title: H3R26C_antiH3K27me3_replicate_2

data_processing:
Reads were mapped using the Rsubread package's align function (version 1.30.6)
Peak calls made with SEACR (version 1.3, stringent, norm 0.01)
Consensus peaks were determined to be peaks that were found in the majority of replicates in at least one mutant or control. Peaks were annotated and genome distribution was determined using the ChIPseeker package (Version 1.28.3)
Pairwise comparisons were made between the control and mutant using DEseq2 using counts from consensus peaks with significant genes considered as (padj < 0.001). Normalized, fragment-extended signal bigWigs were created using the rtracklayer package (Version 1.40.6).
Assembly: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary files format and content: genome wide tracks as bigwig files
Supplementary files format and content: peak calls as bed files
Library strategy: CUT&RUN

extract_protocol:
The CUT&RUN protocol was performed in PCR-tubes per the CUTANA (Epicypher) v1.6 protocol except where otherwise noted. In brief, cells were washed twice in wash buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, EDTA-free Protease Inhibitor) prior to resuspending wash buffer. For each CUT&RUN reaction, 500,000 cells were immobilized to Concanavalin-A beads and incubated overnight at 4 °C with antibody diluted 1:100 in antibody dilution buffer (0.005% Digitonin, 2 mM EDTA, Wash Buffer). pAG-MNase (Epicypher, 15-116) digestion was performed for 2 hours at 4 °C following which CUT&RUN enriched DNA was purified using Phenol-chloroform extraction and Ethanol precipitation.
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used to prepare sequencing libraries with CUT&RUN enriched DNA.


title: T-1

status: Public on Apr 29 2024

type: SRA

city: Shanghai

first: Minrui

last: Liang

state: Shanghai

address: 12 Wulumuqi Zhong Road

country: China

institute: Fudan University

library_source: genomic

data_processing:
1. Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4)
2. Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality
3. The clean reads were mapped to the human genome (assembly human genome hg38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software
4. PCR duplicates were removed using Picard (v2.22.2-0)
5. Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff
6. Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10)
7. Pearson correlation coefficient between biological replicates was calculated using deeptools (v3.4.3) multiBamSummary with default parameters
8. TSS heatmap was generated using deeptools (v3.4.3) computeMatrix reference-point (parameters: -a 5000 -b 5000 --skipZeros )
9. Differential analysis based on detected peaks between group C (or group AT) and group T was performed using R package DESeq2 (v1.26.0) with default parameters
10. Motif analysis based on detected peaks was performed using homer findMotifsGenome.pl (v4.10) with default parameters
11. The resulting histograms (genomic ‘signal maps’) were stored in bigWig files using deeptools (v3.4.3) bamCoverage (parameters: --normalizeUsing RPKM --extendReads 200 --ignoreForNormalization chrX chrY --ignoreDuplicates)
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: Human dermal fibroblasts

growth_protocol: Human dermal fibroblasts were isolated and cultured in Dulbecco’s modified Eagle’s medium-Ham’s F-12 (DMEM/F-12) containing 10% fetal bovine serum (FBS); Before an experiment, dermal fibroblasts were serum-starved in DMEM/F-12 medium containing 0.1% FBS overnight.

extract_protocol:
Dermal fibroblasts (1 × 10^7 cells) were fixed with 1% formaldehyde at room temperature for 10 minutes, quenched with 125 mM glycine and harvested.
ChIP-seq assays, including purification of the enriched DNA, were performed using the ChIP-IT High Sensitivity Kit (#53040, Active Motif, Carlsbad, CA, USA). In brief, chromatin was isolated by adding lysis buffer and fragmented by sonication. DNA was sheared to an average length of 200–500 bp with a EpiShear probe sonicator (#53051, Active Motif, Carlsbad, CA, USA). The input DNA was purified with PCR Purification Kit (#28104, QIAGEN Miami, FL, USA).

treatment_protocol: Dermal fibroblasts were incubated for 48 h with TGFβ (10 ng/ml, #100-21C, PeproTech, Hamburg, Germany), with or without recombinant Adropin34-76 (#032-35, Phoenix Pharmaceuticals, Burlingame, CA, USA) dissolved in sterile distilled water at concentration of 100 ng/ml.

tag: cell type

value: Human dermal fibroblasts

tag: chip-seq antibody

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-603, Novus Biologicals)

tag: treatment

value: TGFb


title: MAFF_Parental_GEM

city: Washington

first: Chan

middle: Dinh Khac

last: Nguyen

state: DC

address: 3970 Reservoir Rd

department: Oncology

country: USA

institute: Lombardi Comprehensive Cancer Center

data_processing:
Read trimming: CutAdapt
Read Alignment: Bowtie2
Read filter: Samtools, MarkDuplicates
Assembly: mm10
Supplementary files format and content: BigWig: Normalized aligned read counts
Library strategy: Cut&Tag

organism: Mus musculus

source_name: Pancreas

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cut&Tag Operate through cell permiabilization with 0.05% Digitonin. Tn5 Transposase cleaves DNA and addition of 6.67 µL 0.5M EDTA, 2 µL 10% SDS and 1.67 µL 20 mg/mL Proteinase K, Incubation at 50C for 1hr and 37C overnight to extract DNA
NEB High Fidelity PCR MasterMix

tag: tissue

value: Pancreas

tag: cell line

value: Murine PDAC cells

tag: genotype

value: KPC

tag: chip antibody

value: MAFF


title: MAFF_Parental_DMSO


title: MAFF_shPrmt1#2_GEM


title: H3R26C_antiH3K27me3_replicate_3

city: Pittsburgh

first: Benjamin

middle: Alexander

last: Nacev

state: PA

address: 5117 Centre Avenue, Suite 2.6b

department: Medicine

institute: University of Pittsburgh

value: mesenchymal progenitor


title: C-3

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-602, Novus Biologicals)

value: Vehicle


title: H3R2C_replicate_3

library_source: transcriptomic

data_processing:
Transcript abundance was determined using Salmon (v0.8.1) and the GENCODE reference transcript sequences
Transcript counts from Salmon were imported into R with the tximport R Bioconductor package (v1.20), and differentially expressed genes were determined with the DESeq2 R Bioconductor package (v1.32)
Assembly: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary files format and content: genome wide tracks as bigwig files

molecule: polyA RNA

extract_protocol:
RNA was  extracted using the RNAeasy kit (Qiagen) with on column DNAase I digestion per manufacturer instructions.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit (New England Biolabs) with polyA selection according to the manufacturer instructions.


title: H3R2C_replicate_2


title: C-2

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-601, Novus Biologicals)


title: BACH1_shPrmt1#2_GEM


title: C-1

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-600, Novus Biologicals)


title: H3R26C_antiH3K4me3_replicate_2


title: H3R2C_replicate_1


title: H3WT__replicate_3


title: H3R26C_antiH3K4me3_replicate_1


title: mT4/shPrmt1#2+GEM_H3K27Ac


title: mT4/shPrmt1#1+DMSO_H3K27Ac


title: H3WT__replicate_2


title: mT4/shPrmt1#1+GEM_H3K27Ac


title: H3R26C_antiHA_replicate_2

value: antiHA


title: H3R26C_antiHA_replicate_3


title: mT4_Parental+GEM_H3K27Ac

value: Parental+GEM


title: H3R26C_antiH3K27me3_replicate_1


title: H3R26C_antiHA_replicate_1


title: H3R26C_antiH3K4me3_replicate_3


title: mT4_Parental+DMSO_H3K27Ac

value: Parental+DMSO


title: BACH1_Parental_GEM


title: H3R26C_IgG_replicate_3

value: IgG


title: primary cells, lymph nodes [Rewild13_GEX]

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Lymph node

extract_protocol:
Single cell suspension from the mesenteric lymph nodes (MLNs) were prepared by mashing the tissues individually through a 70μm cell strainer and washed with RPMI. Cells were then washed with RPMI supplemented with 10% FCS.
Library was performed according to the manufacter’s instructions (10x Genomics). Briefly, pooled samples from each group were then loaded on a 10X Genomics Next GEM chip and single-cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate cDNA and sequencing libraries were performed following 10X Genomics’ protocol. Libraries were pooled and sequenced using Illumina NovaSeq SP 100 cycle as per 10X sequencing recommendations.

value: Mesenteric Lymh node cells

value: Lymph node

tag: strain

value: Various Strains

tag: age

value: 13-15 weeks old


title: BACH1_D10

value: Pancreas

value: GEM 10 days


title: H3R26C_IgG_replicate_1


title: primary cells, lymph nodes [Rewild12_GEX]

description: 10x Genomics


title: mT4/shPrmt1#2+DMSO_H3K27Ac

value: Murine PDAC cells

value: KPC


title: primary cells, lymph nodes [Rewild11_GEX]

description: 10x Genomics


title: SMARCB1_NEPS_NT

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

country: Japan

institute: National Cancer Center Research Institute

data_processing:
Raw sequencing data from ChIP-seq, CUT&RUN-seq, and ATAC-seq were trimmed using fastp version 0.12.4 35 and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5, with parameters –k 1
Prior to all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard-tools version 2.26.11 (Li et al., 2009).
In ChIP-seq and CUT&RUN data, CPM values in the genome tracks were calculated by subtracting those in the input tracks as the background value of each cell.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1 include CPM counts for each sample.

source_name: NEPS

extract_protocol:
Cells were suspended in 1 x Wash Buffer and attached to concanavalin A beads, permeabilized with 100 μL of Antibody Binding Buffer containing digitonin.
Libraries were created by Takara Bio using the ThruPLEX DNA-Seq Kit (Takara, R400674) and amplified for 16 cycles under the following conditions: denaturation at 98°C for 20 s, followed by annealing and extension at 72°C for 50 s. The samples were sequenced by Takara Bio using the NovaSeq 6000 platform (Illumina), with 150 bp paired end reads.

value: NEPS


title: BACH1_D8

value: GEM 8 days


title: H3R17C_antiH3K27me3_replicate_3

value: mesenchymal progenitor


title: SMARCB1_JMURTK2_SMARCB1_NT


title: H3R17C_antiH3K27me3_replicate_2


title: primary cells, lymph nodes [Rewild8_GEX]

description: 10x Genomics


title: SMARCB1_JMURTK2_Mock_NT


title: BACH1_D4

value: GEM 4 days


title: H3WT__replicate_1


title: primary cells, lymph nodes [Rewild14_GEX]

description: 10x Genomics


title: H3R17C_antiH3K27me3_replicate_1


title: H3R26C_IgG_replicate_2


title: BACH1_D2

value: GEM 2 days


title: primary cells, lymph nodes [Rewild7_GEX]

description: 10x Genomics


title: SMARCB1_786O_NT


title: primary cells, lymph nodes [Rewild6_GEX]

description: 10x Genomics


title: RNAPII_JMURTK2_Mock_NT


title: BACH1_DMSO

value: DMSO


title: primary cells, lymph nodes [Rewild10_GEX]

description: 10x Genomics


title: H3R17C_antiH3K4me3_replicate_3


title: H3R17C_antiH3K4me3_replicate_2


title: BACH1_D6

value: GEM 6 days


title: H3R17C_antiH3K4me3_replicate_1


title: RNAPII_JMURTK2_Mock_A485


title: primary cells, lymph nodes [Rewild5_GEX]

description: 10x Genomics


title: Input_NEPS_NT


title: primary cells, lymph nodes [Rewild4_GEX]

description: 10x Genomics


title: primary cells, lymph nodes [Rewild9_GEX]

description: 10x Genomics


title: H3R17C_antiHA_replicate_3

value: antiHA


title: MAFF_D6

value: MAFF


title: MAFF_D4


title: Input_JMURTK2_SMARCB1_NT


title: Input_JMURTK2_Mock_NT

extract_protocol:
Cells were fixed for 15 min at 25°C with 1% formaldehyde. Fixation was stopped by the addition of 125 mM glycine. The fixed cells were washed twice with PBS and chromatin was isolated by addition of lysis buffer, followed by disruption using a Dounce homogenizer.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500, with 75 bp single end reads.


