)


title: A064 V1


title: EUB031

description: ethnicity: European descent


title: K562_dtagknockin_DMSO_12hr_CTCF_input_rep2

data_processing:
Reads were aligned to hg38 using Burrow-Wheeler Aligner (BWA-mem, v  0.7.15)
Sam files were converted to bam files and sorted using Samtools view and sort (v 1.5)
Identical ChIP-seq sequence reads were collapsed to avoid PCR duplicates using Picard Tools MarkDuplicates(v 2.18.5) with Java (v 1.8.0) with parameters VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
Peaks were called using Homer (v. 4.11) getDifferentialPeaksReplicates where -t was replicate ChIP files, -i was the corresponding replicate input files, with parameters -F 10 and -L 4.  Reactivated DNMT1i peaks were called using Homer (v. 4.11) getDifferentialPeaksReplicates where -t was replicate ChIP files for DNMT1i treatment, -b was the replicate ChIP files for DMSO treatment, and -p was the peaks called in the corresponding DNMT1i treatment condition
Bigwig files were constructed from deduplicated bam files using Deeptools2 (v 3.4.3) bamCoverage with --normalizeUsing RPKM and default settings.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files are provided for each ChIP sample.
Supplementary files format and content: Replicate homer peak files are provided for each ChIP condition. Reactivated peak files for 3 days of DNMT1i v. DMSO are also provided.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Cells were lysed and DNA was sonicated with a Branson Sonicator. Immunoprecipitations were carried out overnight for ChIP samples.
ChIP or input DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

treatment_protocol: For DNMT1i experiments, cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. For dTAG-13 experiments, cells were treated at 500nMM dTAG-13 or 0.1% DMSO for 6 hours. All treatments were in duplicate separate cultures.

value: chronic myeloid leukemia


title: Sham-1

value: male

value: adult


title: A043  V1

value: in vivo


title: K562_dtagknockin_DMSO_12hr_CTCF_input_rep1


title: A003 V1


title: EUB030

description: ethnicity: European descent


title: HCT116_HaloTag_CTCF_minus_HaloPROTAC3_24hr_DNMT1i_SON_CutTag_rep1

value: colorectal carcinoma


title: PAML002-CC-VC

city: GLASGOW

first: Alexander

last: Winton

address: Wolfson Wohl Cancer Research Centre, Bearsden

department: School Of Cancer Science

country: United Kingdom

institute: University Of Glasgow

data_processing:
The quality of the FASTQ files was checked using FastQC (V 0.11.9), which showed decent per-base sequence quality but revealed some reads with low quality, along with overrepresented polyG repeats in read 2, a known artifact of two-color system platforms. The reads were then trimmed using fastp (V 0.23.2), with adapter sequence auto-detection and removal, trimming of low-quality bases from both ends, and polyG removal, ensuring no reads below 35 bp were retained. The trimmed reads were aligned to an indexed reference genome (Ensembl release 107, GRCh38) using STAR (V 2.7.10a), generating a BAM file sorted by coordinate and restricted to one primary alignment per read. Finally, gene counts were quantified using FeatureCounts (V 2.0.3), specifying paired-end reads, reverse-strand specificity, and counting exons based on the gene_id attribute from the GTF annotation file.
Differential gene expression analysis was performed using DESeq2 (v1.44.0) and gene set enrichment analysis with fgsea (v1.30.0).
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
Supplementary files format and content: Counts Tables in the form of Text Files

source_name: Bone marrow

growth_protocol: Pediatric mesenchymal stem cells (pMSCs) were isolated from pediatric AML bone marrow mononuclear cells using the plastic adherence method. Cells were cultured under standard conditions (e.g., 37°C, 5% CO2) and characterized for differentiation potential. Cocultures with pediatric AML cells were conducted in 2D format with and without cytokine supplementation. Control liquid cultures (LC) were maintained without coculture.

extract_protocol:
Total RNA was extracted from pediatric AML cells following coculture with pediatric mesenchymal stem cells (pMSCs) using standard RNA isolation techniques. RNA was prepared for downstream RNA sequencing (RNA-seq) analysis to assess transcriptional changes due to coculture conditions.
Quality of sequencing was assessed using FastQC version 0.11.5 (Andrews, 2010), and sequences were trimmed using TrimGalore version 0.4.4_dev (Krueger, 2015) with 3’ end trimming and paired parameters, using a quality score threshold of 20. The reference genome (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz) was obtained via Ensembl (http://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/, 11/01/2018); reads were aligned to the genome using hisat2 (Kim et al. 2015).

treatment_protocol: For the RNA sequencing (RNA-seq) analysis, only the vehicle control (VC) conditions were used. Cells were cultured either in coculture (CC) with pediatric mesenchymal stem cells (pMSCs) or in liquid culture (LC), with no active chemotherapeutic agents added. The vehicle-only treatment was applied to control for any effects of the medium or solvent used in the experimental setup, ensuring the analysis focuses on the transcriptional changes due to coculture and not drug treatment.

