title: Patient sample7:GIST

description:
Patient sample7:GIST
A6402


title: C2C12 scramble (control) 2

status: Public on Mar 31 2023

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from myoblastoma cell line

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Mouse Gene 2.1 ST ArrayStrip (20 h, 292 48 °C)

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cells were grown in standard media as per ATCC protocols

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: Cells were transfected with siRNA pools as per manufacturer's instruction (Dharmacon).

tag: transfection

value: control


title: Patient sample8:GIST

city: GuangZhou

first: Jianrong

last: Guo

address: Dongfengdong Road NO.651

country: China

institute: SYSUCC

description:
Patient sample8:GIST
A6406

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Homo sapiens

source_name: GIST with liver metastasis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: GIST


title: PCW26-N [scATACseq]

type: SRA

city: Chongqing

first: Meryl

last: Liu

address: The First Affiliated Hospital of Chongqing Medical University

description: 10x Genomics

library_source: genomic

data_processing:
Cell Ranger (for scRNA-seq experiments) or Cell Ranger ATAC (for scATAC-seq experiments) was used to demultiplex input files and generate feature-barcode matrices.Downstream processing was preformed in R using Seurat, ArchR, Signac, ChromVar, and Monocle.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: genomic DNA

source_name: fetal retina

extract_protocol:
Fetal eyes at 9–26 weeks of gestation were dissected from fetal and embryonic terminations, collected in DMEM/F-12 (Gibco, Australia), and transferred into a sterile Petri dish. The fetal eye tissue was then sectioned into pieces, followed by digestion in 3 mL of 2 mg/mL papain (brands) for approximately 20 min at 37°C. Using a 30 mL MACS Smart Strainer (Miltenyi), the dissociated fetal eyeball tissue was filtered to guarantee a single-cell suspension. Enzymatic digestion was stopped by the addition of an equal volume of 10% fetal bovine serum (Gibco, Australia) to DMEM/F-12 (Gibco, Australia). The cells were then pelleted and resuspended in an appropriate amount of PBS. A total of 74,571 cells were collected for scRNA-seq and 75,197 cells for scATAC-seq.
Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol. Qubit was used for library quantification before pooling. The final library pool was sequenced on the Illumina NovaSeq 6000 instrument using 150-base-pair paired-end reads.

tag: tissue

value: fetal retina

tag: age

value: 26 post-conceptional weeks


title: PCW26-O [scATACseq]

institute: The First Affiliated Hospital of Chongqing Medical University

description: 10x Genomics

source_name: fetal eye, except retina

value: fetal eye, except retina


title: PCW23 [scATACseq]

description: 10x Genomics

source_name: fetal eye

value: fetal eye

value: 23 post-conceptional weeks


title: PCW20 [scATACseq]

description: 10x Genomics

value: 20 post-conceptional weeks


title: Patient sample16:GIST

description:
Patient sample16:GIST
A6790


title: Patient sample9:GIST

description:
Patient sample9:GIST
A6801


title: C2C12 HTT KO 3

value: HTT KO


title: PCW19 [scATACseq]

description: 10x Genomics

value: 19 post-conceptional weeks


title: Patient sample17:GIST

description:
Patient sample17:GIST
A6803


title: PCW18 [scATACseq]

description: 10x Genomics

value: 18 post-conceptional weeks


title: PCW15 [scATACseq]

description: 10x Genomics

value: 15 post-conceptional weeks


title: Patient sample2:GIST

description:
Patient sample2:GIST
A6411


title: C2C12 HTT KO 2


title: PCW11 [scATACseq]

description: 10x Genomics

value: 11 post-conceptional weeks


title: PCW9 [scATACseq]

description: 10x Genomics

value: 9 post-conceptional weeks


title: PCW11-R [scATACseq]

description: 10x Genomics


title: PCW26-O [scRNAseq]

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA


title: PCW26-N [scRNAseq]

description: 10x Genomics


title: PCW23 [scRNAseq]

description: 10x Genomics


title: PCW18 [scRNAseq]

description: 10x Genomics


title: Patient sample6:GIST

description:
Patient sample6:GIST
A6407


title: PCW9 [scRNAseq]

description: 10x Genomics


title: PCW15 [scRNAseq]

description: 10x Genomics


title: PCW11 [scRNAseq]

description: 10x Genomics


title: PCW14 [scRNAseq]

description: 10x Genomics

value: 14 post-conceptional weeks


title: H1975

city: Guangzhou

first: Liu

last: Huisheng

address: Wushan load

institute: South China University of Technology

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38 (hg38)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.  H1975.fpkm.txt,Sample H1975;H1975OR.fpkm.txt,Sample H1975OR.  Matrix.csv  is a table of gene expression matrices combining the two files.

growth_protocol: H19750R cells and H1975cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

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

treatment_protocol: H1975OR cell line was established by continuous exposure to a gradient concentration of Osimertinib (Selleck, USA) from 0.5 μM to 12.5 μM about six months and maintained in Osimertinib-free medium for 14 days prior to the experiment.

tag: cell line

tag: cell type

value: NSCLC tumor cell

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: phenotype

value: osimertinib-sensitive


title: PCW10 [scRNAseq]

description: 10x Genomics

value: 10 post-conceptional weeks


title: PCW10 [scATACseq]

description: 10x Genomics


title: H1975OR

value: osimertinib

value: osimertinib-resistant


title: PCW14 [scATACseq]

description: 10x Genomics

value: fetal eye


title: ChiRP_GBM8_LacZ

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

country: USA

institute: Brigham and Women's Hospital

data_processing:
library strategy: ChiRP-Seq
Fastqsanger files were mapped to hg19 genome using bowtie2 (default settings)
bigwigs were generated with BamCoverage function from deeptools 3.5.0
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Glioma Stem Cells

extract_protocol:
Monarch PCR and DNA Clean Up Kit (#T1030L, NEB)
Illumina NGS libraries were prepared using the NEBNext Ultra II DNA Kit (NEB, E7645S)

tag: biotinylated oligos

value: LacZ non-human

value: untreated

value: Glioma Stem Cells


title: ChiRP_GBM6_LacZ


title: ChiRP_NHA_HOXDeRNA_activated_siRNA_Control_LacZ

source_name: Immortalized human astrocytes (Sanoda 2001)

value: treated with CRISPRa system with sgRNAs for HOXDeRNA activation for 14 days followed by siRNA treatmant


title: ChiRP_GBM4_LacZ


title: ChiRP_NHA_HOXDeRNA_activated_siRNA_EZH2_LacZ

value: Immortalized human astrocytes (Sanoda 2001)


title: PCW20 [scRNAseq]

description: 10x Genomics

value: 20 post-conceptional weeks


title: 7D,RNAseq,dKO,rep1

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

description: Bulk RNA-seq

data_processing:
The raw data were qualitatively controlled using Fast QC (version 0.11.9), followed by fastp (version 0.23.2) to remove the linker and low-quality reads
Then paired-end clean reads were mapped to the mouse reference genome (mm10)
For CUT&Tag,peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.005,  To create CUT&Tag coverage plots, the locations of the mapped CUT&Tag reads were converted to the bigWig file format by bamCoverage with CPM(Counts Per Million mapped reads),bw files were generated using the deeptools software. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.Peak annotation with homer.
For transcriptome, the mapping files containing the reads matching the mouse genome were used RSEM to calculate gene and transcript expression values, and raw read counts.  We used the DESeq2 R package to analyze the differential expression between the control group and the experimental group, fold change>=2 and qvalue<=0.05. They are thought to be differentially expressed genes. In order to obtain an informative functional interpretation of the differential expression analysis, the DAVID database was used.
Signal tracks were visualized by Integrative Genomics Viewer (IGV)
Assembly: mm10
Supplementary files format and content: bw, narrowPeak or bw, txt

source_name: Mouse testis

extract_protocol:
We used WT and Prmt1 conditional knockout samples for all the experiments through tamoxifen injection for 3 days. For WT CUT&Tag we used C57BL/6J; single cell were were isolated from testis. Further proceeded for library preparation using KIT manual. For RNA-seq we isolated total RNA from testis and for smart-seq2 we used isolted spermatogonia for downstream procedure and library preparation.
CUT&Tag libraries were prepared using Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen)

value: Mouse testis

value: Spermatogonia

tag: cell subtype

value: Germ cell

value: Prmt1 dKO


title: 7D,RNAseq,dKO,rep2

description: Bulk RNA-seq


title: ChiRP_NHA_HOXDeRNA_activated_siRNA_EZH2_Input


title: ChiRP_GBM8_Input


title: 7D,RNAseq,dKO,rep3

description: Bulk RNA-seq


title: C2C12 scramble (control) 1

value: control


title: 7D,RNAseq,WT,rep3

description: Bulk RNA-seq

value: WT


title: C2C12 HTT KO 1

value: HTT KO


title: 7D,RNAseq,WT,rep2

description: Bulk RNA-seq


title: ChiRP_GBM4_Input


title: 7D,RNAseq,WT,rep1

description: Bulk RNA-seq


title: ChIRP_NHA_HOXDeRNA_activated_siRNA_EZH2_rep2

source_name: Immortalized human astrocytes (Sonoda 2001)

value: HOXDeRNA premature


title: 7D,smartseq2,dKO,rep2


title: ChIRP_NHA_HOXDeRNA_activated_siRNA_EZH2_rep1

value: Immortalized human astrocytes (Sonoda 2001)