title: primary cells, lymph nodes [Rewild3_GEX]

description: 10x Genomics

value: Mesenteric Lymh node cells


title: primary cells, lymph nodes [Rewild2_GEX]

description: 10x Genomics

value: Lymph node


title: H3R17C_antiHA_replicate_1


title: MAFF_D2


title: H3R17C_antiHA_replicate_2


title: primary cells, lymph nodes [Rewild1_GEX]

description: 10x Genomics

value: Various Strains


title: MAFF_D10


title: Input_786O_NT


title: MAFF_DMSO


title: H3R17C_IgG_replicate_3

value: IgG


title: 4224

city: Paris

first: Bastien

last: Leclercq

state: Ile-de-France

address: 15 Rue de l'École de Médecine

country: France

institute: INSERM

data_processing:
Quality of raw data was evaluated with FastQC. Poor quality sequences and adapters were trimmed or removed with fastp, using default parameters, to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file
Library orientation, library composition and coverage along transcripts were checked with Picard tools
The transcriptomic data were analyzed on the online platform of the Paris Brain institute (quby.icm-institute.org). Differential expression analysis using edgeR method was assessed to determine the differentially expressed genes (adjusted P-value (FDR), FDR threshold set at 0.05, log2 fold-change threshold set at 0.5)
Assembly: mm10
Supplementary files format and content: Differential expression analysis by EdgeR

source_name: RPE/Choroid/Sclera complex

extract_protocol:
Five months old male P1 hMR transgenic mice (n=3) and their age- and sex-matched wild-type (WT) littermates (n=2) were euthanized, eyes were removed and dissected on ice to isolate the sclera-choroid-RPE complexes, which were immediately frozen in liquid nitrogen
RNA was extracted using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

value: RPE/Choroid/Sclera complex

tag: Sex

value: male

value: P1 hMR


title: MAFF_D8

value: Pancreas

value: Murine PDAC cells

value: KPC


title: H3K27Ac_D10

value: GEM 10 days


title: H3K27me3_JMURTK2_SMARCB1_NT


title: 4223


title: H3K27me3_JMURTK2_Mock_NT


title: 4222


title: H3K27Ac_D8

value: GEM 8 days


title: H3R17C_IgG_replicate_2

value: mesenchymal progenitor


title: H3K27ac_NEPS_NT

value: NEPS


title: H3R17C_IgG_replicate_1


title: H3K27Ac_D4

value: GEM 4 days


title: 4225

value: wild-type


title: H3R8C_antiH3K27me3_replicate_3


title: H3K27ac_JMURTK2_SMARCB1_NT


title: H3K27ac_JMURTK2_Mock_NT2


title: 4253


title: H3K27Ac_D2

value: GEM 2 days


title: H3R8C_antiH3K27me3_replicate_1


title: H3R8C_antiH3K27me3_replicate_2


title: DEN-PB treated MLK3-KO 3

city: Chicago

first: Basabi

last: Rana

state: Illinois

address: 840 S. Wood Street

department: Surgery

institute: University of Illinois at Chicago

description:
used as experimental
RAN083017-025

data_processing:
mapped to mm10 reference with bwa mem
quantified expression with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text of gene expression counts

source_name: Liver tumor tissue

growth_protocol: Mice were housed in the Biologic Resources Laboratory (BRL) facility and maintained on a commercial diet. Sex- and age-matched WT and MLK3-KO mice were used for experiments described here.

extract_protocol:
Water and DEN/PB treated liver tissues were removed from the mice after 11 months in an RNAse free workspace, total RNA was extracted and used for RNA seq. at the Genomic Core, Research Resourse Centre of Uiversity of illinois at Chicago
prepared using strand-specific QuantSeq 3’ mRNAseq library kit (Lexogen, FWD, Cat. No. 015), 50 ng per sample used as input

treatment_protocol: To induce HCC in mice, a single intraperitoneal injection of tumor initiator DEN (5µg/g body weight) was given to 2 weeks (wk)-old WT and MLK3-KO male pups. After 1 wk of lag phase, autoclaved drinking water containing tumor promoter PB (0.05%) was fed continuously to these mice until they were sacrificed at 11 months. Control mice were fed with regular autoclaved water.

value: Liver tumor tissue

value: 11 months


title: H3K27ac_JMURTK2_Mock_NT


title: H3K27Ac_DMSO

value: DMSO


title: DEN-PB treated MLK3-KO 2

description:
used as experimental
RAN083017-024


title: H3K27ac_JMURTK2_Mock_A485


title: 1 month cortex from KO mouse 3 [S_CX_KO3]

city: Philadelphia

first: Thomas

last: Roule

state: Pennsylvania

address: 3501 Civic Center Boulevard  5th Floor CTRB-5400

institute: CHOP

data_processing:
Reads were counted using FeatureCounts from the subread package (v2.0.1) with parameters: -p -C -O.
Differential gene expression analysis was performed with DEseq2 (V1.38.3) excluding genes with less than five reads, and all genes from chromosome X and Y. Differential expression was performed using a linear model and as factor the genotypes.
BigWig files were generated using bamCoverage from the deepTools suite with parameters: --normalizeUsing BPM --binSize 10.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file including read count values for each gene (.txt).
Supplementary files format and content: Coverage files in bigWig format (.bw).

source_name: cortex

extract_protocol:
Mouse brain tissue were dissected on ice, fast froze in liquid nitrogen, and stored in -80˚C until use. On the day of RNA extraction, 50mg to 100mg tissue from each sample was lysed in 1ml TRIzol (15596026, Invitrogen). Addition of 0.2ml chloroform (288306, Sigma-Aldreich) followed by centrifugation was performed to separate the solution into an aqueous phase and an organic phase. Isopropyl alcohol and 75% ethanol (111000200CSPP, Pharmco) was added in sequence to precipitate and wash the RNA pellets.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cortex

value: mix

value: Snx14 KO


title: H3R8C_antiH3K4me3_replicate_2


title: H3R8C_antiH3K4me3_replicate_3


title: H3R8C_antiH3K4me3_replicate_1


title: DEN-PB treated MLK3-KO 1

description:
used as experimental
RAN083017-023


title: 1 month cortex from KO mouse 2 [S_CX_KO2]


title: H3K27Ac_D6

value: GEM 6 days


title: H3K4me3_JMURTK2_SMARCB1_NT


title: H3R8C_antiHA_replicate_3

value: antiHA


title: DEN-PB treated Wild-type 3

description:
used as experimental
RAN083017-022

value: Wild-type


title: H3K27ac_786O_NT


title: H3K4me3_JMURTK2_Mock_NT


title: H3R8C_antiHA_replicate_2


title: 1 month cortex from KO mouse 1 [S_CX_KO1]


title: 1 month cortex from WT mouse 3 [S_CX_WT3]

value: WT


title: DEN-PB treated Wild-type 2

description:
used as experimental
RAN083017-021


title: DEN-PB treated Wild-type 1

description:
used as experimental
RAN083017-020


title: H3K4me1_JMURTK2_SMARCB1_NT


title: H3R8C_antiHA_replicate_1


title: 1 month cortex from WT mouse 2 [S_CX_WT2]


title: Water Control MLK3-KO 2

description:
used as controls
RAN083017-019

source_name: Normal liver tissue

value: Normal liver tissue


title: Water Control MLK3-KO 1

description:
used as controls
RAN083017-018


title: CTCF_JMURTK2_Mock_NT


title: H3K4me1_JMURTK2_Mock_NT


title: H3R8C_IgG_replicate_2

value: IgG


title: 1 month cortex from WT mouse 1 [S_CX_WT1]


title: 1 month cerebellum from KO mouse 3 [S_CB_KO3]

source_name: cerebellum

value: cerebellum


title: Water Control Wild-type 2

description:
used as controls
RAN083017-016


title: CTCF_JMURTK2_Mock_A485


title: 1 month cerebellum from KO mouse 2 [S_CB_KO2]


title: H3R8C_IgG_replicate_1

value: mesenchymal progenitor


title: Water Control Wild-type 1

description:
used as controls
RAN083017-015


title: BRD4_JMURTK2_Mock_NT


title: H3R2C_antiH3K27me3_replicate_3


title: 1 month cerebellum from KO mouse 1 [S_CB_KO1]


title: Neo, ADT-derived cDNA, bio rep2

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline with default settings.The mm10 genome build was used and ADT sequences were concatenated and treated as Custom library.
Further processing was done with Seurat v3.0.2 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: ear

extract_protocol:
We first dissociated mouse ears and MACS enriched CD31+ cells from adult (2 months), adult wounded (day 9 post wounding), and neonatal (P8) samples. The endothelial enriched samples were stained with CD31-Alexa488, NearIR live/dead, and Antibody Derived Tag directed against Icam1, Vcam1, Cxcr4, Flk1 (VEGFR2), and Cd45. We then FACS sorted CD31+, Cdh5CreERT2-Rtom+, and NearIR- live endothelial cells and loaded them into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Single Cell 3ʹ v3 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3 protocol (10x Genomics). For antibody-derived tagged library, we used the QuantaBio Hifi MasterMix following Biolegend's TotalSeqA protocol.
Following the final bead purification, all libraries were pooled as 95% mRNA library and 5% ADT library.

tag: strain background

value: ear

value: endothelial

tag: library type

value: ADT

tag: antibodies/tags

value: Anti-ICAM1/TotalSeq-A0074; Anti-VCAM1/TotalSeq-A0226; Anti-CXCR4/TotalSeq-A0444; Anti-VEGFR2/TotalSeq-A0553; Anti-CD45/TotalSeq-A0096; Rat IgG2b isotype Ctrl/TotalSeq-A0095; Rat IgG2a isotype Ctrl/TotalSeq-A0238


title: H3R2C_antiH3K27me3_replicate_2


title: BRD4_JMURTK2_Mock_A485


title: 1 month cerebellum from WT mouse 3 [S_CB_WT3]


title: H3R8C_IgG_replicate_3


title: RNA_NEPS_NT_24h

extract_protocol:
Cells were lysed and the transposition reaction was performed with the Tn5 Transposase (Illumina, FC121-1030) at 37°C for 30 min. The reaction liquid was purified using the MinElute PCR Purification Kit (Qiagen, 28004).
Five cycles of PCR were conducted using custom Nextera PCR primers 34 and NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB, M0543S). The number of additional PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), using double size selection (left ratio: 1.4x; right ratio: 0.5x) according to the manufacturer’s protocol. The samples were sequenced using the MGI Tech DNBSEQ-G400R sequencer, with 150 bp paired end reads.

