title: Dark3

city: Philadelphia

first: Wei Chun

state: PA

address: 3601 Spruce St

department: Program in Gene Expression and Regulation, Center for Systems and Computational Biology

institute: The Wistar Institute

description: Plant under dark condition

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered out low-quality sequence using Cutadaptor
Sequenced reads were masked for 5'-Ts then mapped to TAIR10 whole genome using Bowtie2. Reads with a mapping quality score (MAPQ) of ≥10 were kept for further analysis.
Reads with ≥2 non-genomic 5'-Ts after alignment were called polyA site supporting (PASS) reads.
pAs within 24 nt from one another were clustered as previously described (Hoque et al., 2013).
Assembly: TAIR10
Supplementary files format and content: csv files include all cluster sites with count values for each sample.

source_name: Plant under dark condition

growth_protocol: The Arabidopsis Columbia ecotype (Col 0) was used as wild-type. Seeds were stratified for three days in the dark at 4°C and then germinated on Murashige and Skoog 0,5x (MS) medium containing 1% agar. Seedlings were grown in Petri dishes with MS medium at a constant temperature of 22°C under constant white light provided by fluorescent tubes with an intensity of irradiance between 70 and 100 μmol/m2sec.

extract_protocol:
Total RNA extraction of seedlings was carried out using RNeasy Plant Mini Kit (Qiagen) following manufacturer’s instructions
The 3'READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 1 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles.

treatment_protocol: Standard treatment protocol: A. thaliana seedlings were grown on MS agar plates (30 seeds per plate) for a period of 1 to 2 weeks and then transferred for 48hr to darkness. After this period, seedlings were kept in dark or transferred to light for 6hr.

tag: ecotype

value: Col 0

tag: sample treatment

value: Dark

value: seedling

tag: library type


title: HFD Mier1 KO 0h 2

status: Public on Dec 31 2022

type: SRA

city: Shanghai

first: Yanhao

last: Chen

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
HAgene.count.matrix.annot.xls
HK_0h_2

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.10.1
Assembly: GRCm39
Supplementary files format and content: Gene counts for each samples

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Liver

tag: genotype

tag: aav treatment

value: AAV-Mier1 sgRNA

tag: treatment

value: PHx 0 h

tag: diet

value: HFD


title: NPC43 scONEseq 086

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

institute: HKUST

description:
RNA+DNA
NPC single cell 086

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

organism: Homo sapiens

source_name: NPC43 cell line

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics

value: nasopharyngeal carcinoma

tag: method

value: scONE-seq


title: NPC43 scONEseq 085

description:
RNA+DNA
NPC single cell 085


title: HFD Mier1 KO 0h 1

description:
HAgene.count.matrix.annot.xls
HK_0h_1


title: R3_146

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

country: United Kingdom

institute: Paul O' Gorman Leukaemia Research Centre

data_processing:
Raw reads were firstly processed through fastp for quality control
Reads were normalised to a reference genome using STAR (v2.5)
Read counts were quantified using featureCounts
Differential expression analysis was performed using DESeq2 (v2_1.6.3)
Genome_build: hg38
Supplementary_files_format_and_content: A tab-delimited text file includes raw gene counts for every gene and every sample.

molecule: polyA RNA

growth_protocol: Cell lines grown in published growth conditions

extract_protocol:
RNA was extracted using a Rneasy plus mini kit (Qiagen, Cat No. 74136)
Done by Novogene

treatment_protocol: Cells spinoculated with supernatant containing lentivirus, generated in 293T. These lentivirus carried either one of two shRNA constructs targeting  NFATC2 or a non-targeting control shRNA. Transduced cells were selected by puromycin treatment 24 hours after spinoculation. Cells were harvested for RNA extraction 48 hours after spinoculation.