title: 7D,smartseq2,WT,rep2


title: ChiRP_NHA_HOXDeRNA_activated_siRNA_Control_rep2


title: ChIRP_NHA_HOXDeRNA_activated_siRNA_Control_rep1


title: 7D,smartseq2,WT,rep1


title: ChiRP_GBM8_rep2


title: Patient 9_TCR

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
10x Genomics
P9_TCR

data_processing:
The demultiplexing, barcoded processing, TCR gene counting were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: *all_contig_annotations.csv: Comma-separated text files.
Supplementary files format and content: *scTCR_seurat_object.rds: Seurat RDS files.
Library strategy: scTCR-seq

source_name: kidney and blood

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

value: T cells

value: kidney and blood

tag: diagnosis

value: ANCA-GN

tag: sample id


title: 7D,smartseq2,dKO,rep1


title: ChiRP_NHA_HOXDeRNA_activated_siRNA_Control_Input


title: 14D,Spermatogonia,H4R3me2s,WT,rep3

description: CUT&Tag

data_processing:
The raw data were qualitatively controlled using Fast QC (version 0.11.9), followed by fastp (version 0.23.2) to remove the linker and low-quality reads
Then paired-end clean reads were mapped to the mouse reference genome (mm10)
For CUT&Tag,peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.005,  To create CUT&Tag coverage plots, the locations of the mapped CUT&Tag reads were converted to the bigWig file format by bamCoverage with CPM(Counts Per Million mapped reads),bw files were generated using the deeptools software. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.Peak annotation with homer.
For transcriptome, the mapping files containing the reads matching the mouse genome were used RSEM to calculate gene and transcript expression values, and raw read counts.  We used the DESeq2 R package to analyze the differential expression between the control group and the experimental group, fold change>=2 and qvalue<=0.05. They are thought to be differentially expressed genes. In order to obtain an informative functional interpretation of the differential expression analysis, the DAVID database was used.
Signal tracks were visualized by Integrative Genomics Viewer (IGV)
Assembly: mm10
Supplementary files format and content: bw, narrowPeak or bw, txt
Library strategy: CUT&TAG

value: Spermatocyte


title: ChiRP_GBM6_Input

value: untreated

value: Glioma Stem Cells


title: ChiRP_GBM8_rep1


title: 14D,Spermatogonia,H3K4me3,WT,rep2

description: CUT&Tag


title: Patient 4_TCR

description:
10x Genomics
P4_TCR


title: 14D,Spermatogonia,H4R3me2s,WT,rep1

description: CUT&Tag


title: Patient 6_TCR

description:
10x Genomics
P6_TCR


title: Patient 8_TCR

description:
10x Genomics
P8_TCR


title: NHA_HOXDeRNA_activated_EZH2_rep2

data_processing:
Fastqsanger files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 with default parameters
PCR duplicates were removed using samtools rmdup version 1.13
resulting aligned Bam files were transformed to Bigwig format without scaling or normalization using deeptools version 3.5.0
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Immortalized astrocytes were maintained in serum‐free Neurobasal media supplemented with N-2 and B-27 Plus Supplements (Gibco™), 3 mM of Gibco® GlutaMAX™ Supplement, 50 units/ml of penicillin and 50 units/ml of streptomycin (Gibco™), 2 μg/ml of heparin (Sigma‐Aldrich), 20 ng/ml of FGF2 (Sigma-Aldrich), and 20 ng/ml of EGF (Sigma-Aldrich). The cells were passaged by dissociation using Neurocult Stem Cells reagent

extract_protocol:
ChIP-Seq was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003. DNA was purified using the Monarch PCR and DNA Clean Up Kit (#T1030L, NEB)
Libraries were prepared according to Illumina's instructions accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7546S, NEB).

tag: chip antibody

value: EZH2 (Cat. 39002, Active Motif)

value: treated with CRISPRa system with sgRNAs for HOXDeRNA activation for 14 days

value: Immortalized human astrocytes (Sanoda 2001)


title: ChiRP_GBM6_rep1


title: 14D,Spermatogonia,H3K27ac,WT,rep1

description: CUT&Tag

value: Mouse testis


title: 14D,Spermatogonia,H3K27ac,WT,rep2

description: CUT&Tag

value: Germ cell


title: 14D,Spermatogonia,H3K4me3,WT,rep1

description: CUT&Tag


title: ChiRP_GBM4_rep2


title: Patient 2_TCR

description:
10x Genomics
P2_TCR


title: ChiRP_GBM6_rep2


title: Patient 3_TCR

description:
10x Genomics
P3_TCR


title: ChiRP_GBM4_rep1


title: NHA_HOXDeRNA_activated_EZH2_rep1


title: Patient 1_TCR

description:
10x Genomics
P1_TCR


title: NHA_Control_EZH2_rep2

value: treated with CRISPRa system with Control sgRNAs for 14 days


title: 14D,Spermatogonia,H4R3me1,WT,rep2

description: CUT&Tag


title: NHA_Control_EZH2_rep1


title: 14D,Spermatogonia,H3R8me2a,WT,rep2

description: CUT&Tag


title: Control 5B_TCR

description:
10x Genomics
C5B_TCR

source_name: blood

value: blood

value: healthy


title: 14D,Spermatogonia,H4R3me2s,WT,rep2

description: CUT&Tag

value: WT


title: Patient 7_TCR

description:
10x Genomics
P7_TCR


title: NHA_HOXDeRNA_activated_H3K27Me3_rep2

value: H3K27Me3 (#9733, Cell Signaling)


title: Patient 5_TCR

description:
10x Genomics
P5_TCR


title: 14D,Spermatogonia,H3R8me2a,WT,rep1

description: CUT&Tag


title: Control 4K_TCR

description:
10x Genomics
C4K_TCR

source_name: kidney

value: kidney


title: Control 4B_TCR

description:
10x Genomics
C4B_TCR

value: T cells


title: NHA_HOXDeRNA_activated_H3K27Me3_rep1


title: Control 3K_TCR

description:
10x Genomics
C3K_TCR


title: 14D,Spermatogonia,H4R3me1,WT,rep1

description: CUT&Tag


title: Control 3B_TCR

description:
10x Genomics
C3B_TCR


title: Control 2_TCR

description:
10x Genomics
C2_TCR

value: kidney and blood


title: 14D,Spermatogonia,H3R2me2a,WT,rep1

description: CUT&Tag


title: NHA_HOXDeRNA_activated_H3K27Ac_rep2

value: H3K27Ac (#4353, Cell Signaling)


title: Control 1_TCR

description:
10x Genomics
C1_TCR


title: Control 5K_TCR

description:
10x Genomics
C5K_TCR


title: NHA_Control_H3K27Ac_rep2


title: 14D,Spermatogonia,H4R3me2a,WT,rep2

description: CUT&Tag

value: Spermatocyte


title: NHA_Control_H3K27Me3_rep2


title: 14D,Spermatogonia,H4R3me2a,WT,rep3

description: CUT&Tag


title: NHA_Control_H3K27Ac_rep1


title: NHA_Control_H3K27Me3_rep1


title: NHA_HOXDeRNA_activated_H3K27Ac_rep1


title: 7D,Spermatogonia,H4R3me2s,dKO,rep1

description: CUT&Tag

value: Spermatogonia

value: Prmt1 dKO


title: NHA_HOXDeRNA_activated_RNAseq_rep3

data_processing:
Fastqsanger files were trimmed to remove Illumina adapters with Trimmomatic (version 0.39)
and aligned to the GRCh37/hg19 genome using HISAT 2.2.1 with the annotation Homo_sapiens.GRCh37.75.gtf (hg19)
bigwigs were generated with BamCoverage function from deeptools 3.5.0
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was isolated with Norgen Biotek kit followed by treatment with DNAse I (Promega) at 37°C for 30 minutes.
Purified total RNA was delivered to Novogene for mRNA library preparation


title: 7D,Spermatogonia,H4R3me2s,WT,rep2

description: CUT&Tag


title: 7D,Spermatogonia,H3K4me3,WT,rep2

description: CUT&Tag


title: NHA_HOXDeRNA_activated_RNAseq_rep2


title: 7D,Spermatogonia,H4R3me2s,WT,rep1

description: CUT&Tag


title: NHA_HOXDeRNA_activated_RNAseq_rep1


title: NHA_Control_RNAseq_rep3


title: 14D,Spermatogonia,H3R2me2a,WT,rep2

description: CUT&Tag


title: 7D,Spermatogonia,H3K4me3,WT,rep1

description: CUT&Tag


title: NHA_Control_RNAseq_rep2


title: 7D,Spermatogonia,H3K27ac,WT,rep2

description: CUT&Tag


title: NHA_Control_RNAseq_rep1


title: 7D,Spermatogonia,H3K27ac,WT,rep1

description: CUT&Tag


title: 7D,Spermatogonia,H4R3me2s,dKO,rep2

description: CUT&Tag


title: fHA_RNAseq_rep3

source_name: fetal human astrocytes

value: fetal human astrocytes

value: untreated


title: fHA_RNAseq_rep2


title: 13-520

city: St. Louis

first: Saravanan

last: Raju

state: MO

address: 660 S Euclid Avenue

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: hdf5 files

source_name: Blood

extract_protocol:
PBMCs were thawed and subject to non-naïve B cell enrichment by magnetic cell selection. Cells were directly submitted for processing on a 10x Chromium instrument.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: B cells

value: Blood

value: Adult


title: 7D,Spermatogonia,H4R3me1,WT,rep1

description: CUT&Tag

value: Mouse testis

value: Germ cell


title: 7D,Spermatogonia,H4R3me1,WT,rep2

description: CUT&Tag


title: 13-506

description: 10x Genomics


title: fHA_RNAseq_rep1


title: 13-516

description: 10x Genomics


title: 7D,Spermatogonia,H3R2me2a,WT,rep2

description: CUT&Tag


title: 7D,Spermatogonia,H3R8me2a,WT,rep1

description: CUT&Tag


title: 7D,Spermatogonia,H3R2me2a,WT,rep1

description: CUT&Tag


title: 7D,Spermatogonia,H3R8me2a,WT,rep2

description: CUT&Tag


title: 501558 Melanoma Atezo

city: Durham

first: Rikhia

last: Chakraborty

state: North Carolina

address: 801 Capitola Drive, Suite 12

institute: Xilis, Inc.