value: NEPS


title: 1 month cerebellum from WT mouse 2 [S_CB_WT2]


title: Neo, mRNA-derived cDNA, bio rep2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: H3R2C_antiH3K4me3_replicate_3


title: RNA_NEPS_A485_2uM_24h

data_processing:
Raw sequencing data were trimmed using trim-galore version 0.6.5-1 and mapped to the hg38 genome using HISAT2 version 2.2.1.
TPM values were calculated using Strand NGS ver 4.0 (TOMY).
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1 include CPM counts for each sample.

extract_protocol:
RNA was collected using the RNeasy Mini Kit (Qiagen).
Library preparation for RNA-seq samples was performed in the Rhelixa using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).


title: H3R2C_antiH3K27me3_replicate_1


title: RNA_JMURTK2_SMARCB1_NT_24h


title: LN_CD44hi_rep3_b2

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
Samples were sequenced on an Illumina NextSeq 500 to produce 75–base pair single-end reads. The raw reads were mapped to the mouse reference transcriptome (Ensembl; Mus musculus version 104) using Kallisto version 0.46.0.
All subsequent analyses were carried out using the statistical computing environment, R version 4.1.0 in RStudio version 1.4.1717 and Bioconductor, version 3.13
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Differentially expressed genes (1.5-fold and 5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Genome_build: Ensembl; Mus musculus version 104
Supplementary_files_format_and_content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary_files_format_and_content: Tab-delimited text filtered (for genes detected at <1 CPM in at least 3 samples), normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method)
Supplementary_files_format_and_content: Tab-delimited text file with study design

source_name: CD8 T cells from dLN

growth_protocol: C57BL/6 mice were infected with L. major and 5 weeks post-infection, mice were euthanized, cells from the infected ear and draining LN cells (dLN) were purified and stained for flow cytometric analysis. Antigen experienced CD8 T cells were purified using FACSAria cell sorter (gating strategy: live, singlets, CD90, CD8+CD44high)

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Poly(A)+-enriched cDNA libraries Illumina TruSeq Stranded mRNA library were prepared. Ribo-Zero Gold rRNA depletion (Illumina) was used to remove ribosomal content
Quality assessment and quantification of RNA preparations and libraries were carried out using an Agilent 4200 TapeStation and Qubit 3, respectively.

value: lymphNodeH

value: CD8 T cells

tag: animal age

value: 6 weeks

value: female


title: RNA_JMURTK2_SMARCB1_A485_2uM_24h


title: SNU-449 ALK targeted inhibition cells (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: SNU-449 cell lines

growth_protocol: HepG2 and SK-HEP1 cells stably expressing either Non-Targeting or ALK Targeted inhibition were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition. SNU449 cells were growth in RPMI-1640 with 10% FBS plus  Penicilline and Streptomycin at the same condition as the other two cell lines.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.

treatment_protocol: HepG2, SK-HEP1 and SNU449 cells stably expressing either Non-Targeting or ALK targeted inhibition were used for preparing the total RNA and to perfrom gene expression array.

tag: genotype/variation

value: ALK Targeted Inhibition cells


title: H3R2C_antiH3K4me3_replicate_2


title: SNU-449 ALK targeted inhibition cells (Replicate_2)


title: H3R2C_antiH3K4me3_replicate_1


title: RNA_JMURTK2_Mock_siNT_96h


title: LN_CD44hi_rep2_b2


title: H3R2C_antiHA_replicate_3

value: antiHA


title: LN_CD44hi_rep1_b2


title: RNA_JMURTK2_Mock_siKREMEN2_96h


title: SNU-449 ALK targeted inhibition cells (Replicate_1)


title: ear_total_rep3_b2

source_name: CD8 T cells from ear


title: H3R2C_antiHA_replicate_2


title: RNA_JMURTK2_Mock_siCBPsip300_96h


title: SNU-449 Non-Target Expressing cells (Replicate_3)

value: Non-Target ALK Expressing control cells


title: Neo, ADT-derived cDNA, bio rep1


title: ear_total_rep2_b2


title: H3R2C_antiHA_replicate_1


title: H3R2C_IgG_replicate_3


title: SNU-449 Non-Target Expressing cells (Replicate_2)


title: Neo, mRNA-derived cDNA, bio rep1


title: H3R2C_IgG_replicate_2


title: Ad-TTR-GOL_persistent_liver_CXCR6-CX3CR1_3

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited text file include sequence read counts of each sample

source_name: liver

extract_protocol:
Samples for RNA-seq were sorted in 1.5 mL reaction tubes including lysis buffer (2xTCL buffer (Qiagen, #1070498) + RNase-free water + beta-mercaptoethanol (1% total volume)).
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

value: 13 weeks


title: 1 month cerebellum from WT mouse 1 [S_CB_WT1]

value: mix

value: WT


title: ear_total_rep1_b2


title: SNU-449 Non-Target Expressing cells (Replicate_1)


title: RNA_JMURTK2_Mock_NT_24h


title: SK-HEP1 ALK targeted inhibition cells (Replicate_2)

source_name: SK-HEP1 cell lines


title: SK-HEP1 ALK targeted inhibition cells (Replicate_3)


title: RNA_HSES2R_siNT_96h


title: Ad-TTR-GOL_persistent_liver_CXCR6-CX3CR1_2


title: SK-HEP1 ALK targeted inhibition cells (Replicate_1)


title: Ad-TTR-GOL_persistent_liver_CXCR6_3

value: hepatic CD8 T cells_CXCR6_TTR_persistent


title: H3R2C_IgG_replicate_1

value: mesenchymal progenitor

value: IgG


title: RNA_HSES2R_siKREMEN2_96h


title: RNA_JMURTK2_Mock_A485_2uM_24h


title: SK-HEP1 Non-Target Expressing cells (Replicate_2)


title: Ad-TTR-GOL_persistent_liver_CXCR6_2


title: Ad-TTR-GOL_persistent_liver_CXCR6_1


title: RNA_HSES2R_A485_2uM_24h


title: SK-HEP1 Non-Target Expressing cells (Replicate_1)


title: H3WT_antiH3K27me3_replicate_3


title: H3WT_antiH3K4me3_replicate_2


title: RNA_HSES2R_siCBPsip300_96h


title: Ad-TTR-GOL_persistent_liver_CXCR6-CX3CR1_1


title: H3WT_antiH3K27me3_replicate_1


title: RNA_G402_A485_2uM_24h


title: H3WT_antiH3K27me3_replicate_2


title: RNA_G402_NT_24h


title: Ad-CMV-GOL_resolved_spleen_CX3CR1_2

source_name: spleen

value: splenic CD8 T cells_CX3CR1_CMV_resolved


title: RNA_786O_NT_24h


title: SK-HEP1 Non-Target Expressing cells (Replicate_3)


title: H3WT_antiH3K4me3_replicate_3


title: Ad-CMV-GOL_resolved_spleen_CX3CR1_3


title: Ad-CMV-GOL_resolved_spleen_CX3CR1_1


title: H3WT_antiHA_replicate_3


title: HepG2/C3A ALK targeted inhibition cells (Replicate_2)

source_name: HepG2/C3A cell lines


title: H3WT_antiH3K4me3_replicate_1


title: HepG2/C3A ALK targeted inhibition cells (Replicate_3)


title: HepG2/C3A Non-Target Expressing cells (Replicate_3)


title: H3WT_antiHA_replicate_2


title: H3WT_antiHA_replicate_1


title: RNA_HSES2R_NT_24h


title: HepG2/C3A ALK targeted inhibition cells (Replicate_1)


title: Ad-CMV-GOL_resolved_liver_CXCR6_2

value: hepatic CD8 T cells_CXCR6_CMV_resolved


title: BEL-A cells, KLF1+/E325K, day 2 of differentiation 2

city: Bristol

first: Jan

last: Frayne

address: Biomedical Sciences Building, University Walk

department: School of Biochemistry

country: United Kingdom

institute: University of Bristol

data_processing:
Hisat2 v2.0.5
For gene expression quantification, featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM (Fragments Per Kilobase of transcript sequence per Millions base pair sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20).
The resulting P-values were adjusted using the Benjamini-Hochberg approach for controlling the false discovery rate. Genes with an adjusted P-value ≤0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing fpkm values for all samples

source_name: BEL-A

growth_protocol: Cells were maintained in expansion medium (Stemspan SFEM (Stem Cell Technologies) supplemented with 50 ng/ml stem cell factor (SCF; R&D Systems), 3 U/ml erythropoietin (EPO; Roche), 1 uM dexamethasone (DEX; Sigma-Aldrich) and 1 ug/ml doxycycline (DOX; Clontech) at 1.0 × 10^5 cells/ml.

extract_protocol:
Total RNA was extracted from 3 biological repeats using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.
Library construction and sequencing were performed by Novogene Co. Ltd. using the NEB Next® Ultra™ RNA Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Cells were seeded in differentiation medium, Iscove’s Modified Basal Medium (IMDM) with glutamine (Biochrom; Merck Millipore), supplemented with 3% (v/v) human AB serum (Sigma-Aldrich), 2% (v/v) fetal bovine serum (Hyclone), 10 μg/ml insulin (Sigma-Aldrich), 3 U/ml heparin (Sigma-Aldrich), 200 μg/ml holo-transferrin (Sanquin), 1 ng/ml interleukin‐3 (IL-3; Roche), 3 U/ml EPO, 10 ng/ml SCF and 1 U/ml penicillin / streptomycin with DOX 1 μg/ml, at 2.0 × 105 cells/ml.

value: BEL-A

value: Erythroid progenitor

value: Erythroid differentiation


title: Ad-CMV-GOL_resolved_liver_CXCR6_3


title: RNA_786O_A485_2uM_24h


title: Ad-CMV-GOL_resolved_liver_CXCR6_1


title: BEL-A cells, KLF1+/E325K, day 2 of differentiation 1


title: H3WT_IgG_replicate_3

extract_protocol:
The CUT&RUN protocol was performed in PCR-tubes per the CUTANA (Epicypher) v1.6 protocol except where otherwise noted. In brief, cells were washed twice in wash buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, EDTA-free Protease Inhibitor) prior to resuspending wash buffer. For each CUT&RUN reaction, 500,000 cells were immobilized to Concanavalin-A beads and incubated overnight at 4 °C with antibody diluted 1:100 in antibody dilution buffer (0.005% Digitonin, 2 mM EDTA, Wash Buffer). pAG-MNase (Epicypher, 15-116) digestion was performed for 2 hours at 4 °C following which CUT&RUN enriched DNA was purified using Phenol-chloroform extraction and Ethanol precipitation.
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used to prepare sequencing libraries with CUT&RUN enriched DNA.