value: Bone marrow

value: Pediatric Acute Myeloid Leukemia (pAML) Blasts

value: Co Culture


title: PAML002-LC-VC

value: Liquid Culture


title: K562_dtagknockin_dtag13_12hr_CTCF_input_rep2


title: A11 V1 N

value: Mild asthma patients

value: Mild asthmatic bronchial epithelium


title: A04 V1 N


title: A078 V1 H


title: PAML001-CC-VC


title: K562_dtagknockin_dtag13_12hr_CTCF_input_rep1


title: PAML001-LC-VC


title: A072 V1 N


title: FR0797-LC-VC

value: Pediatric Mesenchymal Stem Cells (pMSCs)


title: K562_dtagknockin_DMSO_12hr_CTCF_ChIP_rep1

description: K562_dtagknockin_DMSO_12hr_CTCF_rep1_rep2.txt


title: K562_dtagknockin_dtag13_12hr_CTCF_ChIP_rep2

description: K562_dtagknockin_dTAG_12hr_CTCF_rep1_rep2.txt


title: EUB010

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells

value: Blood

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: EUB028

description: ethnicity: European descent


title: A075 V1 H

value: direct bronchoscopy


title: EUB024

description: ethnicity: European descent


title: FR0797-CC-VC


title: K562_dtagknockin_DMSO_12hr_CTCF_ChIP_rep2

value: chronic myeloid leukemia


title: FR0551-LC-VC


title: EUB014

description: ethnicity: European descent


title: EUB012

description: ethnicity: European descent


title: A069 V1 H


title: K562_dtagknockin_dtag13_12hr_CTCF_ChIP_rep1


title: FR0551-CC-VC


title: EUB004

description: ethnicity: European descent


title: A070 V1 H


title: HCT116_HTCTCF_DMSO_1day_CTCF_input_rep2


title: A067 V1 H


title: EUB003

description: ethnicity: European descent


title: FR0376-LC-VC


title: HCT116_HTCTCF_DNMT1i_1day_CTCF_input_rep2


title: A020 V1 H


title: HCT116_HTCTCF_DNMT1i_1day_CTCF_input_rep1


title: AFB215

description: ethnicity: European descent


title: EUB008

description: ethnicity: European descent


title: A023 V1 H


title: FR0376-CC-VC


title: AFB211

description: ethnicity: European descent


title: FR0268-LC-VC


title: Ribo_N6AMT1_2

city: Epalinges

first: Alexis

last: Jourdain

address: Boveresses 155, CP51

department: Immunobiology

country: Switzerland

institute: University of Lausanne

library_source: other

data_processing:
Fastq files were adaptor stripped using cutadapt. Only trimmed reads were retained, with a minimum length of 15 and a quality cutoff of 2 (parameters: -a CTGTAGGCACCATCAAT – trimmed-only –minimum-length = 15 –quality-cutoff = 2)
Histograms were produced of ribosome footprint lengths and reads were retained if the trimmed size was 26 or 34 nucleotides.
Resulting reads were mapped, using default parameters, with HISAT260 using a GRCh38, release 84 genome and index and were removed if they mapped to rRNA or tRNA according to GRCh38 RepeatMasker definitions from UCSC.
A full set of transcripts and CDS sequences for Ensembl release 84 was then established. Only canonical transcripts (defined by knownCanonical table, downloaded from UCSC) were retained with their corresponding CDS. Retained reads were then mapped to the canonical transcriptome with bowtie2 using default parameters.
For analysis, the P-site position of each read was predicted by riboWaltz  and confirmed by inspection. Counts were made by aggregating P-sites overlapping with the CDS and P-sites Per Kilobase Million (PPKMs) were then generated through normalizing by CDS length and total counts for the sample.
Read counts were generated by overlapping with a GRCh38, release 84 gtf.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file include raw count for each sample
Library strategy: Ribosome profiling

molecule: other

growth_protocol: K562 cells were maintained in DMEM containing 1 mM sodium pyruvate (ThermoFisher Scientific) with 25 mM glucose, 10% fetal bovine serum, and 100 U/ml penicillin/streptomycin nder 5% CO2 at 37°C.