tag: cell line

tag: cell type

value: MLL-AF9 human AML cell line

tag: disease state

value: Acute myeloid leukaemia

tag: treatment type

value: NFATC2 Knockdown construct-2


title: Dark1

country: USA

description: Plant under dark condition

organism: Arabidopsis thaliana


title: ATT-CL [A1]

city: Cheonan

first: Ngu

middle: Van

last: Trinh

state: Chungcheongnam

address: 25Bongjeong-ro, Cheonan-si, Korea

country: South Korea

institute: SoonChunHyang Institute of Medi-Bio Science

data_processing:
Sequencing Protocol: NovaSeq 6000 System User Guide Document # 1000000019358 v02
FASTQ files were did quality control using FastQC v0.11.5. Sequenced reads were trimmed using Trimmomatic 0.32 , and masked for low-complexity or low-quality sequence, then mapped to UCSC hg19 using HISAT2 through Bowtie2 aligner
Assembles transcripts were count using Stringtie. Raw counts were normalized using FPKM: Fragments per kilobase of transcript per million read pairs
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

source_name: Breast Epithelial Cell Line

growth_protocol: Cells were grown in DMEM + 10% FBS + 1% PEN/STREP

extract_protocol:
RNA was extracted by RNeasy mini kit
TruSeq Stranded mRNA Sample Preparation Guide. Part # 15031047 Rev. E

treatment_protocol: Cells were grown on suspension and then re-attachment

value: Breast Epithelial Cell Line

tag: collection

value: cluster cells


title: Dark2

description: Plant under dark condition


title: NPC43 scONEseq 084

description:
RNA+DNA
NPC single cell 084


title: R2_146


title: HFD Control 48h 2

description:
HAgene.count.matrix.annot.xls
HC_48h_2

value: AAV-Cre

value: PHx 48 h


title: R1_146


title: Light3

description: Plant under light condition

source_name: Plant under light condition

value: Light


title: NPC43 scONEseq 083

description:
RNA+DNA
NPC single cell 083


title: HFD Control 48h 1

description:
HAgene.count.matrix.annot.xls
HC_48h_1


title: Light2

description: Plant under light condition

value: Col 0


title: R3_143

value: NFATC2 Knockdown construct-1


title: NPC43 scONEseq 082

description:
RNA+DNA
NPC single cell 082


title: Light1

description: Plant under light condition

value: seedling


title: R2_143


title: HFD Control 0h 2

description:
HAgene.count.matrix.annot.xls
HC_0h_2

value: Liver


title: NPC43 scONEseq 080

description:
RNA+DNA
NPC single cell 080


title: HFD Control 0h 1

description:
HAgene.count.matrix.annot.xls
HC_0h_1


title: NCD/Young Control 48h 2

description:
HAgene.count.matrix.annot.xls
NC_48h_2

value: NCD


title: NPC43 scONEseq 081

description:
RNA+DNA
NPC single cell 081


title: NCD/Young Control 48h 1

description:
HAgene.count.matrix.annot.xls
NC_48h_1


title: NPC43 scONEseq 079

description:
RNA+DNA
NPC single cell 079


title: R2_SHX2

description: Control

value: Non-targeting control shRNA


title: NPC43 scONEseq 078

description:
RNA+DNA
NPC single cell 078


title: R1_143


title: NCD/Young Control 0h 2

description:
HAgene.count.matrix.annot.xls
NC_0h_2

value: PHx 0 h


title: R3_SHX2

description: Control


title: R1_SHX2

description: Control


title: NCD/Young Control 0h 1

description:
HAgene.count.matrix.annot.xls
NC_0h_1


title: Combo_THP1_r3

data_processing:
Data quality check was assessed using FastQC version 0.11.5 and sequences trimmed using Trim Galore version 0.4.4_dev
The data was normalised to the reference genome GRCh38. using hisat2
Count matix were generated using featureCounte version 1.6.1
Differential expression analysis carried out by DESeq2 and annotations by biomaRT version 2.34.2
Genome_build: GRCh38
Supplementary_files_format_and_content: A tab-delimited text file includes raw gene counts for every gene and every sample

source_name: THP-1 cells

growth_protocol: THP-1 cells were maintained in RPMI (10% FBS, 1% L_Glut ), fed twice per week and used before passage 20

extract_protocol:
Cells were counted by Trypan Blue Exclusion, washed with PBS and cell pellets frozen at -80 in Qiagen RLT buffer. Triplicates were processed together by Qiagen microRNA extraction kit according to manufacturers instructions - RNA quantities were assessed by Nanodrop and quality assessed using the Agilent RNA integrity 6000 nano kit
RNA libraries were prepared for sequencing using Standard TruSeq Stranded mRNA Illumina protocols followed by a quality check using Agilents High Sensitivity DNA kit

treatment_protocol: Cell were seeded in T25 Treated Culture flasks and treated for 36hrs at 37 degrees 5% CO2 with varying concentrations of drugs all to a final concentration of 0.1% DMSO

value: MLL-AF9 human AML cell

tag: time point

value: 36 hours

tag: agent

value: 5microM 3-7 compound + 5microM olaparib


title: NPC43 scONEseq 077

description:
RNA+DNA
NPC single cell 077

value: nasopharyngeal carcinoma

value: scONE-seq


title: CD21-Cre AtrC/-_S 24h_CDC7i+CDK1i_6 [SD032]