title: HepG2/C3A Non-Target Expressing cells (Replicate_1)


title: H3WT_IgG_replicate_2


title: Ad-CMV-GOL_resolved_liver_CX3CR1_3

value: hepatic CD8 T cells_CX3CR1_CMV_resolved


title: BEL-A cells, wildtype, day 2 of differentiation 2


title: BEL-A cells, wildtype, day 2 of differentiation 3


title: H3WT_IgG_replicate_1


title: After purification [BC2]

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: Analyzed aa frequencies.xlsx>BC2_After purification

data_processing:
Geneious (version 2023.0) was used to process NGS reads for analysis.
trimming low quality ends using the BBDuk Geneious plugin,
mapping the trimmed reads to their respective reference sequence.
a custom Python script was used to generate a matrix of amino acid frequencies at each position.
Data visualization was performed with R (version 4.2.2) using ggplot2 and sequence logo plots were generated using the ggseqlogo R package.
Assembly: Hemagglutinin, Influenza A virus, A/Puerto Rico/8/1934
Supplementary files format and content: excel sheets include frequency of amino acides in each position of hemagglutinin in after purification and before purification libraries

molecule: other

organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Viable mutants

extract_protocol:
DNA fragments were extracted using GeneJET Gel Extraction and DNA Cleanup Micro Kit (Thermo Scientific)
For before library, randomized sequences were cloned into pCIG3 vector. The vector were then electropotated into competent cells and plasmid DNA was extracted and used as template to prepare samples. For after purification library, gDNA was extracted from sorted cells. Sequences was cloned into a soluble hemagglutinin expressing vector based on pDZ vector. Sequencing sample was prepared as described previously.

tag: time point

value: After purification

value: Viable mutants

value: Four codons in Sb site of PR8 hemagglutinin were randomized by mutagenesis.

tag: molecule type

value: plasmid DNA


title: 60d_soybean_seeds_IgG_aChIP-seq_rep2

status: Public on Apr 28 2024

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

organism: Glycine max

source_name: 60d seeds

growth_protocol: For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetativetissues, the plants were planted in greenhouses.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645) and sequenced using an Illumina Novaseq 6000 platform (paired-end 150 bp reads).

value: 60d seeds

value: Williams 82

tag: cell type

value: 60d seeds cells


title: Ad-CMV-GOL_resolved_liver_CX3CR1_1

value: 13 weeks


title: 60d_soybean_seeds_IgG_aChIP-seq_rep1


title: HepG2/C3A Non-Target Expressing cells (Replicate_2)

value: Non-Target ALK Expressing control cells


title: 60d_soybean_seeds_input_rep1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \


title: 60d_soybean_seeds_input_rep2


title: BEL-A cells, KLF1+/E325K, day 2 of differentiation 3


title: interdigital tissue implanted beads, 5-Azacitidine_rep1

city: Mexico City

first: Mario

middle: Alberto

last: Perez-Maldonado

state: Mexico City

address: Circuito Mario de la Cueva s/n

department: Institute of Biomedical Research

country: Mexico

institute: UNAM

description: Bead immediate surrounding tissue

data_processing:
Adapters were trimmed using Galaxy-TrimGalore, automated detection, phredQ score treshold=20.
polyG and polyX extensions were trimmed using Galaxy-fastp.
Alignment was executed using Galaxy-Bismark Maper, PBAT mode (L,0,-0.6,).
Methylation-bias and methylations calls were done with Galaxy-MethylDackel on methylkit format.
Assembly: GRCg6a_v95
Supplementary files format and content: tab-delimited text files, total methylation calls on methylkit format.

organism: Gallus gallus

source_name: Hindlimb 28HH third interdigit

extract_protocol:
Phenol-Chloroform gDNA extraction (see article).
EpiNext High-Sensitivity Bisulfite-seq Kit (Epigentek, P-1056A) and EpiNext NGS Barcode Index Set (Epigentek, P-1060-144), according to manufacturers protocol.
Whole Genome Bisulfite Sequencing - PBAT

treatment_protocol:
250µM 5-Azacytidine soaked Ag1-x2 ionic exchange beads, 4 hours treatment.
50% DMSO soaked Ag1-x2 ionic exchange beads, 4 hours treatment.

value: Hindlimb 28HH third interdigit

value: 5-Azacytidine soaked bead


title: interdigital tissue implanted beads, 5-Azacitidine_rep2

description: Bead immediate surrounding tissue


title: interdigital tissue implanted beads, DMSO_rep2

description: Bead immediate surrounding tissue

value: DMSO soaked bead


title: 60d_soybean_seeds_H3K4me3_aChIP-seq_rep2


title: 60d_soybean_seeds_H3K4me3_aChIP-seq_rep1


title: 60d_soybean_seeds_H3K27me3_aChIP-seq_rep2


title: 60d_soybean_seeds_H3K27me3_aChIP-seq_rep1


title: Carnation_flowers_IgG_aChIP-seq_rep1

organism: Dianthus caryophyllus

source_name: flowers

value: flowers

value: Shencai

value: flowers cells

value: IgG


title: Carnation_flowers_input_rep2


title: Carnation_flowers_IgG_aChIP-seq_rep2


title: Ad-CMV-GOL_resolved_liver_CX3CR1_2

value: hepatic CD8 T cells_CX3CR1_CMV_resolved


title: Carnation_flowers_input_rep1


title: Carnation_flowers_H3K4me3_aChIP-seq_rep1


title: Carnation_flowers_H3K4me3_aChIP-seq_rep2


title: Before purification [BC1]

description: Analyzed aa frequencies.xlsx>BC1_Before purification

value: Before purification


title: Carnation_flowers_H3K27me3_aChIP-seq_rep2


title: Carnation_flowers_H3K27me3_aChIP-seq_rep1


title: BEL-A cells, wildtype, day 2 of differentiation 1

value: BEL-A

value: Erythroid progenitor

value: WT

value: Erythroid differentiation


title: CD8 cells, PBS basophil supernatant, replicate 3

city: Bar Harbor

first: Chih-Hao

last: Chang

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
RNA-seq was performed in a 75-bp paired-end format with a minimum of 40 million reads per sample on the Illumina NextSeq 500 platform, according to the manufacturer’s instructions. RNA-seq reads were filtered and trimmed for quality scores >30 using a custom python script. The filtered reads were aligned to Mus musculus reference genome GRCm38 using RSEM (v1.2.12) equipped with Bowtie2 (v2.2.0) (command: rsem-calculate-expression -p 12 --phred33-quals --seed-length 25 --forward-prob 0 --time --output-genome-bam -- bowtie2). RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package to determine differentially expressed genes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include tpm values for each sample

source_name: CD8 T cells

growth_protocol: Basophils were sort purified and were cultured in complete medium supplemented with 100 units/mL IL-2 and either 3 ng/ml of IL-3 or PBS control for 2 days and their supernatant was  collected by centrifugation. Naive T cells from B6 mouse spleens and lymph nodes were purified and seeded in RPMI-1640 containing 10% FBS, 100 units/mL penicillin, 100 μg/mL streptomycin, 55 μM β-mercaptoethanol, 1% L-glutamine and 1 mM sodium pyruvate. They were stimulated with 0.5 μg/mL αCD28 and 100 units/mL IL-2 on 5 μg/mL αCD3 pre-coated plates for 3 days.All cells were cultured at 37°C in a humidified incubator in the presence of 5% CO2.

extract_protocol:
Total RNA was isolated via miRNeasy mini extraction kit (QIAGEN).
RNA-seq libraries were generated from Poly(A) RNA capture using the Illumina TruSeq RNA Sample preparation kit v2.

treatment_protocol: For treatment the CD8 T cells were supplemented with basophil supernatant supplemented with IL-3 or PBS from day 1 to day 2 post stimulation.

value: CD8 T cells

value: PBS basophil supernatant


title: CD8 cells, IL3 basophil supernatant, replicate 3

value: IL-3 basophil supernatant


title: CD8 cells, PBS basophil supernatant, replicate 2


title: CD8 cells, IL3 basophil supernatant, replicate 2


title: interdigital tissue implanted beads, DMSO_rep1

description: Bead immediate surrounding tissue


title: CD8 cells, IL3 basophil supernatant, replicate 1


title: WT, ATACseq Rep4

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description: 10x Genomics

data_processing:
ATAC-seq Reads were aligned to the GRCm39/mm39 build of the mouse reference genome by using the Subread aligner in the Subread package (version 2.0.6). Only uniquely mapped reads were included. Peaks in each individual sample were called by using Homer (v4.11) with a false discovery rate (FDR) cutoff of <1e-5. The peaks from all the samples were then merged by taking unions of the overlapping peaks; This produced 195818 merged regions. The mapped reads in the individual samples were then assigned to the merged regions by using featureCounts. Multi- assignment of a single read was allowed. Merged regions were required to have at least 10 CPMs in at least 4 samples to be included in the analysis. Read counts were converted to log2-CPM, quantile normalised and precision weighted with the voom function of the limma package. Batch effect was removed by using the removeBatchEffect function in limma. Sample clustering was performed based on multi-dimensional scaling.
A correlation analysis was performed between the 352 DE genes identified in the Avd-G population from the scRNA-seq analysis and the regions of differentially accessible chromatin identified in the luminal cell population from EhfWT and EhfKO samples. Out of the 352 DE genes, 331 genes commonly found between the scRNA-seq data and the ATAC-seq data were included in the correlation analysis. Pearson correlation was performed by first calculating the log2 CPM values of promoter regions of all genes in the ATAC-seq data. The promoter regions were defined as the 5kb up and 2kb down region around the TSS of each gene in the mm39 RefSeq gene annotation. A scatter plot was generated to show the log2 fold changes in scRNA-seq and ATAC-seq data. Gene read coverage track figures show the coverage levels (CPM) of the ATAC-seq reads in the promoter regions of the selected genes. The selected genes have fold changes ≥1.2 in scRNA-seq Avd-G data and in ATAC-seq luminal data. The denominators for calculating CPM values are the number of mapped reads in each library. 50-bp bins in the promoter regions were used.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include log2-CPM values for each library after the filtering step. The supplementary file, raw_read_counts.txt, includes raw read counts for merged peak regions in all the libraries before filtering.