extract_protocol:
Frozen cell pellets were directly resuspended by pipetting in 200 μl of mammalian footprint lysis buffer (20 mM Tris-Cl [pH7.4], 150 mM KCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 2 units/ml Turbo DNase, 0.1 mg/ml cycloheximide). Lysates were incubated on ice for 10 min and then cleared by centrifugation at 20,000 g for 10 min at 4 °C.
1.5 A260 units of lysate was diluted to 200 µl with lysis buffer and digested with 750 units of RNase I in 200 µl lysis buffer at 25 °C for 1 h with 500 rpm agitation in a thermomixer. Reactions were quenched with 200 U SUPERase-in and pelleted through a 900 µl sucrose cushion in a TLA100.3 rotor for 1 h at 100,000 rpm.
Pellets were resuspended in 300 µl TRIzol (Thermo Fisher) and RNA extracted with the Zymo Direct-zol RNA miniprep kit according to the manufacturer’s instructions for purifying total RNA including small RNAs
Fragments were size selected on a 15% TBE-urea PAGE gel  with 15 and 36 nt oligos as size markers, cutting a range from 15 to 36 nt. After gel elution, fragments were dephosphorylated with PNK, and, ligated to preadenylated 3′ linker oBZ407. rRNA depletion was performed with the ribo-zero gold kit (Illumina).
Reverse transcription was performed using protoscript II (NEB) and RT primer oBZ408, and RNA degraded by base hydrolysis. cDNA was gel purified and circularized with Circ Ligase (Lucigen). Libraries were PCR amplified using forward primer oBZ287 (NINI2) and reverse primers bar 11 through 16 (oBZ207-212).
PCR was performed with Phusion DNA polymerase, 1 µM of each primer, and 8 cycles. Amplified libraries were purified away from primers on an 8% native TBE acrylamide gel. After extraction, DNA was quantified by bioanalyzer high-sensitivity DNA chip (Agilent) then equimolarly pooled.

treatment_protocol: Cells were transduced with pLentiCRISPRv2 carrying sgRNA targeting N6AMT1 or control (OR11A1 and OR2M49) by lentiviral infection. 48 h post infection, cells were selected with 10 mg/ml Puromycin for 48 h. Cells were maintained in routine culture media for 10 days post infection before analysis


title: Ribo_N6AMT1_3


title: AFB209

description: ethnicity: European descent


title: HCT116_HTCTCF_DMSO_1day_CTCF_rep1

description: HCT116_HTCTCF_DMSO_1day_rep1_rep2_peaks.txt


title: AFB213

description: ethnicity: European descent


title: HCT116_HTCTCF_DNMT1i_1day_CTCF_rep1

description: HCT116_HTCTCF_DNMT1i_1day_rep1_rep2_peaks.txt


title: HCT116_HTCTCF_DNMT1i_1day_CTCF_rep2


title: A033 V1 N


title: EH01 V1 N

value: Healthy controls

value: Healthy bronchial epithelium


title: AFB208

description: ethnicity: European descent


title: H08 V1 H

value: in vivo


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDMSO_rep3

description: HCT116_HTCTCF_minusHaloPROTAC3_DNMT1i_DMSO_degenes.txt

data_processing:
UMIs were extracted with umi-tools (v 1.1.1) extract and adapters were  trimmed with cutadapt (v 2.7)
Reads were aligned to hg38 using Star aligner (v 2.6.0) with a genome generated using the Ensembl hg38 primary assembly and Ensembl GTF file v 104 with the following settings: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -- peOverlapNbasesMin 40 --peOverlapMMp 0.8 --outSAMattributes NH HI NM MD
Reads were deduplicated with umi-tools dedup ( v 1.1.1) with flags multimapping-detection-method=NH and unpaired-reads=discard
For gene expression analysis, HTseq – count ( v 0.11.2) was used to count reads in genes and generate counts files. For differential exon analysis, the dexseq_prepare_annotation script was used with the -r no option to prepare gff annotation files from ensemble gtf file (v 104) and the dexseq_count.py script was used to create counts files (dexseq.counts files).
DESeq2 (v 1.28) with R (v 4.0.2) was used to process expression count files to get gene expression foldchange values (deseq2_results.csv files). DEXSeq(v 1.34.1). with R (v 4.0.2) was used to process  exon count files and get normalized exon inclusion changes (dexseq_results.csv files)
Assembly: hg38
Supplementary files format and content: The HTSeq raw count files for genes for each individual sample are provided (.counts files). The DEXSeq raw count files for exons for each individual sample are provided (dexseq.counts files).
Supplementary files format and content: The DESeq2 results files with gene folchange and basemean values are provided for each experiment (deseq2_results.csv files). The DEXSeq results files with exon foldchange and basemean values are provided for each experiment (dexseq_results.csv files).

molecule: polyA RNA

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared using the PolyA enrichment kit and Corral mRNA Library Prep Kit  (Lexogen)

treatment_protocol: For DNMT1i experiments, cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. For dTAG-13 experiments, cells were treated at 500nM dTAG-13 or 0.1% DMSO for 6 hours. All treatments were in triplicate separate cultures.