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

data_processing:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>9 required) and proceed on library preparation by using Illumina TruSeq chemistry. Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files.
tpm_values_genes_kallisto.txt:estimated tpm values for each gene (computed from tximport R package)
Supplementary files format and content: txt files containing tpm (transcripts per million) data

source_name: primary B cells

growth_protocol: Purified splenic B (CD43-) cells from mice were cultured in RPMI medium with or without cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
RNA was isolated using TRIzol reagent (Invitrogen). RNA quality was determined using the Bioanalyzer RNA kit (Agilent) and samples with RNA Integrity Number (RIN) higher than 9 were sent for next-generation sequencing
TruSeq Stranded mRNA Library Prep Kit from Illumina was used and the library was sequenced with Illumina NovaSeq 6000.

treatment_protocol: Cells were collected at different time points from 0 to 24 h after cytokine activation. Cells were left untreated or treated with 2.5µM of CDC7i and 2.5µM CDk1i for 14 h

value: anti-CD40 and Il4 activated B cells

value: CD21-Cre AtrC/-

tag: strain

value: mixed 129 BL6


title: Combo_THP1_r2


title: NPC43 scONEseq 076

description:
RNA+DNA
NPC single cell 076


title: U-HO1 cell line

type: RNA

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

description: same as GSM3169088

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were logarithmically transformed and subtracted by the arraymean. Data processing was done via R/Bioconductor using limma and affy packages.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

value: Hodgkin lymphoma cell line


title: CD21-Cre AtrC/-_S 24h_CDC7i+CDK1i_5 [SD031]


title: SUP-HD1 cell line

description: same as GSM3169087


title: NPC43 scONEseq 075

description:
RNA+DNA
NPC single cell 075


title: L-540 cell line

description: same as GSM3169086


title: NPC43 scONEseq 074

description:
RNA+DNA
NPC single cell 074


title: KM-H2 cell line

description: same as GSM3169083


title: Combo_THP1_r1


title: CD21-Cre AtrC/-_S 24h_CDC7i+CDK1i_4 [SD030]


title: CD21-Cre AtrC/-_S_24h_6 [SD029]


title: NPC43 scONEseq 072

description:
RNA+DNA
NPC single cell 072


title: CD21-Cre AtrC/-_S_24h_5 [SD028]


title: 5µM_olaparib_THP1_r2

value: 5microM olaparib


title: 5µM_olaparib_THP1_r1


title: HDLM-2 cell line

description: same as GSM3169082


title: NPC43 scONEseq 071

description:
RNA+DNA
NPC single cell 071


title: NPC43 scONEseq 098

description:
RNA+DNA
NPC single cell 098


title: AM-HLH cell line

source_name: AM-HLH

value: AM-HLH


title: L-428 cell line

description: same as GSM3169085


title: CD21-Cre AtrC/-_S_24h_4 [SD027]


title: 5µM_3-7_compound_THP1_r3

value: 5microM 3-7 compound


title: L-1236 cell line

description: same as GSM3169084


title: 5µM_olaparib_THP1_r3


title: NPC43 scONEseq 070

description:
RNA+DNA
NPC single cell 070


title: AICHI-4 cell line


title: CD21-Cre Atr+/C_S_24h_CDC7i+CDK1i_6 [SD026]

value: CD21-Cre Atr+/C


title: NPC43 scONEseq 073

description:
RNA+DNA
NPC single cell 073


title: 5µM_3-7_compound_THP1_r2


title: CD21-Cre Atr+/C_S_24h_CDC7i+CDK1i_5 [SD025]


title: CD21-Cre Atr+/C_S_24h_CDC7i+CDK1i_4 [SD024]