source_name: mammary gland

extract_protocol:
Thoracic and inguinal mammary glands were resected, lymph nodes removed, and samples collected into cold MEC media (DME-F12 supplemented with 1 mM glutamine, 5µg/ml insulin, 500ng/mL hydrocortisone, 10ng/mL Epidermal growth factor, 5% FBS). Glands were mechanically dissociated with a McIlwain tissue chopper then digested for 1 hour at 37°C in an orbital shaker with 300 U/mL collagenase, 100 U/mL hyaluronidase and 0.1 mg/mL DNAse I in MEC media containing 5% FBS. The resulting suspension was diluted in PBS with 2% FBS and cells pelleted by centrifugation. The cell pellet was further digested in 0.25% trypsin-EGTA with 0.1 mg/mL DNAse I for 3 minutes at 37°C, then diluted in PBS with 10% FBS and cells pelleted by centrifugation. The cell pellet was then digested in 5mg/mL Dispase with 0.1mg/mL DNAseI at 37°C for 5 minutes, then diluted in PBS with 2% FBS. Cells were passed through a 100 mm cell strainer to obtain a single cell suspension, then live cells counted using trypan blue. Single cells were pelleted by centrifugation, then blocked in rat γ-globulin and anti-CD16/CD32 Fcγ III/II receptor antibody with 0.1mg/mL DNAseI for 10 minutes at RT. Antibody incubations were performed at 4°C for 25 minutes. Antibodies used for Fluorescence-activated cell sorting (FACS) were: APC anti-mouse CD31, APC anti-mouse CD45 Antibody, APC anti-mouse TER-119/Erythroid Cells, Pacific Blue anti-mouse CD24 and FITC-anti-mouse CD29. Cells were diluted in PBS with 2% FBS then pelleted by centrifugation, and 0.2mg/ml 7-Aminoactinomycin D added to exclude dead cells. The cell suspension was then filtered through a 40 µm cell strainer and luminal mammary epithelial cells (Ter119–CD31−CD45–CD24+CD29Lo) sorted on a FACS Aria using a 100 µm nozzle.
Nuclei were extracted from 50,000 cells per sample by resuspending in 50 µl of ATAC-seq lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL, 0.01% Digitonin) and incubating on ice for 3 minutes followed by washing with   10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20. Samples were then centrifuged at 500 g for 10 minutes at 4°C and the supernatant discarded.  Transposition of the DNA and ligation of adapters was performed using the Illumina Tagment DNA TDE1 Enzyme and buffer kit (20034197) as per the manufacturer’s instructions. Briefly, DNA was digested by incubation with Tn5 Transposase enzyme at 37°C for 30 minutes. Transposed DNA was then purified using the Qiagen MinElute reaction cleanup kit (Qiagen, 28204), and partially PCR-amplified using Nextera custom barcoded primers for 5 cycles. To reduce GC-bias, the number of additional PCR cycles required was determined to be 9 cycles (14 cycles in total) by using a SYBR Green q-RT-PCR reaction and calculating the number of cycles corresponding to 1/3 of the maximum fluorescent intensity. Libraries were then purified by AMPure XP magnetic bead purification (Beckman Coulter A63880). DNA quantity and quality was assessed using the Tapestation 2000 system (Agilent).

value: Luminal mammary epithelial cells

value: mammary gland

value: Adult, 18.5 days pregnant


title: WT, ATACseq Rep2

description: 10x Genomics


title: Ehf_KO, ATACseq Rep3

description: 10x Genomics

value: EhfKO


title: Ehf_KO, scRNA-seq

description: 10x Genomics

data_processing:
Raw 10x Chromium scRNA-seq data were quantified using the cellCounts function in Bioconductor package Rsubread (ver 2.6.4). Sequencing reads were mapped to the GRCm38/mm10 reference genome. Mapped reads were deduplicated and counted to the NCBI mouse RefSeq genes (build 38.1) to produce unique molecular identifier (UMI) counts for each gene in each cell. Genes that failed to express in at least three cells in at least one sample were excluded from analysis. An expressed gene in a cell has at least one UMI count. Mitochondrial genes, ribosomal genes and genes with no known symbols were all excluded from analysis. Cells were excluded from analysis if they expressed < 200 genes or > 5000 genes, or had > 20% of mitochondrial gene content, or had > 40% of ribosomal gene content. Seurat (version 4.0.4) was used to perform t-distributed stochastic neighbour embedding (t-SNE) dimension reduction and unsupervised cell clustering.
The unsupervised cell clustering was performed by using shared nearest neighbour (SNN) modularity optimisation with a resolution parameter of 0.8 and nearest neighbour number of 20.
Assembly: mm10
Supplementary files format and content: gzipped sparse matrix files (in the Matrix Market format) of UMI counts

extract_protocol:
Thoracic and inguinal mammary glands were resected, lymph nodes removed, and samples pooled from 18.5 dP females of the same genotype into cold MEC media (DME-F12 supplemented with 1 mM glutamine, 5µg/ml insulin, 500ng/mL hydrocortisone, 10ng/mL Epidermal growth factor, 5% FBS). Glands were mechanically dissociated with a McIlwain tissue chopper then digested for 1 hour at 37°C in an orbital shaker with 300 U/mL collagenase, 100 U/mL hyaluronidase and 0.1 mg/mL DNAse I in MEC media containing 5% FBS. The resulting suspension was diluted in PBS with 2% FBS and cells pelleted by centrifugation. The cell pellet was further digested in 0.25% trypsin-EGTA with 0.1 mg/mL DNAse I for 3 minutes at 37°C, then diluted in PBS with 10% FBS and cells pelleted by centrifugation. The cell pellet was then digested in 5mg/mL Dispase with 0.1mg/mL DNAseI at 37°C for 5 minutes, then diluted in PBS with 2% FBS. Cells were passed through a 100 mm cell strainer to obtain a single cell suspension, then live cells counted using trypan blue. Single cells were pelleted by centrifugation, then blocked in rat γ-globulin and anti-CD16/CD32 Fcγ III/II receptor antibody with 0.1mg/mL DNAseI for 10 minutes at RT. Antibody incubations were performed at 4°C for 25 minutes. Antibodies used for Fluorescence-activated cell sorting (FACS) were: APC anti-mouse CD31, APC anti-mouse CD45 Antibody, APC anti-mouse TER-119/Erythroid Cells. Cells were diluted in PBS with 2% FBS then pelleted by centrifugation, and 0.2mg/ml 7-Aminoactinomycin D added to exclude dead cells. The cell suspension was then filtered through a 40 µm cell strainer and mammary epithelial cells (Ter119–CD31−CD45–) sorted on a FACS Aria using a 100 µm nozzle.
Mammary glands from two females per genotype were pooled. The 10x Chromium Single cell 3’ V3 kit was used for freshly sorted mammary epithelial cell capture and cDNA preparation according to the 10x single cell 3’ protocol.

value: Mammary epithelial cells


title: Ehf_KO, ATACseq Rep2

description: 10x Genomics


title: 15d_maize_seeds_H3K27me3_aChIP-seq_rep1

organism: Zea mays

value: 15DPA seeds cells


title: 15d_maize_seeds_H3K4me3_aChIP-seq_rep1


title: 15d_maize_seeds_H3K27me3_aChIP-seq_rep2


title: Ehf_KO, ATACseq Rep1

description: 10x Genomics


title: CD8 cells, PBS basophil supernatant, replicate 1


title: WT, ATACseq Rep3

description: 10x Genomics


title: WT, ATACseq Rep1

description: 10x Genomics


title: WT, scRNA-seq

description: 10x Genomics


title: 7th day after vaccinated under persistent HBsAg stimulation, WT Replicate 1

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to GRcm38 Genome by using Hisat2
Raw count were calculated by using featurecounts
Assembly: GRcm38
Supplementary files format and content: tab-delimited txt files include raw count values for each Sample

source_name: CD45.2+ E6F6-B cells

extract_protocol:
The CD45.2+ E6F6-B cell were sorted and stored in RNA Later Solution (Thermo Fisher Scientific) for a maximum of 24 h at 4 °C. Lung tissue was homogenized using TissueLyser II (Qiagen, Hilden, Germany) and RNA extraction was performed according to the manufacturer’s instructions (QIAamp Viral RNA Mini Kit (Qiagen)).
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: CD45.2+ E6F6-B cells

tag: time

value: 7th day


title: 15d_maize_seeds_H3K4me3_aChIP-seq_rep2


title: 15d_maize_seeds_IgG_aChIP-seq_rep2

source_name: 15DPA seeds

value: 15DPA seeds

value: IgG


title: 7th day after vaccinated under persistent HBsAg stimulation, WT Replicate 2

tag: treatment


title: 15d_maize_seeds_IgG_aChIP-seq_rep1

tag: tissue


title: 15d_maize_seeds_input_rep2

tag: cell line


title: HCT8_DDP_3

city: wuhan

first: Qingming

last: Wu

state: Hubei

address: huangjiahu east

institute: wuhan university of science and technology

data_processing:
Raw reads sequence data (.fastq files) was acquired and filtered.
HISAT2 was used to perform reads alignment.
Ballgown and R were used to analyze differential gene expression and visulation.
DEseq2 was used to produce plots and differential expression tables.
Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: colorectal cancer chemo-resistant cell lines

growth_protocol: chemo-sensitive and chemo-resistant cells were maintained in RPMI1640 medium supplemented with 10% FBS. All the cells were incubated in a 37 humifidified CO2 chamber equipped with 5%CO2.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including non-coding RNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: molecule subtype

value: non-coding RNAs and mRNAs

tag: phenotype

value: chemo-resistant


title: HCT8_DDP_2


title: 28th day after vaccinated under persistent HBsAg stimulation, WT Replicate 1

value: 28th day


title: 15d_maize_seeds_input_rep1


title: 21st day after vaccinated under persistent HBsAg stimulation, WT Replicate 3

value: 21st day


title: HCT8_DDP_1


title: HCT8_5_FU_3


title: Ehf_KO, ATACseq Rep4

description: 10x Genomics

tag: strain


title: HCT8_5_FU_2


title: 21st day after vaccinated under persistent HBsAg stimulation, WT Replicate 1


title: 14th day after vaccinated under persistent HBsAg stimulation, WT Replicate 3

value: 14th day


title: HCT8_2

source_name: colorectal cancer chemo-sensitive cell lines

value: chemo-sensitive


title: 14th day after vaccinated under persistent HBsAg stimulation, WT Replicate 1


title: HCT8_5_FU_1


title: HCT8_3


title: HCT8_1


title: 7th day after vaccinated under persistent HBsAg stimulation, WT Replicate 3


title: 28th day after vaccinated under persistent HBsAg stimulation, WT Replicate 3


title: 7th day after vaccinated under persistent HBsAg stimulation, WT Replicate 4


title: Negative Control, E6F6-B sorted from CD45.2+ E6F6-TG Mice, Replicate 2

value: Negative Control

value: 0 day


title: Negative Control, E6F6-B sorted from CD45.2+ E6F6-TG Mice, Replicate 3


title: 7th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 3


title: 21st day after vaccinated under persistent HBsAg stimulation, WT Replicate 4


title: 7th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 4


title: 7th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 1


title: 28th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 3


title: 21st day after vaccinated under persistent HBsAg stimulation, WT Replicate 2


title: 7th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 2


title: 21st day after vaccinated under persistent HBsAg stimulation, HBV Replicate 2


title: 28th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 1


title: 21st day after vaccinated under persistent HBsAg stimulation, HBV Replicate 1


title: 14th day after vaccinated under persistent HBsAg stimulation, WT Replicate 2


title: Negative Control, E6F6-B sorted from CD45.2+ E6F6-TG Mice, Replicate 4


title: 28th day after vaccinated under persistent HBsAg stimulation, WT Replicate 2


title: 14th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 4


title: 28th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 2


title: 14th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 2


title: 21st day after vaccinated under persistent HBsAg stimulation, HBV Replicate 4


title: 21st day after vaccinated under persistent HBsAg stimulation, HBV Replicate 3


title: Vcam1 KO-2

city: Pittsburgh

first: Partha

last: Dutta

address: 200 Lothrop Street

institute: University of Pittsburgh

description: Atheorsclerotic macrophages were sorted

data_processing:
CLC Genomics Workbench v 11.0.1
The RNA-Seq analysis is done in several steps using CLC Genomics Workbench: First, all genes are extracted from the reference genome (using annotations of type gene). Other annotations on the gene sequences are preserved (e.g. CDS information about coding sequences etc). Next, all annotated transcripts (using annotations of type mRNA) are extracted. If there are several annotated splice variants, they are all extracted. Note that the mRNA annotation type is used for extracting the exon-exon boundaries.
Next, the reads are mapped against all the transcripts plus the entire gene
From this mapping, the reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated. After that, putative exons are identified.
Fold change in gene expression was calculated
Assembly: mm10
Supplementary files format and content: The excel file includes RPKM values for each Sample.