value: colorectal carcinoma


title: Ribo_N6AMT1_1


title: AFB207

description: ethnicity: European descent


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDMSO_rep2


title: HCT116_HTCTCF_DMSO_1day_CTCF_rep2


title: AFB205

description: ethnicity: European descent


title: Ribo_Ctrl_3

value: Control


title: FR0268-CC-VC

value: Bone marrow


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDMSO_rep1


title: EH03 V1 N


title: H05 V1 N


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDNMT1i_rep3


title: H16 V1 N


title: AFB203

description: ethnicity: European descent


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDNMT1i_rep1


title: RNA_N6AMT1_2

data_processing:
Fastq files were adaptor stripped using cutadapt with a minimum length of 15 and a quality cutoff of 2 (parameters: -a NNNNNNCACTCGGGCACCAAGGAC –minimum-length = 15 –quality-cutoff = 2).
Resulting reads were mapped, using default parameters, with HISAT2 using a GRCh38, release 84 genome and index.
Read counts were generated by overlapping with a GRCh38, release 84 gtf.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file include raw count for each sample

extract_protocol:
Frozen cell pellets were directly resuspended by pipetting in 200 μl of mammalian footprint lysis buffer (20 mM Tris-Cl [pH7.4], 150 mM KCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 2 units/ml Turbo DNase, 0.1 mg/ml cycloheximide). Lysates were incubated on ice for 10 min and then cleared by centrifugation at 20,000 g for 10 min at 4 °C.
200 µl of trizol was added to an 0.5 A260 aliquot, and RNA was purified with the Zymo Direct-zol RNA miniprep kit according to the manufacturer’s instructions for purifying total RNA.
RNA-seq libraries were prepared using the Illumina TruSeq stranded total RNA-seq kit with ribozero gold human/mouse/rat rRNA depletion following the manufacturer's instructions.


title: Ribo_Ctrl_2


title: AFB195

description: ethnicity: European descent


title: HCT116_HTCTCF_minusHaloPROTAC_1dayDNMT1i_rep2


title: H15 V1 H


title: Ribo_Ctrl_1


title: H10 V1 N


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDMSO_rep3


title: H14 V1 N


title: RNA_N6AMT1_3


title: AFB197

description: ethnicity: European descent


title: H12 V1 N


title: H07 V1 N


title: AFB193

description: ethnicity: European descent


title: RNA_N6AMT1_1


title: AFB192

description: ethnicity: European descent


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDMSO_rep2


title: H09 V1 N


title: RNA_Ctrl_2


title: AFB204

description: ethnicity: European descent


title: RNA_Ctrl_3


title: AFB190_R

description: ethnicity: European descent


title: AFB190

description: ethnicity: European descent


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDMSO_rep1


title: H06 V1 N


title: H04 V1 N


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDNMT1i_rep3


title: RNA_Ctrl_1


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDNMT1i_rep2


title: H03 V1 N


title: HCT116_HTCTCF_plusHaloPROTAC3_1dayDNMT1i_rep1


title: AFB182_R

description: ethnicity: European descent


title: H02 V1 N


title: AFB182

description: ethnicity: European descent


title: A549 control

city: wenzhou

first: sunhui

last: xing

address: Ouhai district Chashan Street higher education park

institute: wenzhou medical university

description: without YHM18

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameter- mismath cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: lung

growth_protocol: HCT116 and A549 cells were incubated at 37 ℃ in 5% CO2 and maintained in McCoy's 5A and RPMI-1640 medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Libraries Prep Kit following manufacturer's protocols.

treatment_protocol: The active compound in our study is a novel pyrimidine derivative named YHM18. The control group was cultured in nomral medium. The treated group was challenged in 2µM YHM18 for 48h.

value: lung

value: human non-small cell lung cancer cells A549

value: epithelial cell

value: WT

value: Cultured in common medium


title: H01 V1 H


title: EndoC-βH1 with ARGI overexpression, replicate 3

city: Donostia - San Sebastian

first: Koldo

last: Garcia

address: Paseo Beguiristain S/N

country: Spain

institute: Biodonostia HRI

data_processing:
Reads were trimmed using Trimmomatic 0.39, with default settings
Reads were aligned by means of HISAT2 using as reference Human Genome assembly hg38
HTseq-count to get the counts of each transcript
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each sample

growth_protocol: EndoC-βH1 cells were seeded at an approximate density of 70.000-75.000 cells/cm2 on culture plates pre-coated with Matrigel-fibronectin (100mg/ml and 2 mg/mL, respectively) (Sigma-Aldrich) at 37°C, 5% CO2 in complete OPTIβ1 medium (Human Cell Design). Cells were passed every 7 days

extract_protocol:
48 hours after transfection cells were lysed and total RNA was purified using a silica-column-based prurification system from Macherey-Nagel (Nucleospin RNA Mini Kit, ref#740955.50
Sequencing libraries were prepared using “TruSeq Stranded Total RNA Human” kit (Illumina Inc., Cat.# RS-122-2201), following “TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E)”.