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expressions between the different groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes (DEGs) for each comparison.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-delimited text files include hit counts for each sample

source_name: Melanoma

extract_protocol:
Samples were washed with PBS and centrifuged at 500 g for 5 minutes. They were then resuspended in 100 µl Arcturus PicoPure RNA Extraction Buffer (Applied Biosystems) and stored at –80ºC. RNA was isolated using Arcturus PicoPure RNA Isolation Kit as per manufacturer’s protocol.
Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera™ XT kit and analyzed for concentration (Qubit DNA assay and NanoDrop; Thermo Fisher Scientific), size distribution (Agilent® Bioanalyzer) and quantification of viable sequencing templates via qPCR. Sequencing was performed on the Illumina HiSeq 2500 in Rapid Run Mode with 2x150 bp paired-end configuration.

treatment_protocol: After 5 to 7 days of culture, MOS generated from matched skin and tumor biopsies from 2 melanoma patients were dispensed to 3 wells on a flat-bottom 96-well plate. The MOS suspension was mixed gently with a wide bore pipette and 20 µl of MOS suspension was dispensed to each well of PBS and mixed well. The number of MOS in each well was counted and the average concentration of MOS/µl was calculated. The desired volume of MOS suspension was transferred to a new centrifuge tube and spun at 300 g for 5 minutes. The supernatant was removed, and the MOS were resuspend in the appropriate culture media at a concentration of 100 MOS/50 µL. The desired number of MOS was added to each well of a non-TC treated 96- or 24-well plate. All MOS handling steps were completed using a wide bore pipette. MOS was then treated with either atezolizumab (350 µg/ml), or immunoglobulin G4 (10 µg/ml) for 120 hours. PBS was added to empty wells to prevent evaporation. Post-treatment droplets were collected in 1.5 ml tubes and centrifuged at 500 g for 5 minutes. Supernatant was removed. Samples were resuspended in Cell Recovery Solution (Corning) and incubated at room temperature for 10 minutes to remove matrigel matrix remaining after drug treatment.

value: Melanoma

tag: sample type

value: MOS

value: Unknown

value: Atezolizumab

tag: clinical response

value: resistant


title: 501559 Skin Atezo

source_name: Skin

value: Skin


title: 7D,Spermatogonia,H4R3me2a,WT,rep3

description: CUT&Tag

value: WT


title: 501894 Melanoma Atezo

value: hospice, no treatment


title: SW480 cells, siTIP60-11, replicate 3

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

country: Japan

institute: The University of Tokyo

description: 1 × 60 bp SE

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.33).
Trimmed sequence reads were aligned to human genome (hg38) using STAR aligner (v2.7.3a).
Raw gene counts from the read alignments were obtained using RSEM (v1.3.3).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

source_name: Colon

growth_protocol: HCT116 and SW480 cells were maintained in McCoy's 5A Modified Medium and Leibovitz's L-15 Medium, respectively, supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
RNA was extracted from the cells using RNeasy Plus Mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's instructions.

treatment_protocol: The cells were transfected with 10 nM of siRNA using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and harvested after 48 hours of incubation.

value: Colon

value: Colorectal cancer

value: TIP60-11 siRNA


title: 14D,Spermatogonia,H4R3me2a,WT,rep1

description: CUT&Tag

value: Spermatocyte


title: 7D,Spermatogonia,H4R3me2a,WT,rep1

description: CUT&Tag

value: Spermatogonia


title: SW480 cells, siTIP60-11, replicate 2

description: 1 × 60 bp SE


title: 7D,Spermatogonia,H4R3me2a,WT,rep2

description: CUT&Tag


title: SW480 cells, siTIP60-2, replicate 1

description: 1 × 60 bp SE

value: TIP60-2 siRNA


title: SW480 cells, siTIP60-2, replicate 2

description: 1 × 60 bp SE


title: SW480 cells, siTIP60-2, replicate 3

description: 1 × 60 bp SE


title: SW480 cells, siTIP60-11, replicate 1

description: 1 × 60 bp SE


title: SW480 cells, siBRD8-36, replicate 3

description: 1 × 60 bp SE

value: BRD8-36 siRNA


title: SW480 cells, siBRD8-36, replicate 2

description: 1 × 60 bp SE


title: 501895 Skin Atezo


title: SW480 cells, siControl, replicate 3

description: 1 × 60 bp SE

value: Control siRNA


title: SW480 cells, siBRD8-6, replicate 2

description: 1 × 60 bp SE

value: BRD8-6 siRNA


title: SW480 cells, siControl, replicate 2

description: 1 × 60 bp SE


title: SW480 cells, siBRD8-6, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siTIP60-11, replicate 1

description: 1 × 60 bp SE


title: HCT116 cells, siTIP60-2, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siTIP60-11, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siTIP60-11, replicate 2

description: 1 × 60 bp SE


title: HCT116 cells, siBRD8-36, replicate 2

description: 1 × 60 bp SE


title: HCT116 cells, siBRD8-6, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siControl, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siBRD8-36, replicate 1

description: 1 × 60 bp SE


title: Daoy_shDDX3X_2

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon miR-592 expression.
Assembly: GRCh37-hg19
Supplementary files format and content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

source_name: Medulloblastoma cell line

growth_protocol: Daoy and its polyclonal populations expressing DDX3X shRNA in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Librarieswere prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq 2500 platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of shRNA expression and exogenous wild type or mutant DDX3X expression

value: Daoy

value: Medulloblastoma cell line

value: shRNA targeting open reading frame of DDX3X expressing Daoy cells


title: HCT116 cells, siBRD8-6, replicate 1

description: 1 × 60 bp SE


title: HCT116 cells, siControl, replicate 2

description: 1 × 60 bp SE


title: HCT116 cells, siTIP60-2, replicate 1

description: 1 × 60 bp SE


title: Daoy_shDDX3X_1

value: shRNA targeting 3'-UTR of DDX3X expressing Daoy cells


title: Daoy_parental_WT1

value: parental Daoy cell line


title: ALI culture, IL4 treated, donor 3, scRNAseq

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

data_processing:
De-multiplexing and alignment to the hg38 human genome, identification of unique molecular identifiers (UMI) and barcode filtering were performed using the ‘CellRanger’ toolkit (version 3.1.0) provided by 10X Genomics.
Then, we considered only cells with at least 200 expressed genes and a total UMI count above 500, where a gene is counted as expressed if we found at least one UMI mapped to it.
We further filtered out cells that had 20% or more of their gene counts mapped to mitochondrial genes, since higher percentages indicate stressed or dying cells.
We did not apply a maximum library size filter. Then, we applied scrublet (version 0.2.3) to determine potential doublets in each sample and filtered out all cells with a doublet score above 0.2. Finally, we filtered out all genes that were expressed in less than 10 cells.
To compute scran size factors, we first divided cells from all samples by library size with the median of total UMI count per cell (pp.normalize_total in scanpy) and subsequently scaled with log+1.
Then, we computed a PCA with 50 principal components and used the PCA space to compute the 30 nearest neighbors (pp.neighbors in scanpy).
We then clustered with the Louvain algorithm at resolution 0.5, computed size factors using scran to scale the count matrix and scaled the result with log+1.
We then computed the 3,000 most highly variable genes based on mean and dispersion (pp.highly_variable_genes in scanpy with the flavor ‘cell_ranger’ to compute normalized dispersions), thereby accounting for differences across batches.
To correct for batch effects, we scaled the normalized gene expression matrix to mean 0 and variance 1 for each gene and applied Scanorama v. 1.7 using the embedding output.
To compute cell density per condition (Fig. 2D), we used the tl.density_embedding function in scanpy using a Gaussian kernel estimate.
Further, we computed the k-nearest neighbor graph with k=30 on the embedding output and used a UMAP to represent the data in a two-dimensional embedding and data visualization (tl.umap).
We used scanpy v. 1.5.1 in Python 3.8.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Upper bronchial airways

growth_protocol: 3D-air-liquid interface cultures were grown from low passage primary human bronchial epithelial cells (NHBE, Lonza, Walkersville, MD) cells in PneumaCult-Ex Plus expansion medium (Stemcell Technologies, Cologne, Germany) according to the manufacturer’s instructions.