title: 3µM_3-7_compound_THP1_r3

value: 3microM 3-7 compound


title: NPC43 scONEseq 068

description:
RNA+DNA
NPC single cell 068


title: NPC43 scONEseq 067

description:
RNA+DNA
NPC single cell 067


title: 3µM_3-7_compound_THP1_r2


title: NPC43 scONEseq 066

description:
RNA+DNA
NPC single cell 066


title: CD21-Cre Atr+/C_S_24h_5 [SD022]


title: 3µM_3-7_compound_THP1_r1


title: NPC43 scONEseq 065

description:
RNA+DNA
NPC single cell 065


title: NPC43 scONEseq 069

description:
RNA+DNA
NPC single cell 069


title: 5µM_3-7_compound_THP1_r1


title: patient 3, healthy dermis

city: London

first: Magdalena

last: Plotczyk

address: Royal School of Mines, Prince Consort Road

department: Bioengineering

institute: Imperial College London

hyb_protocol: Samples were hybridized onto Affymetrix Human Genome U133 Plus 2.0 Array and analysed using Nugen Ovation WTA Pico System V2.

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

data_processing: Transcriptomic Analysis Console (TAC) was used to perform a one-way ANOVA on the dataset to identify 422 transcripts that were significantly (P < 0.01) and differentially (fold change <- 1.5 or > 1.5) regulated between fibrotic dermis of stretched scars and dermis of the surrounding healthy skin. The intensity values of the samples were normalised and summarised using RMA algorithm.

source_name: dermis excised from healthy skin

label_protocol: RNA was used to synthesize first-strand complementary DNA (cDNA) using Nugen Ovation V2. This was then converted to double-stranded cDNA, and used as a template for in vitro transcription to generate cRNA using the Nugen Encore Biotin Module.

growth_protocol: During the study, full-thickness skin samples were collected from 3 patients who had their stretched scars excised for aesthetic reasons. Excised samples (approximately 1 cm x 2 cm) were embedded in OCT (optimal cutting temperature) medium and stored at −80°C.

extract_protocol: To isolate total RNA, skin samples of stretched scars and the surounding healthy skin were cryosectioned at the thickness 20 µm. Scar dermis was dissected using 23G needles under a stereomiscrocope. After homogenization with QIAshredder (Qiagen), RNA was isolated using RNeasy Plus Mini Kit (Qiagen). The quality of isolated RNA was tested using Agilent 2100 Bioanalyser.

tag: condition

value: healthy


title: DMSO_THP1_r3

value: 0.1percent DMSO (control)


title: NPC43 scONEseq 064

description:
RNA+DNA
NPC single cell 064


title: CD21-Cre AtrC/-_G0_0h_3 [SD018]

value: non-activated B cells


title: CD21-Cre Atr+/C_S_24h_4 [SD021]


title: HD-70 cell line


title: DMSO_THP1_r2

value: MLL-AF9 human AML cell


title: CD21-Cre Atr+/C_S_24h_6 [SD023]


title: NPC43 scONEseq 063

description:
RNA+DNA
NPC single cell 063


title: CD21-Cre AtrC/-_G0_0h_2 [SD017]


title: patient 2, stretched scar dermis

source_name: dermis excised from fibrotic skin of stretched scars

value: scar


title: CD21-Cre AtrC/-_G0_0h_1 [SD016]


title: NPC43 scONEseq 062

description:
RNA+DNA
NPC single cell 062


title: DMSO_THP1_r1

value: 36 hours


title: patient 2, healthy dermis


title: patient 1, healthy dermis


title: NPC43 scONEseq 061

description:
RNA+DNA
NPC single cell 061

value: nasopharyngeal carcinoma


title: CD21-Cre Atr+/C_G0_0h_3 [SD015]


title: patient 3, stretched scar dermis


title: NPC43 scONEseq 060

description:
RNA+DNA
NPC single cell 060

value: scONE-seq


title: PET_8T

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

institute: Asan Medical Center

description: gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then the raw RNA-seq data were processed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized read counts for each gene.

source_name: liver cancer

growth_protocol: freezing liquid nitrogen

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit with 1 ug of total RNA.