treatment_protocol: pCMV6 control vector or ARGI-overexpressing vector were trasfected using Lipofectamine-2000 (ThermoFisher) using manufacturer's instructions

value: Pancreatic beta cells

value: ARGI overexpressing vector transfection


title: HCT116 treat

description: with YHM18

source_name: colon

value: colon

value: human colorectal cancer cells HCT116

value: treated with a novel pyrimidine derivative(YHM18:2um) for 48h


title: AFB180

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells

value: Blood

value: CD14+ Monocytes

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: EndoC-βH1 with ARGI overexpression, replicate 1


title: EndoC-βH1 with ARGI overexpression, replicate 2


title: HCT116 control

description: without YHM18


title: AFB175

description: ethnicity: European descent


title: AFB170

description: ethnicity: European descent


title: AFB171

description: ethnicity: European descent


title: SH_tau_2

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4
Reads were mapped using TopHat2 v2.1.0 (--no-convert-bam --no-coverage-search -x 1 -g 1)
Counting of reads per gene was done using featureCounts v1.5.0
RPMs and RPKMs were calculated using the statistical environment R (v 3.4.1).
Assembly: GRCh38.92
Supplementary files format and content: xls file containing read counts/RPMs/RPKMs per gene

extract_protocol:
RNA was extracted with the NucleoSpin (Macherey-Nagel) RNA extraction kit according to the manufacturer’s instructions
Library preparation was done using Illumina’s TruSeq stranded mRNA kit following the manufacturer’s description.

value: Tau overexpression


title: SH_tau_3


title: GFP negative H3K4me1 cells

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

data_processing:
FASTQC run for quality of sequencing
Trimming the poor-quality reads and the adapters
Alignment using STAR
Convert sam to bam, Sorting the aligned coordinates, Indexing the bam file using Samtools
Peak calling using macs2
Assembly: Zv10
Supplementary files format and content: BED and broadPeak files containing the ChIP-Seq regions

organism: Danio rerio

source_name: Heart

extract_protocol:
1 µg of H3K4me1 antibody (ab8895, Abcam) was added to the cell lysates. Enhancer regions were incubated with magnetic Dynabeads™ Protein G (ThermoFisher Scientific) on a wheel at 4°C overnight. Beads have been washed for 10 min rotating on a wheel at 4°C with the following buffers: once with dilution buffer (165mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA pH 8.0, 16.7 mM Tris HCl pH 8.0), twice with low salt buffer (150 mM NaCl, 0.5% sodium deoxycholate, 0.1% SDS, 1% Nonidet P-40, 1 mM EDTA pH 8.0, 50 mM Tris HCl pH 8.0), twice with high salt buffer (500 mM NaCl, 0.5% sodium deoxycholate, 0.1% SDS, 1% Nonidet P-40, 1 mM EDTA pH 8.0, 50 mM Tris HCl pH 8.0), once with TE buffer (0.25 mM EDTA pH 8.0, 10 mM Tris HCl pH 8.0). Immunoprecipitated DNA was eluted by vortexing twice for 15 min at room temperature with 100 µl elution buffer (1% SDS, 100 mM sodium bicarbonate) each. DNA was de-crosslinked by adding NaCl to a final concentration of 0.3M with subsequent incubation at 65°C overnight, followed by purification (Qiagen MinElute PCR Purification Kit, #28004).
Libraries have been prepared using the Clontech SMARTer ChIP-Seq Kit (Protocol 021115). A single equimolar pool was made based upon size-adjusted qPCR quantitation results, followed by denaturation of 14 pM used for c-bot hybridisation and cluster generation in an Illumina HiSeq 1500 High output run (Illumina Protocol 15006165 Rev K Oct 2012). Our samples were sequenced using 50 bp single reads (Illumina HiSeq High output Mode, Illumina Protocol 15035788 Rev D, Apr 2014).

value: Heart

value: Primary cells

value: non-cardiomyocytes

value: Control

tag: gfp status

value: GFP negative

tag: chip antibody

value: H3K4me1 antibody (ab8895, Abcam)


title: GFP positive H3K4me1 cells

value: Cardiomyocytes

value: GFP positive


title: SH_tau_1


title: Control EndoC-βH1, replicate 3

value: Pancreatic beta cells

value: pCMV6 control vector transfection


title: Control EndoC-βH1, replicate 2


title: A549 treat

description: with YHM18

value: lung

value: human non-small cell lung cancer cells A549

value: epithelial cell

value: WT


title: AFB169

description: ethnicity: European descent

data_processing:
Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus
Normalized Beta values