extract_protocol:
NHBEs were purchased from Lonza
Chromium Next GEM Single Cell 5ʹ Library Kit v1.1 (10x Genomics)

treatment_protocol: When epithelial cultures generated a dense epithelial tissue-like structure displaying a TEER-value of 600 V/OHM, hydrocortisone was withdrawn from the supplements, and the organoid cultures were stimulated with or without the addition of 50 ng/ml IL-4 (R&D Systems, Minneapolis, MN). Medium with fresh IL-4 was exchanged every other day. The culture of NHBE show donor dependent differences, however, after day 21 at the earliest, a TEER of >700 V/OHM was used as threshold for harvesting completely differentiated organoid cultures. The cultures were subsequently subjected to single-cell RNA sequencing

value: Airway epithelium

value: Upper bronchial airways

tag: condition

value: grass pollen-allergic


title: HCT116 cells, siTIP60-2, replicate 2

description: 1 × 60 bp SE

value: Colon


title: SW480 cells, siBRD8-36, replicate 1

description: 1 × 60 bp SE

value: Colorectal cancer


title: ALI culture, medium, donor 3, scRNAseq

description: Chromium Next GEM Single Cell 5ʹ Library Kit v1.1 (10x Genomics)


title: SW480 cells, siBRD8-6, replicate 1

description: 1 × 60 bp SE


title: ALI culture, IL4 treated, donor 2, scRNAseq


title: HCT116 cells, siControl, replicate 1

description: 1 × 60 bp SE


title: ALI culture, medium, donor 2, scRNAseq


title: SW480 cells, siControl, replicate 1

description: 1 × 60 bp SE


title: ALI culture, IL4 treated, donor 1, scRNAseq


title: ALI culture, medium, donor 1, scRNAseq


title: HCT116 cells, siBRD8-36, replicate 3

description: 1 × 60 bp SE


title: HCT116 cells, siBRD8-6, replicate 2

description: 1 × 60 bp SE


title: M059J CRISPR ATRX KO_rep 2

first: David

middle: M

last: Ashley

state: NC

address: 203 Research Dr, MSRB1

department: Neurosurgery

institute: Duke University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis- match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: M059J cells were obtained from ATCC (Manassas, VA). Cells were maintained in DMEM/F12 medium containing 2.5mM L-glutamine, 15mM HEPES, 0.5mM sodium pyruvate, 1.2g/L sodium bicarbonate and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted from monolayer cell cultures using miRNeasy Mini kit (Qiagen, Germantown, MD). 100ng of RNA was used for cDNA prep and construction of sequencing libraries.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatment

value: Glioma

value: ATRX KO


title: M059J CRISPR ATRX KO_rep 3


title: M059J CRISPR ATRX KO_rep 1


title: vThO-Day112

city: New Haven

first: In-Hyun

last: Park

state: CT

address: 10 AMISTAD ST # 201B

department: Genetics

institute: Yale University

description: 10 Genomics

data_processing:
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
Assembly: hg19
Supplementary files format and content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: Ventral thalamic organoid

extract_protocol: Library was constructed by the manufacter's protocol (Chromium reagent 3' v2, 10X Genomics)

value: Ventral thalamic organoid

value: H1 hESCs

value: 112 days

value: 100ng/ml SHH at day14-22


title: M059J CRISPR control_rep 1

value: ATRX WT


title: M059J CRISPR control_rep 2


title: vThO-Day36

description: 10 Genomics


title: M059J CRISPR control_rep 3


title: ThO-Day36

description: 10 Genomics

source_name: Thalamic organoid

value: Thalamic organoid

value: 36 days


title: Mouse crescentic glomerulonephritis TCR

description:
10x Genomics
cGN_TCR

value: T cells

value: kidney

value: crescentic glomerulonephritis

value: cGN

tag: strain


title: NoCKN_6h-rep3

city: Research Triangle Park

first: Sara

middle: A

last: Grimm

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Reads were mapped to the mm10 reference genome via STAR v2.5 with parameters "--outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Subread featureCounts v1.5.0-p1 used to collect counts per gene with parameter "-s2" using NCBI Curated RefSeq gene models as downloaded from the UCSC Table Browser timestamped January 10 2020.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM", then converted to bigWig format with UCSC utility bedGraphToBigWig.
DEGs identified via DESeq2 v1.28.1 at FDR 0.05.
Assembly: mm10
Supplementary files format and content: counts per gene per sample in tab-delimited text format
Supplementary files format and content: DEG list in tab-delimited text fomat
Supplementary files format and content: normalized depth tracks in bigWig format

source_name: spleen and skin-draining LNs

extract_protocol:
RNA was isolated via NucleoSpin RNA XS kit (Takara Bio) following the manufacturer's instruction.
Libraries were constructed via Illumina TruSeq RNA sample prep kit.

tag: Sex

value: male

value: spleen and skin-draining LNs

value: MACS-purified naive CD4+ T cells

value: anti-CD3 and -CD28


title: CCL19_6h-rep2

tag: tissue

value: anti-CD3 and -CD28 + rCCL19


title: NoCKN_6h-rep2


title: CCL19_6h-rep3


title: NoCKN_6h-rep1


title: CCL19_6h-rep1


title: RPE-ICRF193-RAD21-1

city: Berlin

first: Maria

last: Valieva

address: Ihnestraße 63

institute: MPIMG

data_processing:
Single-end reads from ChIP-seq experiments were mapped with bowtie (v2.2.6) to the reference genome hg19.
Mapped reads were filtered for mapping quality MAPQ ≥10, and duplicates were removed using samtools (v1.8).
Reads were extended to 200bp and scaled by the total number of unique reads (total count of reads/106) to produce coverage tracks that could be visualized in UCSC. Tracks were reformatted in the bigWig file
Assembly: hg19
Supplementary files format and content: bigWig (except for Input sample)

growth_protocol: RPE1 cells were grown in DMEM, supplemented with 10% FCS and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor
For the ChIP-seq library preparation we have followed Illumina's TruSeq Chip Sample Preparation Guide including NextFlex UDIs.  have followed Illumina's TruSeq Chip Sample Preparation Guide including NextFlex UDIs.

treatment_protocol: Cells were treated with 1) DMSO for 18h 2) doxorubicin, for 18h with two final concentrations: either 340 uM 3 or 200 uM 3) ICRF193 for 18h with a final concentration 5uM

value: Human retinal pigment epithelial

value: Abcam; ab992; lot GR221348-8; dilution 1:150


title: RPE-ICRF193-RAD21-2


title: RPE-ICRF193-CTCF-1

value: Active Motif; 613111; lot 34614003; dilution 1:150


title: RPE-DOX034-RAD21-1


title: RPE-ICRF193-CTCF-2


title: RPE-DOX034-CTCF-1


title: RPE-DOX034-CTCF-2


title: RPE-DOX02-RAD21-2


title: RPE-DOX02-CTCF-2


title: Asxl2KO-H2AK119ub1

city: Tianjin

first: Rui

last: Li

state: Tianjin

address: Qixiangtai Road No.22

department: Department of Cell Biology, School of Basic Medical Sciences

institute: Tianjin Medical University

data_processing:
ChIP-seq datasets were performed using the AQUAS processing pipeline
ChIP-seq clean reads were aligned to the mouse reference genome assembly GRCm38 (mm10), and only unique mapped reads were used for subsequent analysis.
Peaks for histone modifications were called using MACS2, while peaks for polycomb group proteins were called using SPP.
Assembly: mm10

growth_protocol: Mouse ESC culture and the generation of Asxl2KO ESCs through CRISPR/Cas9 technique were performed as previously described. Briefly, proper amounts of ESCs were seeded on 0.1% gelatin-coated plates in GMEM medium (Gibco) supplemented with 15% FBS, 2 mM L-glutamine, 1×Penicillin/Streptomycin, 1×non-essential amino acids, 0.5 mM β-mercaptoethanol, and 100 U/ml leukemia inhibitory factor. To delete Asxl2, the specific sgRNA was designed to target Exon 5 of mouse Asxl2 and cloned into pX458 vector (Addgene #48138).

extract_protocol:
Chromatin preparation was performed as previously described. First, 2×107 cells were crosslinked with 1% formaldehyde for 10 min at room temperature (RT) and then quenched with 0.125 M glycine for another 5 min. Then cells were washed with ice cold PBS and lysed in SDS Buffer (100 mM NaCl, 50 mM Tris-Cl pH8.1, 5 mM EDTA pH 8.0, 0.5% SDS, 1×Protease inhibitor cocktail (PIC)). After spinning, Nuceli were resuspended in appropriate volume of ice-cold IP Buffer (100 mM NaCl, 50 mM Tris-Cl pH8.1, 5 mM EDTA pH 8.0, 0.3% SDS, 1.0% Triton X-100) for sonication using a BioRuptor sonicator (Diagenode). After centrifugation at 16,000 ×g for 20 min at 4°C, the fragmented chromatin was divided into different aliquots that were incubated overnight at 4°C with primary antibodies (RING1B CST 5694s, SUZ12 CST 3737S, RYBP MILLIPORE AB3637). Next, 30 μl protein G magnetic beads were incubated with the reaction for another 3 hrs at 4°C. Then beads were washed 3 times with high salt buffer (1% Triton X-100, 0.1% SDS, 500 mM NaCl, 2 mM EDTA, pH 8.0, 20 mM Tris-HCl, pH 8.0). After reversal of the crosslinking, ChIP DNA was purified for qPCR analysis or library preparation.WT or Asxl2KO cells were washed twice in wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1×Protease inhibitor cocktail). Meanwhile Concanavalin A beads (Bangs Laboratories, BP531) were activated by washing twice in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM MnCl2, 1mM CaCl2), followed by mixing with the cells at RT for 15min. The supernatant was then removed and beads were resuspended in 100 μL antibody buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1×PIC; 0.05% Digitonin 2 mM EDTA and 30% BSA). Then 1 μg H2AK119ub1 antibody was added and incubated overnight at 4 ℃. On the next morning, the supernant containing primary antibody was removed and the beads were incubated in 100 μL of Dig-Wash buffer (20 mM HEPES pH 7.5,150 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 1×PIC) containing the secondary antibody at RT for 1 hr. Then the pellets were washed in 800 μl Dig-wash Buffer for 3 times. Meanwhile 1:200 dilution of pA-Tn5 adapter complex (~0.04 μM) was prepared in Dig-300 Buffer (0.05% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine,1×PIC). Then the beads were incubated with pA-Tn5 at RT for another 1 hr. After 3 times washing by Dig-300 Buffer, the pellets were resuspended in 50 μL Tagmentation buffer (10mM MgCl2 in Dig-300 Buffer) and incubated at 37 °C for 1 hr. Then Stop buffer (2.25 μL of 0.5 M EDTA, 2.75 μL of 10% SDS and 0.5 μL of 20 mg/mL Proteinase K) was added and incubated at 50 °C for 1 hr. To extract DNA from the reaction, 300 μl hydroxybenzene-chloroform-Isoamyl alcohol were added, thoroughly mixed and centrifuged for 5 min at 16,000 g. The aqueous phase was collected and mixed with 300 μl chloroform. After centrifuging for another 5 min at 16000 g, aqueous phase was then mixed with 750 μl ethanol overnight at 4℃. The samples were centrifuged for 15 min at 16000 g at 4℃. After being washed twice in 1 mL 80% ethanol, the DNA was resuspended in 22 μL TE buffer and used for library amplification (Vazyme).
Libraries for both ChIP and Input samples were prepared using TD503 Kit (Vazyme) according to the manufacturer’s instruction. The successfully prepared libraries were sequenced as 150 bp paired-end reads on Illumina NovaSeq 6000 platform.