source_name: Aorta

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Aorta

value: plaque macropahges

tag: genotype

value: LysMcre/+ Vcam1fl/fl

value: High fat diet


title: Vcam1 KO-3

description: Atheorsclerotic macrophages were sorted


title: 14th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 1


title: 14th day after vaccinated under persistent HBsAg stimulation, HBV Replicate 3


title: Vcam1 KO-1

description: Atheorsclerotic macrophages were sorted


title: Negative Control, E6F6-B sorted from CD45.2+ E6F6-TG Mice, Replicate 1


title: 20d_rice_seeds_H3K4me3_aChIP-seq_rep1

organism: Oryza sativa

source_name: seeds

value: seeds

value: Zhonghua 11

value: seeds cells

tag: chip antibody


title: 15d_rice_seedlings_H3K4me3_CUT&Tag_rep2

source_name: seedlings

value: seedlings

value: seedlings cells


title: 20d_rice_seeds_H3K4me3_aChIP-seq_rep2


title: 15d_rice_seedlings_H3K4me3_CUT&Tag_rep1


title: WT-1

description: Atheorsclerotic macrophages were sorted

value: LysM+/+ Vcam1fl/fl


title: 20d_rice_seeds_H3K27me3_aChIP-seq_rep1


title: WT-2

description: Atheorsclerotic macrophages were sorted


title: 20d_rice_seeds_H3K27me3_aChIP-seq_rep2


title: Potato_tuber_input_rep2

organism: Solanum tuberosum

source_name: tubers

value: tubers

value: Atlantic potato

value: tubers cells


title: 15d_rice_seedlings_H3K4me3_eChIP-seq_rep1

value: Minghui 63


title: Potato_tuber_H3K27me3_aChIP-seq_rep2


title: 15d_rice_seedlings_H3K4me3_aChIP-seq_rep1


title: 15d_rice_seedlings_H3K4me3_aChIP-seq_rep2


title: Potato_tuber_IgG_aChIP-seq_rep2

value: IgG


title: Potato_tuber_H3K4me3_aChIP-seq_rep1


title: Potato_tuber_H3K4me3_aChIP-seq_rep2


title: Potato_tuber_IgG_aChIP-seq_rep1


title: Potato_tuber_input_rep1


title: Potato_tuber_H3K27me3_aChIP-seq_rep1


title: MCMKO268

city: Augusta

first: Jianqiu

last: Zou

state: GA

address: 1460 Laney Walker Blvd

department: VBC

institute: Augusta University

data_processing:
Differentially expressed genes were defined by Padj<0.05 and a fold change larger than 1.5.
Pathway enrichment analysis was carried out using Metascape with a nominal threshold of P<0.05.
Assembly: mm10
Supplementary files format and content: Excel file, with the pfkm of each sample per colume

source_name: Heart ventricle

extract_protocol:
Mouse ventricles were minced and treated with RNAlater (Thermo Fisher Scientific). Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. The isolated RNA was subjected to RNA-sequencing analysis performed by Novogene via Next Generation Sequencing.
The library construction was performed by Novogene using library preperation kit following manual.

value: Heart ventricle

value: Cardiomyocytes

value: Tamoxifen


title: MCMWT207

value: WT


title: MCMKO264


title: MCMWT265


title: MCMKO267


title: WT-3

state: PA

description: Atheorsclerotic macrophages were sorted

value: Aorta

value: plaque macropahges


title: 15d_rice_seedlings_H3K4me3_eChIP-seq_rep2


title: dCdN10_DE

city: Beijing

first: Wulan

last: Deng

address: Beijing Haidian District Yiheyuan Road #5

department: BIOPIC

institute: Peking University

description: Homozygote cell line with the endogenous FOXA2 protein both N- and C-terminally deleted, differentiated to definitive endoderm, clone #10

data_processing:
Base-calling performed with CASAVA
RNA-Seq reads quality control performed with FastQC (version 0.10.1)
RNA-Seq reads were aligned to the hg38 genome assembly using STAR RNA-Seq aligner (version 2.7) with the following options: --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
We used Samtools (version 1.9) to convert STAR output .sam files into .bam files, and to sort and index them
We used HTSeq (version 0.11.1) to count how many reads overlapped an annotated gene (GENECODE v32 annotations) with the following options: htseq-count --stranded=no -f bam --additional-attr=gene_name -m union)
BigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2913022398 --ignoreDuplicates
Assembly: hg38
Supplementary files format and content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary files format and content: text files containing the output of HTSeq, i.e. read counts in each annotated Ensemble gene (GENECODE v32 annotations)

source_name: definitive endoderm

growth_protocol: H7 hESCs (WiCell, WAe007-A) were cultured on plates pre-coated with 1% (v/v) Geltrex (Thermo Fisher, A1413302) with complete Essential 8 medium (Thermo Fisher, A1517001). Accutase (Thermo Fisher, A1110501) was used for cell dispersion and ROCK inhibitor Thiazovivin at 2 μΜ final concentration was used in the culture medium for the first day after re-plating cells.

extract_protocol:
Total RNA was isolated using TRIzol following the manufacturer’s instructions
RNA library was generated using the Solexa rapid library protocol.

treatment_protocol:
hESCs were differentiated to DE using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601).
hESCs were differentiated to APS and DE with a two-day protocol using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601) or following the protocol in the report (Loh et al., 2014)

tag: foxa2 protein

value: deletion of CTD (A297-S463) and NTD (M1-K155)


title: dC11_APS

description: Homozygote cell line with the endogenous FOXA2 protein C-terminally deleted, differentiated to anterior primitive streak, clone #11

source_name: anterior primitive streak

treatment_protocol:
hESCs were differentiated to APS using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601).
hESCs were differentiated to APS and DE with a two-day protocol using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601) or following the protocol in the report (Loh et al., 2014)

value: deletion of CTD (A297-S463)


title: dCdN10_APS

description: Homozygote cell line with the endogenous FOXA2 protein both N- and C-terminally deleted, differentiated to anterior primitive streak, clone #10


title: KO21_DE

description: Homozygote FOXA2 Knock-out clone #21 differentiated to definitive endoderm

value: FOXA2 Knock-out


title: dC11_DE

description: Homozygote cell line with the endogenous FOXA2 protein C-terminally deleted, differentiated to definitive endoderm, clone #11


title: MCMWT261


title: KO1_DE

description: Homozygote FOXA2 Knock-out clone #1 differentiated to definitive endoderm


title: KO1_APS

description: Homozygote FOXA2 Knock-out clone #1 differentiated to anterior primitive streak


title: MCMKO209


title: KO21_APS

description: Homozygote FOXA2 Knock-out clone #21 differentiated to anterior primitive streak


title: Arabidopsis_MYC_aChIP-seq_rep2

organism: Arabidopsis thaliana

source_name: 15d seedlings

value: 15d seedlings

value: 15d seedlings cells

value: MYC


title: WT_ES

description: wild type H7 cell line

source_name: embryonic stem cells

treatment_protocol:
None
hESCs were differentiated to APS and DE with a two-day protocol using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601) or following the protocol in the report (Loh et al., 2014)

value: wild type


title: PANC1PSB_PS04ULAPANC1PSBS383_GAAGAGCTT_L003_R1_001

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
The PLATE-Seq FASTQ files were pseudoaligned to the GRCh38 human transcriptome (mRNA & ncRNA) and gene expression was quantified using kallisto (version 0.44.0), tximport package (Soneson et al., 2015), and biomaRt package (Durinck et al., 2009).
The gene expression was quantified as both raw counts (i.e. sequencing fragments per genomic locus) and transcripts per million (i.e. sequencing fragments per genomic locus normalized for transcript/gene length and sample sequencing depth).
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)

source_name: PDA tumor

growth_protocol: Panc1 and Aspc1 pancreatic cancer cells were cultured in white 96-well tissue culture-treated plates at optimized density, in 100 μl of Dulbecco's Modified Eagle Medium (DMEM) media supplemented with 10% fetal bovine

extract_protocol:
After 24 h of incubation, the plates were treated with following drugs: RAF inhibitors – Sorafenib, Dabrafenib, RAF709, PLX8394, GDC-0879; MEK inhibitors – Trametinib, Cobimetinib, Binimetinib, Selumetinib, Rafametinib; and ERK inhibitors – SCH772984, Ulixertinib, AZD0364, Ravoxertinib. Each drug was dosed at the concentration at which the cells were 80% viable after 48 h of treatment. After 24 h of treatment, the medium was replaced with 100 ml of FBS supplemented with 10% DMSO and the plates were frozen at −80 °C prior to PLATE-Seq.
Detailed protocol for preparation of the automated PLATE-SEQ experiment was described by Bush et al. (Bush et al., 2017).
Samples were sequenced using PlateSeq approach