value: CD14+ Monocytes, resting cells

value: Blood

value: CD14+ Monocytes


title: Diabetic ulcer, control, bio rep 3

city: Zhongshan

first: Chenyan

last: Long

address: Sunwen East Road, Zhongshan City, Guangdong Province

institute: ZhongshanCity People’s Hospital

data_processing:
Standard transcriptome sequencing data analysis process
The Cutadapt software was used to filter the raw data, including removing adapters and low-quality reads for sequencing
The FastQC software was performed to quality control on filtered data
The high quality reads were mapped to  reference genomes using HISAT2 software
Read count extraction and normalization were performed using Stringtie
Assembly: GRCm39
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Mus musculus

source_name: Ulcer skin tissue

extract_protocol:
Total RNA was extracted  using RNeasy Plus Mini Kit (Qiagen), 1.5 μg was used for library construction
The sequencing library was constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

value: Ulcer skin tissue

tag: disease state

value: Diabetic


title: Control EndoC-βH1, replicate 1


title: K562_dtagknockin_DMSO_6hr_rep2

value: chronic myeloid leukemia


title: AFB163

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: SH_ctrl_1

value: control vector expression


title: AFB168

description: ethnicity: European descent


title: K562_dtagknockin_dtag13_6hr_rep3


title: GFP negative input cells

value: Heart

value: Primary cells

value: non-cardiomyocytes

value: Control

value: GFP negative


title: SH_ctrl_3


title: PDGF-B library sorted for high binding to 50 nM PDGFRbeta-Fc

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: PDGF-B positive sort 50nM PDGFRbeta

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script (Fragment A): python Paired_read_fuser.py --path directory/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.bz2 --read2 sample_R2.fastq.bz2 --wtseq TCTCTCGGGTCACTCACCATCGCCGAACCAGCCATGATAGCGGAGTGCAAAACACGGACGGAAGTCTTTGAAATCAGCAGACGCTTGATTGATAGAACCAACGCCAATTTCCTGGTATGGCCGCCGTGCGTGGAAGTTCAACGCTGT --read1_overlap_start 32 --read1_overlap_end 179 --read2_overlap_start 85 --read2_overlap_end 232 --mode B
Fuser script (Fragment B): python Paired_read_fuser.py --path directory/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.bz2 --read2 sample_R2.fastq.bz2 --wtseq AGCGGTTGCTGTAACAACAGAAATGTACAATGCAGACCTACACAGGTACAGCTCCGGCCAGTACAGGTTCGCAAGATAGAAATCGTCCGAAAAAAGCCTATCTTTAAGAAAGCTACCGTGACCTTGGAGGACCATCTGGCTTGTAAGTGCGAAACAGTCGCCGCA --read1_overlap_start 20 --read1_overlap_end 185 --read2_overlap_start 43 --read2_overlap_end 208 --mode B
Aligner script (Fragment A): python2.7 Fused_read_aligner.py --path directory/ --infile sample_R1.fast_B_qc1 --referenceDNA TCTCTCGGGTCACTCACCATCGCCGAACCAGCCATGATAGCGGAGTGCAAAACACGGACGGAAGTCTTTGAAATCAGCAGACGCTTGATTGATAGAACCAACGCCAATTTCCTGGTATGGCCGCCGTGCGTGGAAGTTCAACGCTGT --referenceAA SLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRC --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
Aligner script (Fragment B): python2.7 Fused_read_aligner.py --path directory/ --infile sample_R1.fast_B_qc1 --referenceDNA AGCGGTTGCTGTAACAACAGAAATGTACAATGCAGACCTACACAGGTACAGCTCCGGCCAGTACAGGTTCGCAAGATAGAAATCGTCCGAAAAAAGCCTATCTTTAAGAAAGCTACCGTGACCTTGGAGGACCATCTGGCTTGTAAGTGCGAAACAGTCGCCGCA --referenceAA SGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAA --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues
In Excel, the log(base2) enrichment ratio of the wild type sequence was subtracted from the log(2) enrichment ratios for all single mutations.  The minimum log(2) enrichment ratio for severely depleted mutants was set at -10.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

growth_protocol: Yeast (strain EBY100) were cultured in SDCAA medium overnight at 30 deg C, then protein expression was induced at a density of OD(600nm) = 0.5 in SGCAA for ~8 h at 30 deg C.  Yeast were then transferred to 24 deg C for a further ~20 h.

extract_protocol:
Plasmid DNA was harvested from unsorted and sorted cells.  The PDGF-B insert was amplified for deep sequencing in two PCR steps; in the first, primer overhangs added sequences for annealing to the Illumina sequencing primers, and in the second, primer overhangs added unique barcodes and Illumina adaptors.
Primer pair for 1st round of PCR (Fragment A): PDGF_FragA_DeepSeq_For (TCTTTCCCTACACGACGCTCTTCCGATCTCATATGGGAGGGAGTTCTGC) and PDGF_FragA_DeepSeq_Rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTGTTGTTACAGCAACCGC).
Primer pair for 1st round of PCR (Fragment B): PDGF_FragB_DeepSeq_For (TCTTTCCCTACACGACGCTCTTCCGATCTGCGTGGAAGTTCAACGCTG) and PDGF_FragB_DeepSeq_Rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTAAGCTCGAGACCGCCGCTA).
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a HiSeq 2500 using a 2x250 nt paired end protocol.