treatment_protocol: untreatment

value: mouse embryonic stem cells

tag: antibody


title: RPE-DOX02-RAD21-1

tag: cell line


title: ThO-Day112

description: 10 Genomics

value: H1 hESCs

tag: age

value: 100ng/ml SHH at day14-22


title: WT-H2AK119ub1

tag: cell type

tag: genotype

value: WT


title: RPE-DOX02-CTCF-1

tag: treatment


title: RPE-DMSO-RAD21-2

value: DMSO


title: RPE-DMSO-RAD21-3


title: RPE-DMSO-CTCF-2


title: RPE-DMSO-CTCF-3


title: RPE-DMSO-RAD21-1


title: RPE-DMSO-CTCF-1


title: RPE-ICRF193 5uM

data_processing:
FASTQ files were processed using the Juicer pipeline v1.5.6, CPU version, which was set up with BWA v0.7.17 to map short reads to reference genome hg19, from which haplotype sequences were removed and to which the sequence of Epstein–Stein–Barr Virus (NC_007605.1) was added.
Replicates were processed individually. Mapped and filtered reads were merged afterwards. A threshold of MAPQ ≥ 30 was applied for the generation of Hi-C maps with Juicer tools v1.7.5
Assembly: hg19
Supplementary files format and content: .hic

extract_protocol:
cells were washed twice with PBS and digested with Trypsin–EDTA 0.05% (Gibco) for 10 min at 37 °C. A 40-µm cell strainer was used to obtain single cells. The cell suspension was pelleted at 300g for 5 min and resuspended with cold 10% FCS. Subsequently, the cells were fixed by adding an equal volume of 4% formaldehyde (Sigma-Aldrich). The suspension was mixed for 10 min while shaking at room temperature in 50 ml tubes. Exactly after 10 min the fixation was quenched with 500 µl 1.425 M glycine (Merck) on ice. The suspension was pelleted at 400g for 8 min and resuspended in cold lysis buffer (50 mM Tris, pH 7.5; 150 mM NaCl; 5 mM EDTA; 0.5% NP-40; 1.15% Triton X-100; protease inhibitors (Roche)). Next we followed Hi-C protocol.
Universal sequencing adaptor were added using the NEBnext Ultra DNA Library Kit (NEB) according to the supplier’s recommendation. The PCR cycle number was adjusted to 4–12 based on the initial DNA concentration. The final libraries were purified using AMPure Beads (Beckman Coulter) and samples were sequenced with Ilumina Hi-Seq technology according to the standard protocols.

treatment_protocol: Cells were treated for 18h with one of the reagents 1) DMSO, 2) ICRF193  in final concentration 5uM or doxorubicin in final concentration 3) 200 nM and 4) 340 nM.

value: ICRF193 5 uM

tag: time


title: RPE-doxorubicin 02uM

value: doxorubicin 0.2 uM


title: RPE-DMSO


title: RPE-doxorubicin 034uM

value: doxorubicin 0.34 uM


title: CT2A CRISPR ATRX KO clone KO-B_rep 2

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis- match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: CT2A cells were a kind gift of Peter Fecci (Duke University Medical Center, Durham NC). Cells were maintained in DMEM (high glucose) containing 10% FBS.

value: Glioma

value: ATRX KO


title: CT2A CRISPR control_rep 1

value: ATRX WT


title: CT2A CRISPR ATRX KO clone KO-C_rep 1


title: CT2A CRISPR ATRX KO clone KO-B_rep 1


title: CT2A CRISPR ATRX KO clone KO-A_rep 2


title: CT2A CRISPR ATRX KO clone KO-C_rep 2


title: CT2A CRISPR ATRX KO clone KO-A_rep 1


title: CT2A CRISPR control_rep 2


title: Donor_5_Macula

first: Taku

last: Tanaka

address: 2-10-1 Okura, Setagaya

department: Ophthalmology

institute: National Center for Child Health and Development

hyb_protocol: 0.6 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Human Gene Expression Microarrays 8 × 60 K v2 (Agilent Technologies) for 17 hours at 65°C in a hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C with Gene Expression Wash Buffer 2 (Agilent Technologies), then air-dried immediately.

scan_protocol: Slides were scanned on an Agilent G2505C microarray scanner at 100% PMT and 3 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalized signal intensity (75th percentile shift normalized) calculated from the processed signal after Feature Extraction using the GeneSpring software version 12.1 (Agilent).

source_name: donor5, retina, macula region

label_protocol: Total RNAs (50 ng) extracted from the macular and peripheral regions of retina were used to prepare Cy3-labelled target cRNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) followed by RNeasy column purification (QIAGEN).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) in accordance with the manufacturer’s instructions. The concentration and purity of the isolated RNA was evaluated using a NanoDrop LITE (Thermo Fisher Scientific, Waltham, MA, USA). The integrity of the RNA samples was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Donor eyes were obtained from 6 patients (age 1-17 months) with retinoblastoma and peters anomaly after enucleation. The tumor-free neural retina was immediately dissociated from the eye with forceps and surgical scissors. The macula region and peripheral retina were dissected from the neural retina using forceps and scissors and directly transferred to a tube containing RNA extraction solution.

tag: disease

value: peters anomaly

value: retina

tag: gender

value: male

tag: age in month


title: CT2A Parental_rep 2


title: HSAPN3

city: Beijing

first: yanru

last: duan

state: Beijing

address: Beijing, Chaoyang

institute: Capital Medical University

data_processing:
Illumina  software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using HiSeq 4000 and paired-end clean reads were aligned to the reference genome using HiSeq 4000.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: aorta

extract_protocol:
The total RNA was isolated from mouse aortic tissue by TRIzol method (Invitrogen).
The mRNA Library was generated by NEB Next Ultra Directional RNA Library Prep Kit for Illumina (#E7530L, NEB, Ispawich, USA) according to the ' 'manufacturer's protocol.

treatment_protocol: The mice were randomized to feed a high-fat diet (HFD) (60% kcal fat, D12492i; Research Diets Inc.) or a standard diet control (ND, D12450Bi) for 12 weeks to induce 2 type diabetes

value: aorta

value: APPL1 knockdown

value: High-fat feeding


title: Donor_6_Periphery

source_name: donor6, retina, peripheral region


title: Donor_4_Macula

source_name: donor4, retina, macula region

value: female


title: CT2A Parental_rep 1


title: Donor_4_Periphery

source_name: donor4, retina, peripheral region


title: HSAPN2

growth_protocol: The mice were randomized to feed a high-fat diet (HFD) (60% kcal fat, D12492i; Research Diets Inc.) or a standard diet control (ND, D12450Bi)


title: HAPN3


title: HAPN1


title: HAPN2


title: HFD3


title: HFD2


title: HFD1


title: WT1

value: Normal-diet feeding


title: Donor_6_Macula

source_name: donor6, retina, macula region


title: Donor_5_Periphery

source_name: donor5, retina, peripheral region


title: Ring1a-/-Ring1bf/fERT2cre+4-OHT -H2AK119ub1

data_processing:
ChIP-seq datasets were performed using the AQUAS processing pipeline
ChIP-seq clean reads were aligned to the mouse reference genome assembly GRCm38 (mm10), and only unique mapped reads were used for subsequent analysis.
Peaks for histone modifications were called using MACS2, while peaks for polycomb group proteins were called using SPP.
Genome_build: mm10

value: mouse embryonic stem cells


title: WT-H3K27me3

value: WT


title: Asxl2KO-CUT&TAG-H2AK119ub1


title: WT-SUZ12


title: Asxl2KO-SUZ12


title: Asxl2KO-RYBP

value: RYBP(Millipore AB3637)


title: HSAPN1


title: WT-CUT&TAG-H2AK119ub1


title: WT-RING1B

value: RING1B(CST 5694S)


title: Asxl2KO-RING1B


title: WT-input


title: Asxl2KO-input


title: WT3


title: WT2


title: WT-RYBP


title: lung.NET.84 [mRNA]

city: Madrid

first: GarciaCarbonero

last: Lab

state: Comunidad de Madrid

address: Av/ Córdoba s/n

department: Centro de Oncología Experimental

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

description: FFPE.tumor.tissue

hyb_protocol: Standardized array hybridization process recommended by Affymetrix was used.