value: PDA tumor

value: Human PDA cell line

value: DMSO


title: PANC1PSB_PS04ULAPANC1PSBS384_TGCGGATCA_L003_R1_001

value: UNTREATED


title: PANC1PSB_PS04ULAPANC1PSBS376_TAGCCGGTT_L003_R1_001


title: WT_APS

description: wild type H7 cell line differentiated to anterior primitive streak


title: Arabidopsis_MYC_aChIP-seq_rep1


title: PANC1PSB_PS04ULAPANC1PSBS372_GTATCCCAA_L003_R1_001


title: PANC1PSB_PS04ULAPANC1PSBS374_CCCAAGTAG_L003_R1_001


title: MCMWT208

value: Heart ventricle


title: PANC1PSB_PS04ULAPANC1PSBS375_TGGGTCATG_L003_R1_001

value: Binimetinib


title: Arabidopsis_dryseed_H3K4me3_aChIP-seq_rep1

source_name: dry seed

value: dry seed

value: dry seed cells


title: PANC1PSB_PS04ULAPANC1PSBS363_ATCGTGTCA_L003_R1_001


title: Arabidopsis_dryseed_H3K27me3_aChIP-seq_rep2


title: WT_DE

description: wild type H7 cell line differentiated to definitive endoderm


title: PANC1PSB_PS04ULAPANC1PSBS365_AGTTGTGGA_L003_R1_001

value: Ulixertinib


title: Arabidopsis_dryseed_H3K4me3_aChIP-seq_rep2


title: E14.5

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: scATAC on gonads

library_source: genomic single cell

data_processing:
Sequencing data were processed using the Bio-Rad ATAC-Seq Analysis Toolkit, which performed FASTQ debarcoding, read trimming, alignment, bead filtration, bead deconvolution, cell filtration and peak calling.
For generation of the fragments file, which contain the start and end genomic coordinates of all aligned sequenced fragments, sorted bam files were further process with “bap-frag” module of BAP
Assembly: mm10
Supplementary files format and content: Fragments file

source_name: Gonad

extract_protocol:
Embryos were collected from pregnant female C57BL/6J mice at E11.5, E12.5, E13.5 and E14.5, which the day with the presence of vaginal plugs was defined as E0.5. For the embryos at E11.5, whole genital ridges (including gonad and mesonephros) were dissected. For the embryos at E12.5, E13.5 and E14.5, gonads were dissected free of the mesonephros. The sexing step was omitted to reduce the sample processing time, and the gonads from both sexes were pooled in equal numbers for subsequent steps. The XX and XY gonads at the same time points were pooled together. Each time point contains at least 6 embryos.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ATAC-Seq Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed with PCR amplification as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads. Barcoded amplicons were further amplified for 8 cycles. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were sequenced on HiSeq 2000 with 150 bp paired-end reads.

value: Gonad

tag: age

value: Embryonic day 14.5


title: Arabidopsis_dryseed_H3K27me3_aChIP-seq_rep1


title: E12.5

description: scATAC on gonads

value: Embryonic day 12.5


title: Arabidopsis_MBD7-MYC_aChIP-seq_rep2


title: PANC1PSB_PS04ULAPANC1PSBS361_TTAGGGCCT_L003_R1_001

value: Dabrafenib


title: PANC1PSB_PS04ULAPANC1PSBS362_ATCACACTG_L003_R1_001

value: Refametinib


title: Arabidopsis_input_rep2

value: 15d seedlings cells


title: PANC1PSB_PS04ULAPANC1PSBS360_TAGTAGCGA_L003_R1_001


title: Sugarcane_stalks_input_rep1

organism: Saccharum officinarum

source_name: stalks

value: stalks

value: Funong 155002

value: stalks cells


title: Sugarcane_stalks_H3K4me3_aChIP-seq_rep2


title: Arabidopsis_input_rep1


title: Sugarcane_stalks_H3K4me3_aChIP-seq_rep1


title: PANC1PSB_PS04ULAPANC1PSBS371_GCATAGTGA_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: Sugarcane_stalks_H3K27me3_aChIP-seq_rep2


title: Arabidopsis_MBD7-MYC_aChIP-seq_rep1

value: MYC


title: Arabidopsis_FLAG_input_rep2


title: Arabidopsis_CAMTA3-FLAG_aChIP-seq_rep2

value: FLAG


title: Arabidopsis_CAMTA3-FLAG_eChIP-seq_rep1


title: PANC1PSB_PS04ULAPANC1PSBS339_CTCTGCTAG_L003_R1_001

value: Sorafenib


title: PANC1PSB_PS04ULAPANC1PSBS338_TGGGACACA_L003_R1_001


title: PANC1PSB_PS04ULAPANC1PSBS352_GGGACTTAA_L003_R1_001


title: Arabidopsis_FLAG_input_rep1


title: cirrhotic liver, paired control, rep4

city: Cambridge

first: Ben

last: Leaker

state: MA

address: 77 Massachusetts Avenue

department: HST

institute: MIT

data_processing:
Raw data quality was assessed with FastQC v0.11.9
Reads were trimmed with Cutadapt v3.4 and Trim Galore v0.6.7
Pseudo-alignment and transcript abundance estimation were performed with Salmon v1.5.2
Reads were imported to R with tximport and converted to gene-level data with the tx2gene option. Differential expression was calculated using DESeq2 v4.2.2
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPMs for each sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Samples were placed in RNAlater (Thermo Fisher Scientific) and stored at 4C overnight, then at -20C until ready to use. RNA extraction was performed using the RNeasy midi kit with proteinase K digestion and on-column DNase digestion according to manufacturer instructions (Qiagen, Hilden, Germany).
Libraries were prepared using NEBNext Ultra II (New England Biolabs, Ipswich, USA) with poly(A) selection

treatment_protocol: Laser-treated samples were ablated with a fractional CO2 laser. Untreated samples from the same liver were collected for paired controls

value: liver

tag: disease

value: cirrhosis

value: control


title: Sugarcane_stalks_input_rep2


title: PANC1PSB_PS04ULAPANC1PSBS336_TGCGTAAGG_L003_R1_001

value: DMSO


title: E13.5

description: scATAC on gonads

value: Gonad

value: Embryonic day 13.5


title: PANC1PSB_PS04ULAPANC1PSBS350_CTCCATTCC_L003_R1_001

value: Ravoxertinib


title: PANC1PSB_PS04ULAPANC1PSBS349_CTCCACAGA_L003_R1_001

value: Cobimetinib


title: PANC1PSB_PS04ULAPANC1PSBS348_GGTGCCTTA_L003_R1_001

value: UNTREATED


title: PANC1PSB_PS04ULAPANC1PSBS353_GTTGGCCTA_L003_R1_001

value: Trametinib


title: Arabidopsis_CAMTA3-FLAG_eChIP-seq_rep2

value: 15d seedlings cells


title: Sugarcane_stalks_H3K27me3_aChIP-seq_rep1

value: stalks

value: Funong 155002

value: stalks cells


title: E11.5

description: scATAC on gonads

value: Embryonic day 11.5


title: PANC1PSB_PS04ULAPANC1PSBS326_ATGGAAGTG_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: cirrhotic liver, paired control, rep2

value: liver


title: Arabidopsis_CAMTA3-FLAG_aChIP-seq_rep1

value: FLAG


title: cirrhotic liver, laser treated, rep4

value: cirrhosis

value: fractional laser


title: cirrhotic liver, laser treated, rep3


title: cirrhotic liver, paired control, rep3

value: control


title: PANC1PSB_PS04ULAPANC1PSBS329_TCGACTCGA_L003_R1_001


title: PANC1PSB_PS04ULAPANC1PSBS325_ACACACACG_L003_R1_001

value: Binimetinib


title: cirrhotic liver, laser treated, rep2


title: PANC1PSB_PS04ULAPANC1PSBS341_AATACGGGA_L003_R1_001

value: Selumetinib


title: PANC1PSB_PS04ULAPANC1PSBS316_TCATCCCTG_L003_R1_001

value: Dabrafenib


title: cirrhotic liver, paired control, rep1


title: PANC1PSB_PS04ULAPANC1PSBS324_CTCTCATGA_L003_R1_001

value: DMSO


title: PANC1PSB_PS04ULAPANC1PSBS305_ACGTAACGC_L003_R1_001

value: Ravoxertinib


title: healthy liver, paired control, rep4

value: healthy


title: Mouse0 Trametinib rep1

city: Boulder

first: Edward

middle: Boyi

last: Chuong

state: CO

address: JSC Biotech Building, 3415 Colorado Ave

department: BioFrontiers Institute and Molecular, Cellular & Developmental Biology Department

institute: University of Colorado Boulder

description: HCT116 cell line-based xenograft

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=r k=31 mink=11 hdist=1 qtrim=r trimq=10 tpe tbo' and mapped to hg38 using hisat2 v2.1.0 with options '--rna-strandness RF --no-softclip'. Aligned fragments with an alignment score less than 10 were removed with samtools v1.10. Samples were mapped to Gencode genes in the GENCODE v34 annotation using featureCounts v1.6.2 with options '-s 2 -t exon -g gene_id -0 -p'. For visualization, aligned fragments were converted to stranded, CPM normalized bigwigs using deepTools bamCoverage v3.0.1.
Differentially expressed genes were called using DESeq2 v1.32.0 with design '~ condition'. For the CRISPR-KO differential expression analysis, normalized count data is derived from DESeq2 comparisons between the KO (3 replicates) vs untreated HCT116 samples (2 replicates). For the CRISPRi differential expression analysis, GFP (2 replicates) were used as the control. Genes with zero counts across all samples were removed.
Assembly: hg38
Supplementary files format and content: CPM normalized signal tracks in UCSC bigwig format
Supplementary files format and content: Tab-delimited text files including unnormalized counts and DESeq2 normalized counts

source_name: HCT116 cell line-based xenograft

growth_protocol: HCT116 cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in McCoy’s 5A (Gibco #16600082) supplemented with 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
RNA from HCT116 was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057).
Libraries were generated with 500 ng RNA using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to the manufacturer's instructions. Briefly, single-indexed adapters (KAPA #KK8700) or unique dual-indexed adapters (KAPA #KK8727) were added to each sample at a final concentration of 78 nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups. Purified, adapter-ligated samples were amplified for 11 cycles according to the manufacturer's instructions and purified using a 1.0X KAPA Pure Bead cleanup.

treatment_protocol: HCT116 cells were either untreated or treated with 1 uM Cobimteinib or 100 ng/mL TNF-alpha for 24h. For the HCT116 cell line-based xenografts, HCT116 cells were engrafted into two immunodeficient mice, which were dosed at 0.125 mg/kg trametinib or vehicle by oral gavage daily for 21 days.