treatment_protocol: Yeast were electroporated with the PDGF-B SSM library, and after induction were incubated with 30 nM or 50 nM PDGFRbeta ectodomain fused to IgG Fc.  After washing, bound receptor was stained with anti-IgG-APC, and surface expressed PDGF-B was detected with anti-myc-FITC.  FITC-positive yeast (i.e. expressing PDGF-B) were binned into two gates for FACS collection.  The “positive selection” gate collected the 3% of cells with the highest APC fluorescence, while the “negative selection” gate collected the 3% of cells with lowest APC fluorescence.  From the two populations, it is possible to determine whether PDGF-B mutations increase receptor binding, decrease receptor binding, or are simply not expressed.

tag: protein

value: PDGF-B

tag: sort gate

value: 3% of the total yeast population that express PDGF-B and have high binding to PDGFRbeta-Fc

tag: molecule subtype

value: plasmid DNA


title: K562_dtagknockin_DMSO_6hr_rep3


title: GFP positive Input cells

value: Cardiomyocytes

value: GFP positive


title: SH_ctrl_2


title: Diabetic ulcer, control, bio rep 2

tag: time


title: K562_dtagknockin_DMSO_6hr_rep1


title: Diabetic ulcer, control, bio rep 1


title: AFB161

description: ethnicity: European descent

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions followed by ethanol precipitation

value: CD14+ Monocytes, resting cells

value: Blood


title: AFB155

description: ethnicity: European descent

value: CD14+ Monocytes


title: K562_dtagknockin_dtag13_6hr_rep2


title: Diabetic ulcer, Platelet-Rich Plasma treatment, bio rep 3

value: Ulcer skin tissue

value: Diabetic

value: Platelet-Rich Plasma treatment


title: Wildtype PDGF-B: Control for sequencing errors

description: PDGF-B wild type DNA


title: Diabetic ulcer, Platelet-Rich Plasma treatment, bio rep 2


title: AFB165

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: PDGF-B library sorted for high binding to 30 nM PDGFRbeta-Fc

description: PDGF-B positive sort 30nM PDGFRbeta


title: PDGF-B library sorted for weak or absent binding to 50 nM PDGFRbeta-Fc

description: PDGF-B negative sort 50nM PDGFRbeta

value: 3% of the total yeast population that express PDGF-B and have low binding to PDGFRbeta-Fc


title: K562_dtagknockin_dtag13_6hr_rep1

value: chronic myeloid leukemia


title: Non-diabetic ulcer, control, bio rep 3

value: Non-diabetic


title: PDGF-B library sorted for weak or absent binding to 30 nM PDGFRbeta-Fc

description: PDGF-B negative sort 30nM PDGFRbeta


title: Non-diabetic ulcer, control, bio rep 2

value: Control


title: HCT116wt_DMSO_3days_rep3

value: colorectal carcinoma


title: ChIP-seq Input

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The sequences were basecalled by Illumina RTA.
Sequenced reads were trimmed with adaptor sequences (cutadapt v1.9.1) and mapped to the mouse genome (GRCm38, emsembl release 93) by Bowtie2 (v2.3.4.1). Mitochondrial and duplicated reads were removed by SAMtools (v1.9) and Picard (v2.9.0), respectively.
Peaks were found by MACS3 (v3.0.0a6) and visualized by deepTools (v3.1.1).
Assembly: mm10(GRCm38)
Supplementary files format and content: a narrowPeak file including Chrom, ChromStart, ChromEnd, Name, Score, Strand, SignalValue, pValue, qValue, and Peak.
Supplementary files format and content: a bigWig file

source_name: Colon

growth_protocol: DKK2 knockout colon cancer organoids were isolated using Gibco TrypLETM Express Enzyme (12605101) following the manufacture's protocols. Those  isolated cells were plated in 1:1 ratio of Matrigel (Corning, 356231) and the minimal medium mix. The minimal medium contained 1x B27 supplement (Thermo, 12587010), 1x Glutamax (Gibco, 35050061) and 1x Penicillin/Streptomycin (Thermo, 15140122) in advanced DMEM-F12 (Thermo, 12634010). Colon cancer organoids were cultured in the minimal medium. The culture medium was replaced every other day. Eight days cultured organoids were harvested for sequencing.

extract_protocol:
Eight days cultured organoids were isolated as single cells using TrypLE (Thermo, 12605010) and washed with PBS three times. Chromatin Immunoprecipitation was performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010054) and recombinant Anti-HNF4-alpha antibody, ChIP Grade (Abcam, ab181604) following the manufacturers' protocols.
ChIP-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using the KAPA HyperPrep kit and sequenced on the Illumina HiSeq 2500 (150 bp paired-end run).