scan_protocol: Arrays were scanned using a GC3000 laser confocal scanner (Affymetrix), and microarray image data were analyzed by GeneChip Operating Software (GCOS 1.4 Affymetrix).

data_processing: CEL files were processed in R with affy package using the function expresso. Background correction method was RMA, the normalization method was quantiles, pm correction was pmonly and the summary method was medianpolish.

label_protocol: cDNA was prepared following the GeneChip WT PLUS Reagent Kit labeling protocol.

extract_protocol: Total RNA, containing small RNA, was extracted from FFPE tissue samples using Recover All TM Total Nucleic Acid Isolation Ambition Kit (Applied Biosystems, Foster City, CA, USA).

value: lung

value: tumor

tag: grade

tag: death


title: lung.NET.83 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.78 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.86 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.77 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.80 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.81 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.72 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.69 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.74 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.82 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.76 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.85 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.70 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.64 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.73 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.66 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.59 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.61 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.65 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.63 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.57 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.58 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.75 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.60 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.68 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.54 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.56 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.55 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.52 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.53 [mRNA]

description: FFPE.tumor.tissue


title: S.sanguinis + Pg supernatant in Glucose, anoxic conditions replicate 3

city: Portland

first: Emily

last: Helliwell

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB433

institute: Oregon Health and Science University

description:
Ss_PgSN_Glu_N2_3
PhenoRNA_dataframe.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 2.10 command --nextseq-trim=20
Assembly: Trimmed sequence reads were mapped to S.sanguinis SK36 reference GCA_000014205.1_ASM1420v1_genomic.fna.gz using BWA-MEM under default parameters
.sam files were converted to .bam, and filtered for paired reads using samtools
htseq-count was used to create count tables for each library (yield .counts files)
DEseq2 was used to create normalized count tables
Supplementary files format and content: tab-delimited text files include DEseq2-normalized counts and phenotypic data across all samples "PhenoRNA_dataframe.txt"
Supplementary files format and content: tab-delimited text file includes DEseq2-normalized counts for oxic sample comparison "O2_ncounts.txt"
Supplementary files format and content: tab-delimited text file includes DEseq2-normalized counts for anoxic sample comparison "N2_ncounts.txt"
Supplementary files format and content: tab-delimited text file includes DEseq2-normalized counts for P.gingivalis treatment comparison "Pg_ncounts.txt"

organism: Streptococcus sanguinis

source_name: bacterial cell

growth_protocol: Streptococcus sanguinis SK36 was grown for 18hrs in chemically-defined media (CDM) for 18hrs, until late log-growth phase.

extract_protocol:
RNA was extracted from whole cells using a Trizol-based protocol, genomic DNA was digested using TURBO DNaseI according to manufacters protocol and samples were cleaned using Qiagen RNeasy kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded with rRNA and Globin Depletion kit following manufacturer's protocols.

treatment_protocol:
CDM was supplemented with either 1.7% sucrose or 3.4% glucose, cultures were incubated either in oxic (95% O2, 5%CO2) or anoxic (N2, CO2, H2) conditions, 37C.
When specified, Corynebacterium durum 33277, Filifactor alocis, Porphyromonas gingivalis W83, or 15ml of BHI filtered from P.gingivalis W83 culture.

value: bacterial cell

value: Glucose, anoxic condition + Pg supernatant


title: S.sanguinis +Pg supernatant in Glucose, anoxic conditions replicate 2

description:
Ss_PgSN_Glu_N2_2
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, +Pg supernatant


title: C.durum+S.sanguinis +Pg supernatant in Glucose, anoxic conditions replicate 2

description:
Cd_Ss_PgSN_Glu_N2_2
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, + C.durum +Pg supernatant


title: C.durum+S.sanguinis +Pg supernatant in Glucose, anoxic conditions replicate 3

description:
Cd_Ss_PgSN_Glu_N2_3
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, +C.durum +Pg supernatant


title: C.durum+S.sanguinis +P.gingivalis in Glucose, anoxic conditions replicate 2

description:
Cd_Ss_Pg_Glu_N2_2
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, + C.durum +P.gingivalis


title: C.durum+S.sanguinis +P.gingivalis in Glucose, anoxic conditions replicate 3

description:
Cd_Ss_Pg_Glu_N2_3
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, +C.durum +P.gingivalis


title: S.sanguinis +P.gingivalis in Glucose, anoxic conditions replicate 2

description:
Ss_Pg_Glu_N2_2
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, +P.gingivalis


title: lung.NET.51 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.50 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.49 [mRNA]

description: FFPE.tumor.tissue


title: S.sanguinis + P.gingivalis in Glucose, anoxic conditions replicate 3

description:
Ss_Pg_Glu_N2_3
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition + P.gingivalis


title: lung.NET.47 [mRNA]

description: FFPE.tumor.tissue

value: female


title: C.durum+S.sanguinis +F.alocis in Glucose, anoxic conditions replicate 3

description:
Cd_Ss_Fa_Glu_N2_3
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, +C.durum +F.alocis


title: lung.NEC.41 [mRNA]

description: FFPE.tumor.tissue

value: male


title: lung.NEC.43 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.39 [mRNA]

description: FFPE.tumor.tissue


title: S.sanguinis + F.alocis in Glucose, anoxic conditions replicate 3

description:
Ss_Fa_Glu_N2_3
PhenoRNA_dataframe.txt

value: WT

value: Glucose, anoxic condition + F.alocis


title: lung.NEC.45 [mRNA]

description: FFPE.tumor.tissue


title: lung.NEC.46 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.48 [mRNA]

description: FFPE.tumor.tissue


title: lung.NET.42 [mRNA]

description: FFPE.tumor.tissue


title: C.durum+S.sanguinis +F.alocis in Glucose, anoxic conditions replicate 2

description:
Cd_Ss_Fa_Glu_N2_2
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, + C.durum +F.alocis


title: lung.NET.44 [mRNA]

description: FFPE.tumor.tissue

value: lung


title: lung.NET.38 [mRNA]

description: FFPE.tumor.tissue

value: tumor


title: lung.NET.40 [mRNA]

description: FFPE.tumor.tissue


title: S.sanguinis +F.alocis in Glucose, anoxic conditions replicate 2

description:
Ss_Fa_Glu_N2_2
PhenoRNA_dataframe.txt

value: bacterial cell

value: Glucose, anoxic condition, +F.alocis


title: C.durum+S.sanguinis in Glucose, anoxic conditions replicate 3

description:
Cd_Ss_Glu_N2_3
N2_ncounts.txt
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition, C.durum


title: S.sanguinis in Glucose, anoxic conditions replicate 3

description:
Ss_Glu_N2_3
N2_ncounts.txt
Pg_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, anoxic condition


title: C.durum+S.sanguinis in Glucose, anoxic conditions replicate 2

description:
Cd_Ss_Glu_N2_2
N2_ncounts.txt
Pg_ncounts.txt
PhenoRNA_dataframe.txt


title: S.sanguinis in Glucose, anoxic conditions replicate 2

description:
Ss_Glu_N2_2
N2_ncounts.txt
Pg_ncounts.txt
PhenoRNA_dataframe.txt


title: C.durum+S.sanguinis in sucrose, anoxic conditions replicate 2

description:
Cd_Ss_Suc_N2_2
N2_ncounts.txt
PhenoRNA_dataframe.txt

value: Sucrose, anoxic condition, C.durum


title: S.sanguinis in sucrose, anoxic conditions replicate 2

description:
Ss_Suc_N2_2
N2_ncounts.txt
PhenoRNA_dataframe.txt

value: Sucrose, anoxic condition


title: gastroenteropancreatic.NET.33 [mRNA]

description: FFPE.tumor.tissue

value: small intestine


title: gastroenteropancreatic.NET.34 [mRNA]

description: FFPE.tumor.tissue

value: stomach


title: C.durum+S.sanguinis in Glucose, oxic conditions replicate 3

description:
Cd_Ss_Glu_O2_3
O2_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, oxic condition, C.durum


title: gastroenteropancreatic.NET.28 [mRNA]

description: FFPE.tumor.tissue

value: colorectal


title: panc1_bruchaseseq6h_TGFb72h

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: panc1 bruchaseseq 72h TGFb replicate 1

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Assembly: hg38
Supplementary files format and content: The columns of the genes.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length (7) read count (8) RPKM

growth_protocol: Cell lines were cultured in the appropriate medium (RPMI-1640 for BxPC-3 and DMEM for PANC-1) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (GIBCO) at 37°C with 5% CO2.

extract_protocol:
For bruseq and BruChaseseq, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: PANC-1 cells were treated with TGF-β or vehicle control for 1, 24, or 72h before Bru-seq and BruChase-seq analyses. KMT2D was knocked out in BxPC-3 cells using CRISPR/cas9. Bru-seq analyses were performed in two KMT2D-knockout BxPC-3 clones (KO1 and KO2) comparing to a control BxPC-3 cell line.