value: HCT116 cell line-based xenograft

value: colorectal cancer

value: wildtype

value: Trametinib

tag: timepoint

value: 21 days


title: Mouse95 Vehicle rep2

description: HCT116 cell line-based xenograft

value: Vehicle


title: Mouse95 Vehicle rep1

description: HCT116 cell line-based xenograft


title: healthy liver, paired control, rep2

value: liver


title: healthy liver, paired control, rep3


title: PANC1PSB_PS04ULAPANC1PSBS304_AGTCTGAAC_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Cobimetinib


title: healthy liver, laser treated, rep2

value: fractional laser


title: PANC1PSB_PS04ULAPANC1PSBS303_CGTGGTTTT_L003_R1_001


title: healthy liver, paired control, rep1

value: control


title: cirrhotic liver, laser treated, rep1

value: cirrhosis


title: PANC1PSB_PS04ULAPANC1PSBS317_GCTGATGTT_L003_R1_001

value: Refametinib


title: Mouse0 Trametinib rep2

description: HCT116 cell line-based xenograft


title: PANC1PSB_PS04ULAPANC1PSBS315_TAGCAATCC_L003_R1_001

value: Ulixertinib


title: healthy liver, laser treated, rep4


title: PANC1PSB_PS04ULAPANC1PSBS313_GCATATCGT_L003_R1_001


title: Sparsely granulated somatotroph adenoma 7

city: Gwang-ju

first: Yeongmin

last: Kim

address: Chundamguagiro

department: BMSE

country: South Korea

institute: GIST

data_processing:
Trimmomatix(Version 0.36)
STAR(Version 2.7.10) using GRCh38.109
Picards's MarkDuplicates function(Version 3.0.0)
HTseq(Version 2.0.2)
Assembly: GRCh38.109
Supplementary files format and content: counts

source_name: Pituitary gland

extract_protocol:
RNeasy mini kit
Illumina TruSeq Stranded Total RNA Library Prep Gold Kit

value: Pituitary cell

value: adenoma


title: PANC1PSB_PS04ULAPANC1PSBS300_CCGAAGGTT_L003_R1_001

value: DMSO


title: healthy liver, laser treated, rep3

value: healthy


title: PANC1PSB_PS04ULAPANC1PSBS312_ACATCGGTT_L003_R1_001


title: PANC1PSB_PS04ULAPANC1PSBS302_GTAGGTAGG_L003_R1_001


title: Sparsely granulated somatotroph adenoma 6


title: PANC1PSB_PS04ULAPANC1PSBS293_GGGATTAAG_L003_R1_001


title: Poplar_dormant_2-year_branches_IgG_aChIP-seq_rep2

organism: Populus

source_name: dormant branches

value: dormant branches

value: dormant branches cells

value: IgG


title: PANC1PSB_PS04ULAPANC1PSBS291_TTTCGGTCG_L003_R1_001

value: Selumetinib


title: Sparsely granulated somatotroph adenoma 5


title: Sparsely granulated somatotroph adenoma 4


title: Sparsely granulated somatotroph adenoma 3


title: Sparsely granulated somatotroph adenoma 2


title: Poplar_dormant_2-year_branches_IgG_aChIP-seq_rep1


title: Normal pituitary 6

value: Healthy


title: healthy liver, laser treated, rep1

value: liver


title: Poplar_dormant_2-year_branches_H3K4me3_aChIP-seq_rep1


title: Poplar_dormant_2-year_branches_H3K4me3_aChIP-seq_rep2


title: PANC1PSB_PS04ULAPANC1PSBS289_CCGTGTCTT_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Sorafenib


title: PANC1PSA_PS03ULAPANC1PSAS288_TCGTATCAC_L003_R1_001

value: UNTREATED


title: Normal pituitary 3


title: Normal pituitary 4


title: Sparsely granulated somatotroph adenoma 1


title: Poplar_dormant_2-year_branches_H3K27me3_aChIP-seq_rep2


title: Normal pituitary 1


title: Densely granulated somatotroph adenoma 11


title: NNE_PFOS_2_1

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

data_processing:
BGI MGI2000
RNA concentration, RNA integrity number and 28S/18S ratio were detected with an Agilent 2100 instrument and Agilent RNA 6000 nano Reagents Part 1, to determine its quality. Qualified samples were sequenced on an MGISEQ-2000 platform. Raw reads with low-quality base ratios exceeding 20% or unknown base ratios exceeding 5% or containing sequencing adapter were removed with the SOAPnuke.
Clean reads were mapped to the reference genome and the reference coding gene set using HISAT2 and Bowtie2 respectively.
Gene expression levels were calculated with RSEM and differential expression analysis was performed with DESeq2.
Genes with fold change  greater than 2 and FDR (false discovery rate) less than or equal to 0.001 were considered to be differentially expressed genes (DEGs).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: CSV file with mRNA expression value for each sample

source_name: Blastocyst

growth_protocol: H1 hESCs were cultured in mTeSR Plus medium. NNE differentiation was induced by repalcing homemade Essential 6 (E6) medium containing 10 ng/mL BMP4, 10 μM SB431542 and 10 μM SU5402 for 2 days, then from day 3 to day 10, the medium remained the same as on day 0, but with a decreased concentration of BMP4 (5 ng/mL) added to sustain the differentiation process. Global monolayer differentiation was initiated by supplying homemade Essential 6 (E6) medium to H1 hESCs and keeping culturing for 8 days or 16 days.

extract_protocol: Total RNA extraction was obtained with the TRNzol Reagent for all samples according to the manufacturers’ instructions. 2 μg of total RNA was used to construct RNA-seq libraries.

treatment_protocol: Add PFOA, PFHxA, PFBA, PFOS, PFHxS, and PFBS with 10 μM concentration at the very beginning of differentiation.

value: Blastocyst

value: Non-neural ectodermal cells differentiated from H1

value: WT

value: PFOS 10 μM


title: NNE_PFOS_1_1

address: 双清路18号林业大学北门


title: Densely granulated somatotroph adenoma 8

value: Pituitary cell

value: adenoma


title: Normal pituitary 2


title: PANC1PSA_PS03ULAPANC1PSAS280_TATGCAGCA_L003_R1_001


title: Densely granulated somatotroph adenoma 9


title: PANC1PSA_PS03ULAPANC1PSAS279_CTTACCTAC_L003_R1_001

value: Binimetinib


title: Densely granulated somatotroph adenoma 7


title: PANC1PSA_PS03ULAPANC1PSAS278_CGTAGAGCT_L003_R1_001


title: NNE_PFOA_2_1

address: 双清路18号林业大学北门

value: PFOA 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS276_GAAGTGGAG_L003_R1_001


title: Densely granulated somatotroph adenoma 6


title: Densely granulated somatotroph adenoma 5


title: Densely granulated somatotroph adenoma 4


title: PANC1PSA_PS03ULAPANC1PSAS275_GGAAGACCA_L003_R1_001

value: DMSO


title: Densely granulated somatotroph adenoma 3


title: NNE_PFOA_1_1

address: 双清路18号林业大学北门


title: NNE_PFHxS_2_1

address: 双清路18号林业大学北门

value: PFHxS 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS287_CGTTACCAT_L003_R1_001


title: Densely granulated somatotroph adenoma 1


title: PANC1PSA_PS03ULAPANC1PSAS269_CATAGCGAG_L003_R1_001

value: Ulixertinib


title: Poplar_dormant_2-year_branches_H3K27me3_aChIP-seq_rep1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

value: dormant branches

value: dormant branches cells


title: hypoxia2

city: qingdao

first: Qiuxia

last: Ji

address: jiangsu road

institute: qingdao university

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCh38.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

growth_protocol: THP-1 cell were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (P/S) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Standard cell culture conditions are applied, with hypoxia treatment.

value: hypoxia


title: hypoxia3


title: PANC1PSA_PS03ULAPANC1PSAS267_CTTAAGCCT_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: Densely granulated somatotroph adenoma 10


title: hypoxia1


title: NNE_PFHxS_1_1

address: 双清路18号林业大学北门


title: NNE_PFHxA_2_1

address: 双清路18号林业大学北门

value: PFHxA 10 μM


title: control3

value: control


title: PANC1PSA_PS03ULAPANC1PSAS266_TGGTGCAAA_L003_R1_001

value: Refametinib


title: NNE_PFHxA_1_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Non-neural ectodermal cells differentiated from H1

value: WT


title: control2


title: PANC1PSA_PS03ULAPANC1PSAS265_TCGCGAACA_L003_R1_001

value: Dabrafenib


title: control1


title: Densely granulated somatotroph adenoma 2

value: Pituitary cell

value: adenoma


title: NNE_PFBS_2_1

address: 双清路18号林业大学北门

value: PFBS 10 μM


title: OPBG-GBM-001

city: Utrecht

first: Konstantinos

last: Vazaios

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

data_processing:
cutadapt v2.10 used for sequence trimming
Trimmed sequences were mapped to human GRCh38.p13 reference based on Burrow-Wheeler Transformation using STARv2.5.4. default settings
Mapped reads indexed and sorted into BAM with samtools v1.10
Further processing and normalization of counts was performed using EdgeR (Ensemble ids aggregated into unique Gene symbols, raw counts <10 in less than 70% or total gene counts in all samples <15 were removed before TMM normalization and CPM calculation)
Assembly: hu GRCh38.p13
Supplementary files format and content: tab-delimited text file includes log2-transformed CPMs for each sample used for the discovery of correlating genes
Supplementary files format and content: tab-delimited text file includes log2-transformed CPMs for each sample used for validation of correlating genes

source_name: High Grade Glioma

extract_protocol:
RNA was harvested using the miRvana™ miRNA isolation kit (Ambion)
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420S/L)

value: High Grade Glioma


title: NNE_PFBS_1_1

address: 双清路18号林业大学北门


title: PANC1PSA_PS03ULAPANC1PSAS257_GTGAACCAT_L003_R1_001

value: Trametinib


title: VUMC-DIPG-11


title: PANC1PSA_PS03ULAPANC1PSAS264_CACTAAGCA_L003_R1_001

value: UNTREATED


title: VUMC-DIPG-F


title: PANC1PSA_PS03ULAPANC1PSAS256_GGACTGGAT_L003_R1_001


title: NNE_PFBA_2_1

address: 双清路18号林业大学北门

value: PFBA 10 μM


title: VUMC-EPN-01

source_name: Ependymoma

value: Ependymoma

value: PFA


title: NNE_DMSO_2_1

address: 双清路18号林业大学北门

value: 0.1% DMSO


title: KNS-42


title: NNE_PFBA_1_1

address: 双清路18号林业大学北门


title: VUMC-EPN-05


title: PANC1PSA_PS03ULAPANC1PSAS252_AAGCATAGC_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: NNE_DMSO_1_1

address: 双清路18号林业大学北门


title: PANC1PSA_PS03ULAPANC1PSAS253_GTAGTGCTC_L003_R1_001

value: Cobimetinib


title: PANC1PSA_PS03ULAPANC1PSAS254_TACATGCCC_L003_R1_001

value: Ravoxertinib


title: E6_D8_PFOS_2_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H28

value: PFOS 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS245_CTCGCGAAA_L003_R1_001

value: Selumetinib


title: VUMC-ATRT-04

source_name: Atypical teratoid/rhabdoid tumor

value: Atypical teratoid/rhabdoid tumor

value: MYC


title: VUMC-EPN-06


title: PANC1PSA_PS03ULAPANC1PSAS243_GGGTTGACT_L003_R1_001

value: Sorafenib


title: E6_D8_PFOS_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H27

value: WT


title: E6_D8_PFOA_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H26

value: PFOA 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS242_ATAGTCGCC_L003_R1_001


title: VUMC-ATRT-01

value: SHH


title: PANC1PSA_PS03ULAPANC1PSAS240_ATGTGTCGC_L003_R1_001

value: DMSO


title: E6_D8_PFOA_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H25


title: VUMC-ATRT-03


title: PANC1PSA_PS03ULAPANC1PSAS233_TAGCTCTCA_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: E6_D8_PFHxS_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H24

value: PFHxS 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS230_AACGGGTTC_L003_R1_001