value: Colon

value: Dkk2 knockout colon cancer organoids carrying mutations in Apc, Kras and Tp53 genes

value: Organoids

value: Input control


title: HCT116wt_DMSO_3days_rep1


title: Diabetic ulcer, Platelet-Rich Plasma treatment, bio rep 1


title: AFB144

description: ethnicity: European descent


title: AFB154

description: ethnicity: European descent


title: AFB147

description: ethnicity: European descent


title: AFB151

description: ethnicity: European descent


title: ChIP-seq IgG

value: IgG antibody


title: Naive PDGF-B library

description: PDGF-B naive SSM library

value: PDGF-B

value: plasmid DNA


title: HCT116wt_DNMT1i_3days_rep1


title: AFB146

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells

value: Blood

value: CD14+ Monocytes


title: Non-diabetic ulcer, control, bio rep 1

value: Ulcer skin tissue


title: HCT116wt_DNMT1i_3days_rep3


title: HCT116wt_DNMT1i_3days_rep2


title: AFB148

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: AFB140

description: ethnicity: European descent


title: HCT116wt_DMSO_3days_rep2


title: AFB138

description: ethnicity: European descent


title: ChIP-seq HNF4A

value: HNF4A antibody


title: RNA-seq AOMDSS Dkk2 KO3

description:
AOMDSS_KO3
AOMDSS_deseq2_normalized_counts.txt

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
The sequencing reads were aligned onto Mus musculus GRCm38/mm10 reference genome using the TopHat v2.1.0 software or Kallisto v0.45.0. The mapped reads were transformed into the count matrix with default parameters using the HTSeq v0.8.0 software, then normalized using the DESeq v2 software. Differentially expressed genes (DEGs) were identified using the same software based on a negative binomial generalized linear model. Sleuth was used to analyze statistical significance of kallisto data.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM
Supplementary_files_format_and_content: a text file including gene identifiers and normalized counts

source_name: Colitis-induced cancer cells from azoxymethane and dextran sodium sulfate treated tamoxifen-inducible Dkk2 knockout mice

growth_protocol: Colon cancer organoids (AKP and KO) were isolated as single cell or multple cells using Gibco TrypLETM Express Enzyme (12605101) following the manufacture's protocols. Those  isolated cells were plated in 1:1 ratio of Matrigel (Corning, 356231) and the minimal medium mix. The minimal medium contained 1x B27 supplement (Thermo, 12587010), 1x Glutamax (Gibco, 35050061) and 1x Penicillin/Streptomycin (Thermo, 15140122) in advanced DMEM-F12 (Thermo, 12634010). Organoids were cultured in the minimal medium and the medium was replaced every other day. Eight days cultured organoids were harvested for sequencing.

extract_protocol:
RNA was purified from colon cancer organoids using QIAGEN miRNeasy kit (217004) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed following Illumina TruSeq Stranded mRNA protocol (20020594). The RNA-seq libraries were sequenced on the Illumina Nextseq 500 (42 bp paired-end run) and Illumina HiSeq 2500 instrument platform (76 bp single-end sequencing) for organoids and colitis-induced cancer cells, respectively.

treatment_protocol: 12.5 mg/kg of azoxymethane (AOM, Sigma, A5486) was administered to 6 weeks old Lgr5CreERT2-IRES-EGFP/+-Dkk2fl/fl mice via intra-peritoneal injection. Lgr5+/+-Dkk2fl/fl littermate mice were used as controls.  After 5 days, mice were treated with 2.5 % of dextran sodium sulfate (DSS, MP biomedicals, molecular mass 36,000–50,000 Da) in the drinking water for 5 days followed by 14 days of regular water. This cycle was performed three times. 7 days after DSS treatment in each cycle, 200 μl of tamoxifen (10 mg/ml in sunflower oil, Sigma, T5648) was delivered into Lgr5CreERT2-IRES-EGFP/+-Dkk2fl/fl mice and their littermate controls by intra-peritoneal injection every other day, total three injections per DSS cycle.

value: Primary cancer cells


title: AFB136

description: ethnicity: European descent


title: RNA-seq AOMDSS Dkk2 KO2

description:
AOMDSS_KO2
AOMDSS_deseq2_normalized_counts.txt


title: K562wt_DMSO_3days_rep1

value: chronic myeloid leukemia


title: RNA-seq AOMDSS Dkk2 KO1

description:
AOMDSS_KO1
AOMDSS_deseq2_normalized_counts.txt


title: K562wt_DNMT1i_3days_rep3


title: AFB139

description: ethnicity: European descent


title: K562wt_DNMT1i_3days_rep2


title: AFB126

description: ethnicity: European descent


title: K562wt_DMSO_3days_rep3


title: K562wt_DMSO_3days_rep2