value: TGF-b

tag: time point

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruChase-seq

tag: time between end of bru labeling and rna extraction

value: 6 hours

tag: labeling agent

value: Bromouridine (Bru)


title: gastroenteropancreatic.NET.25 [mRNA]

description: FFPE.tumor.tissue

value: male


title: gastroenteropancreatic.NET.29 [mRNA]

description: FFPE.tumor.tissue

value: tumor


title: panc1_bruseq0h_TGFb72h

description: panc1 bruseq 72h TGFb replicate 1

value: bruseq

value: 0 hours


title: S.sanguinis in sucrose, anoxic conditions replicate 3

description:
Ss_Suc_N2_3
N2_ncounts.txt
PhenoRNA_dataframe.txt

tag: strain

value: bacterial cell

value: WT


title: panc1_bruchaseseq6h_TGFb24h

description: panc1 bruchaseseq 24h TGFb replicate 1

tag: cell line


title: gastroenteropancreatic.NET.26 [mRNA]

description: FFPE.tumor.tissue

value: female


title: C.durum+S.sanguinis in Glucose, oxic conditions replicate 2

description:
Cd_Ss_Glu_O2_2
O2_ncounts.txt
PhenoRNA_dataframe.txt


title: C.durum+S.sanguinis in sucrose, anoxic conditions replicate 3

description:
Cd_Ss_Suc_N2_3
N2_ncounts.txt
PhenoRNA_dataframe.txt

value: Sucrose, anoxic condition, C.durum


title: gastroenteropancreatic.NET.27 [mRNA]

description: FFPE.tumor.tissue

value: pancreas


title: lung.NET.36 [mRNA]

description: FFPE.tumor.tissue

value: lung


title: gastroenteropancreatic.NET.30 [mRNA]

description: FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.32 [mRNA]

description: FFPE.tumor.tissue


title: gastroenteropancreatic.NET.23 [mRNA]

description: FFPE.tumor.tissue

value: apendix


title: C.durum+S.sanguinis in Glucose, oxic conditions replicate 1

description:
Cd_Ss_Glu_O2_1
O2_ncounts.txt

value: Glucose, oxic condition, C.durum


title: gastroenteropancreatic.NET.24 [mRNA]

description: FFPE.tumor.tissue

value: stomach


title: gastroenteropancreatic.NEC.21 [mRNA]

description: FFPE.tumor.tissue

value: colorectal


title: gastroenteropancreatic.NET.22 [mRNA]

description: FFPE.tumor.tissue


title: S.sanguinis in Glucose, oxic conditions replicate 3

description:
Ss_Glu_O2_3
O2_ncounts.txt
PhenoRNA_dataframe.txt

value: Glucose, oxic condition


title: S.sanguinis in Glucose, oxic conditions replicate 2

description:
Ss_Glu_O2_2
O2_ncounts.txt
PhenoRNA_dataframe.txt


title: gastroenteropancreatic.NET.18 [mRNA]

description: FFPE.tumor.tissue

value: small intestine


title: S.sanguinis in Glucose, oxic conditions replicate 1

description:
Ss_Glu_O2_1
O2_ncounts.txt


title: panc1_bruchaseseq6h_TGFb1h

description: panc1 bruchaseseq 1h TGFb replicate 1

value: TGF-b

value: 0.5 hours

value: bruChase-seq

value: 6 hours

value: Bromouridine (Bru)


title: gastroenteropancreatic.NET.19 [mRNA]

description: FFPE.tumor.tissue

value: tumor

value: male


title: gastroenteropancreatic.NET.20 [mRNA]

description: FFPE.tumor.tissue

value: female


title: panc1_bruseq0h_TGFb24h

description: panc1 bruseq 24h TGFb replicate 1

value: bruseq

value: 0 hours


title: W9706, drought for Day7 rep3

city: Ithaca

first: yuan

last: jiang

address: 306 Tower Rd

institute: cornell university

data_processing:
The library fragments were selected to be 200-250 bp in length. Then, library preparations were sequenced on an Illumina HiSeq 2500 platform, and paired-end reads were generated.
Clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data according to the instructions. Then, the clean reads were mapped to the Zea mays B73 reference genome V4 with STAR, and the mismatch limitation was set to 1.
Assembly: Zea mays B73 reference genome V4
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: leaf

growth_protocol: three seeds were sown into a 1000 mL plastic b  eaker with soil and transferred to the growth chamber with the following settings until the three-leaf stage: temperature 26°C, photoperiod 14 h/10 h (light/dark) and relative humidity 50±5%.

extract_protocol:
Total RNA of the third leaf samples was isolated using TRIzol reagent and the UItrapure RNA kit (Cowin Biotech) following the manufacturer’s protocols. The RNA was treated with DNase I (RNase Free) to remove the DNA (Cowin Biotech). The RNA was tested using gel electrophoresis to check its integrity. The concentration of the RNA was determined by the Implen NanoPhotometer P360.
Sequencing libraries were generated using the NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions.

treatment_protocol: I had modified it in the main text. The maize seeds were soaked in water for one day, and transferred into a 1000ml breaker. Because it could be easy to control the water content for drought stress.

tag: tissue

value: leaf

value: drought


title: panc1_bruchase6h_CTL

description: panc1 bruchaseseq CTL replicate 1

value: vehicle control


title: TLGK974_5: endothelial cells from CT2A tumors in LGK974 treated mice, rep4

city: Xi’an

first: Lei

last: Zhang

address: No. 620, West Chang'an Avenue

institute: Shaanxi Normal University

data_processing:
Sequences were processed to remove adapter and low-quality bases by FastQC (v0.11.5).
Reads were aligned to mouse genome and transcriptome using STAR (v2.5.3a).
Read counts and FPKM per sample were generated by StringTie(v1.3.1c)
Assembly: GRCm38.98
Supplementary files format and content: CSV file includes FPKM values for each sample, generated by StringTie.

organism: Mus

source_name: brain tumor

extract_protocol:
Total RNA was extracted from each sample with Qiagen RNAeasy plus mini kit  following manufacturer's recommendations.
RNA librarys were prepared for sequencing using standarded Illumina protoclos.

value: brain tumor

tag: cell type

value: endothelial


title: panc1_bruseq0h_TGFb1h

description: panc1 bruseq 1h TGFb replicate 1


title: S.sanguinis in sucrose, oxic conditions replicate 3

description:
Ss_Suc_O2_3
O2_ncounts.txt
PhenoRNA_dataframe.txt

value: bacterial cell

tag: genotype

value: WT

value: Sucrose, oxic condition


title: W9706, drought for Day7 rep2

tag: treatment


title: TLGK974_4: endothelial cells from CT2A tumors in LGK974 treated mice, rep3


title: W9706, drought for Day7 rep1


title: TLGK974_2: endothelial cells from CT2A tumors in LGK974 treated mice, rep2


title: B73, drought for Day7 rep2

value: B73, WT


title: TLGK974_1: endothelial cells from CT2A tumors in LGK974 treated mice, rep1


title: B73, drought for Day7 rep3


title: Tcontrol_3: endothelial cells from CT2A tumors in control mice, rep2


title: C.durum+S.sanguinis in sucrose, oxic conditions replicate 1

description:
Cd_Ss_Suc_O2_1
O2_ncounts.txt

value: Sucrose, oxic condition, C.durum

tag: time


title: S.sanguinis in sucrose, oxic conditions replicate 2

description:
Ss_Suc_O2_2
O2_ncounts.txt
PhenoRNA_dataframe.txt


title: BxPC3_bruseq0h_KO2

description: BxPC3 bruseq KO2 replicate 1

tag: genotype/variation

value: KO

value: 0.5 hours


title: panc1_bruseq0h_CTL

description: panc1 bruseq CTL replicate 1

value: Bromouridine (Bru)


title: S.sanguinis in sucrose, oxic conditions replicate 1

description:
Ss_Suc_O2_1
O2_ncounts.txt


title: BxPC3_bruseq0h_WT

description: BxPC3 bruseq WT replicate 1


title: BxPC3_bruseq0h_KO1

description: BxPC3 bruseq KO1 replicate 1


title: PGP1_DE_CTD-2501M5.1-KO-RIP-Input-rep3

status: Public on Mar 30 2023

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. RIPseq peaks were analyzed by Macs2 callpeak (V2.1.1).
Assembly: GRCh38
Supplementary files format and content: TPM for RNAseq
Supplementary files format and content: peak bed for RIPseq

source_name: differentiated CTD-2501M5.1-KO endoderm cells

growth_protocol: hPSCs were treated with IMEM-F12 as basal medium, supplemented with 0.2% BSA, 1% Penicillin-Streptomycin and 100ng/mL Activin A  for the three days.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: C.durum+S.sanguinis in sucrose, oxic conditions replicate 3

description:
Cd_Ss_Suc_O2_3
O2_ncounts.txt
PhenoRNA_dataframe.txt


title: PGP1_DE_CTD-2501M5.1-KO-RIP-Input-rep2

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed


title: PGP1_DE_WT-RIP-Input-rep3

description:
RIPseq
WT_RIP_summits.bed

source_name: differentiated endoderm cells


title: PGP1_DE_CTD-2501M5.1-KO-RIP-Input-rep1

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed


title: Tcontrol_1: endothelial cells from CT2A tumors in control mice, rep1


title: PGP1_DE_WT-RIP-Input-rep1

description:
RIPseq
WT_RIP_summits.bed


title: gastroenteropancreatic.NET.17 [mRNA]

description: FFPE.tumor.tissue

value: small intestine

value: tumor

tag: gender


title: PGP1_DE_WT-RIP-Input-rep2

description:
RIPseq
WT_RIP_summits.bed


title: C.durum+S.sanguinis in sucrose, oxic conditions replicate 2

description:
Cd_Ss_Suc_O2_2
O2_ncounts.txt
PhenoRNA_dataframe.txt


title: Pax7Cre_Run2

status: Public on Mar 21 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description:
10x snRNAseq
Single cell RNA

data_processing:
Mapping was performed by cellranger.
Cellbender was used to remove empty droplets and ambient RNA.
scDblFinder was used to exclude potential doublets.
Downstream analysis was performed by Seurat.
Assembly: GRCm39
Supplementary files format and content: Raw count matrices from Cell Ranger. barcodes.tsv, features.tsv, matrix.mtx files.

source_name: Myogenic progenitor cells

growth_protocol: 12-week-old mice were used for the experiment.

extract_protocol:
On day 6 of CTX-induced skeletal muscle regeneration, TA muscles of both hindlimb legs were dissected, digested, and subjected to flow cytometry. After exclusion of doublets and dead cells, myogenic progenitor cells were sorted based on the expression of alpa7 integrin and the exclusion of CD45/CD31/sca1. Subsequently, single cell suspension was generated using Chromium.
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry).

treatment_protocol: Intramuscular injection of Cardiotoxin was performed under anaesthesia to induce muscle regeneration.

value: Skeletal muscle

value: Myogenic progenitor cells

value: WT (Pax7Cre)

value: Cardiotoxin-induced muscle regeneration


title: Pax7CremiR501flox_Run1

description:
10x snRNAseq
Single cell RNA

value: miR-501 KO (Pax7CremiR-501fl/Y)


title: Pax7Cre_Run1

description:
10x snRNAseq
Single cell RNA


title: B73, drought for Day7 rep1

value: leaf

value: drought


title: Pax7CremiR501flox_Run2

description:
10x snRNAseq
Single cell RNA


title: Ishikawa scRNAseq, 0,2,4 and 8 hours of e2 treatment_multiseq_barcodes

status: Public on Mar 15 2023

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

library_source: other

data_processing:
Sequencing output was processed from reads to counts using the 10x Genomics Cell Ranger v3.1.0 pipeline
MULTI-seq calls were processed using the demultiplex R pipeline and mapped back to the E2 timepoints
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: Ishikawa

growth_protocol: T-47D and Ishikawa cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco).

extract_protocol:
Sample preparation was performed according to the 10x Genomics sample prep user guide for Cultured Cells
Cells were separated into single-cell emulsions using the 10x Genomics Chromium Controller with a targeted recovery of 10,000 cells.
Sequencing libraries were prepared using the 10X Genomics Next GEM Single Cell 3' Gene Expression Library prep v3.1
MULTI-seq libraries were prepared according to the protocol described in McGinnis et al. Nature Methods 2019

treatment_protocol:
Cells were treated with 10nM 17beta-estradiol (E2) for 0 (vehicle treated), 2, 4, and 8 hours.
Cells from different timepoints were labeled via MULTI-seq as described in McGinnis et al. Nature Methods 2019, then mixed prior to sequencing

value: Ishikawa

value: Endometrial Adenocarcinoma

value: 10nM e2 (2,4 and 8 hours) or DMSO (0 hours)

value: 0,2,4 and 8 hours (de-multiplexed by MULTI-seq barcodes)


title: T-47D scRNAseq, 0,2,4 and 8 hours of e2 treatment_GEX

value: Ductal carcinoma, mammary gland


title: Ishikawa scRNAseq, 0,2,4 and 8 hours of e2 treatment_GEX


title: T-47D scRNAseq, 0,2,4 and 8 hours of e2 treatment_multiseq_barcodes


title: Thymic_cells_GEX

city: Minneapolis

first: Kristin

last: Hogquist

state: MN

address: 2101 6th St SE

institute: University of Minnesota

description:
Genotypes: WT, IFNAR_KO, IFNAR_DRKO
Single-cell RNAseq 10X Genomics

data_processing:
10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Each gel bead in emulsion (GEM) was identified and all gene specific reads were mapped via cellranger count (ver. 4.0.0) using the mouse reference genome (mm10) or antibody specific tags (HTOs and ADTs).
Gene level quantification was completed using cellranger count software (ver. 4.0.0) using a custom GTF (derived from GENCODE, version M23, Ensembl 98). HTO/ADT counts were generated by cellranger count using the specific antibody-oligo tags sequences used in this experiment. WT, IFNAR_KO and INFAR_DRKO (strain) were classified using HTO counts respectively via Seurat's HTOdemux function.
Raw counts data was imported into R (ver 4.0.0) for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc. primarily using the Seurat R package (ver. 3.2.2). Although ADT data were generated they were not used in this analysis. Additionally, there was HTO tagged population (OT-I) that was sequenced but that was also excluded from all analyses.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Supplementary_files_format_and_content: GEX_*.txt: Tab-delimited text files that contain raw GEX counts.
Supplementary_files_format_and_content: HTO_*.txt: Tab-delimited text files that contain raw HTO counts for every tagged GEM.
Supplementary_files_format_and_content: features.csv has the feature barcode sequence for all cell samples sequenced in the original sequencing run.
Supplementary_files_format_and_content: seurat-object_all_cells_GEX_HTO_metadata.txt has metadata, including hashtag ID and HTO classification, for all sequenced cells.

source_name: murine thymocytes

extract_protocol:
An RNeasy micro kit (Qiagen) was used to isolate RNA obtained from each sample per the manufacturer’s instructions.
For 10X Genomics scRNA-seq, we generated libraries that measure: (1) mRNA transcript expression (RNA) and (2) tissue-specific hashtag oligos (HTO). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations and sequenced in a NovaSeq.

treatment_protocol: Thymus cells from different strains were obtained from organs digested with collagenase D (1 mg/ml). CD90.2-expressing thymocytes were depleted with magnetic-activated sorting. Enriched cells were stained with anti-MHC-II antibodies, and live MHC-II+ cells were FACS-sorted with a FACSAria (BD Biosciences). These cells were used for RNA extraction.

value: MHC-II+ thymocytes

value: mixed sample (non-demultiplexed)

tag: age

value: 5 weeks


title: 220228_L2 wild-type infected rep2

status: Public on Feb 13 2023

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
An initial ANOVA-like pass of differential expression testing was performed. Genes that did not significantly vary between any of the three treatments were culled from downstream analysis.
Differential expression testing was performed using default paramters to identify differentially expressed genes in either L2-wt or L2ΔCTL0480-infected samples relative to the mock-infected control, accounting for variation between replicates.
Assembly: hg19
Supplementary files format and content: CLC file containing raw counts, TPM, and FDRP values for every gene and sample.

source_name: Primary endocervical epithelial cells

growth_protocol: Human primary endocervical epithelial cells (PCS-480-011, Lot 80306190) were cultured at 37C with 5% atmospheric CO2 in Cervical Epithelial Cell Basal Medium (CECBM, ATCC PCS-480-032) supplemented with all contents of the Cervical Epithelial Growth Kit (ATCC PCS-080-042), per manufacturer's instructions. Chlamydia trachomatis serovar L2/434/Bu was originally obtained from Dr. Ted Hackstadt (Rocky Mountain National Laboratory, NIAID), and the L2ΔCTL0480 mutant strain was provided by Dr. Derek Fisher and Dr. Erika Lutter.

extract_protocol:
Primary cells were harvested for Total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers’ protocols, and were subsequently assayed for fragmentation using an Agilent Bioanalyzer 2100.
cDNA library preparation of intact samples was performed using the NuGEN Universal mRNA-Seq Library Preparation kit, according to the manufacturer's protocol.

treatment_protocol: Primary cells cultured to confluence (6-7 days) seeded on fibronectin-coated 6-well plates (Corning 354402) were washed with pre-warmed Hanks Buffered Saline Solution (HBSS) prior to inoculation with Chlamydia-containing CECBM at a multiplicity of infection (MOI) of 2. Tissue culture plates were centrifuged at 4C and 500 rcf (Eppendorf 5810 R tabletop centrifuge, A-4-81 rotor) for 15 minutes to synchronize infection. Inoculum was then aspirated, and cells were washed with chilled HBSS prior to the addition of pre-warmed KSFM. Infected cultures were then returned to the tissue culture incubator until 24 hours post-infection.

value: Primary endocervical epithelial cells

value: L2 wild-type infected

tag: infection time

value: 24 hpi


title: Thymic_cells_HTO


title: 220228_Mock-infected rep3

value: Mock-infected


title: 220228_L2 wild-type infected rep1


title: HCT116 cells, siNRF1-MG132

status: Public on Mar 18 2023

city: Kyotanabe

first: Akira

last: Kobayashi

address: 1-3 Tatara Miyakodani

institute: Doshisha University

hyb_protocol: Samples were hybridized to the Affymetrix Human Gene 1.0 ST Arrays. GeneChip fluidics station 450 was used for processing of the arrays.

scan_protocol: Array scanning was performed with the GeneChip scanner 3000-7G.

data_processing:
Images were analyzed with the GeneChip operating software (Affymetrix). Expression console and Transcription analysis console (Affymetrix) were used to identify the gene expression.
RMA expression value derived from Expression Console software

label: Biotin

source_name: HCT116 cells

label_protocol: Total RNA was processed with the Ambion WT Expression Kit (Affymetrix) accord- ing to the manufacturers’ instructions. cRNA was then fragmented, labelled using the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HCT116 cells were cultured in DMEM/high glucose medium (Wako) supplemented with 10% FBS (Nichirei Biosciences), 40 µg/ml streptomycin, and 40 units/ml penicillin (Wako). Cells were cultured in 37˚C with 5% CO2 incubator.

extract_protocol: RNA was extracted and purification using ISOGEN II (NIPPON GENE) according to the manufacturer's protocol

treatment_protocol: Transfection of siRNA was performed using RNAiMAX (Invitrogen). After 48 h from siRNA transfection, cells were treated with DMSO or 1 µM MG132 (Peptide Institute) for 16 h.

value: colon

tag: Sex

value: male

value: NRF1 KD


title: 220228_Mock-infected rep2


title: 220228_Mock-infected rep1


title: HCT116 cells, siControl-DMSO

value: control

value: DMSO