treatment_protocol: fresh frozen tissue

value: liver

value: HCC


title: CD21-Cre Atr+/C_G0_0h_2 [SD014]

value: mixed 129 BL6


title: PET_89T

description: gene expression


title: NPC43 scONEseq 059

description:
RNA+DNA
NPC single cell 059


title: PET_88T

description: gene expression


title: patient 1, stretched scar dermis


title: patient 2, time point 6 months after hair follicle transplantation

data_processing: Transcriptomic Analysis Console (TAC) was used to perform a one-way ANOVA on the dataset to identify 719 transcripts that were significantly (P < 0.01) and differentially (fold change <- 1.5 or > 1.5) regulated between the four time points (0 mo, 2 mo, 4 mo, 6 mo). The intensity values of the samples were normalized and summarized using RMA algorithm.

source_name: interfollicular skin dermis excised from a scar 6 months after hair follicle transplantation

growth_protocol: During the study, 3 mm punch biopsies were taken from the scar dermis from two patients at four time points: prior to transplantation (time point 0 mo), then again at 2, 4, and 6 months after hair follicle transplantation. Excised biopsies were embedded in OCT (optimal cutting temperature) medium and stored at −80°C.

extract_protocol: To isolate total RNA, 3 mm biopsies from four time points (0, 2, 4, and 6 month after hair follicle transplantation) were cryosectioned at the thickness 20 µm. Scar dermis was dissected using 23G needles under a stereomiscrocope. After homogenization with QIAshredder (Qiagen), RNA was isolated using RNeasy Plus Mini Kit (Qiagen). The quality of isolated RNA was tested using Agilent 2100 Bioanalyser.

tag: individual

value: patient 2

value: hair follicle transplantation

tag: time after hair follicle transplantation

value: 6 months

value: scar dermis


title: patient 2, time point 4 months after hair follicle transplantation

source_name: interfollicular skin dermis excised from a scar 4 months after hair follicle transplantation

value: 4 months

tag: tissue


title: patient 2, time point 2 months after hair follicle transplantation

source_name: interfollicular skin dermis excised from a scar 2 months after hair follicle transplantation

value: 2 months


title: CD21-Cre Atr+/C_G0_0h_1 [SD013]

tag: genotype

value: CD21-Cre Atr+/C


title: CD21-Cre AtrC/-_S_24h_3 [SD012]

value: anti-CD40 and Il4 activated B cells

value: CD21-Cre AtrC/-


title: NPC43 scONEseq 058

description:
RNA+DNA
NPC single cell 058


title: PET_9T

description: gene expression


title: patient 1, time point 6 months after hair follicle transplantation

value: patient 1


title: PET_86T

description: gene expression


title: NPC43 scONEseq 057

description:
RNA+DNA
NPC single cell 057


title: patient 2, time point 0 months (before hair follicle transplantation)

source_name: skin dermis excised from a scar

value: control

value: 0 months


title: PET_84T

description: gene expression


title: NPC43 scONEseq 056

description:
RNA+DNA
NPC single cell 056

value: nasopharyngeal carcinoma


title: CD21-Cre AtrC/-_S_24h_2 [SD010]


title: NPC43 scONEseq 092

description:
RNA+DNA
NPC single cell 092

value: scONE-seq


title: NPC43 scONEseq 055

description:
RNA+DNA
NPC single cell 055


title: CD21-Cre AtrC/-_G1_10h_2 [SD009]


title: F2_D1 individual, grown at 16C [T16_P1.A6_F2_D1]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P1.A7_F2_D1]

tag: treatment


title: PET_82T

description: gene expression

value: liver

value: HCC


title: patient 1, time point 4 months after hair follicle transplantation

value: hair follicle transplantation


title: NPC43 scONEseq 054

description:
RNA+DNA
NPC single cell 054


title: CD21-Cre AtrC/-_S_24h_1 [SD008]

value: mixed 129 BL6


title: PET_81T

description: gene expression


title: patient 1, time point 0 months (before hair follicle transplantation)

value: scar dermis


title: patient 1, time point 2 months after hair follicle transplantation


title: CD21-Cre AtrC/-_G1_10h_3 [SD011]


title: NPC43 scONEseq 052

description:
RNA+DNA
NPC single cell 052


title: CD21-Cre AtrC/-_G1_10h_1 [SD007]


title: PET_7T

description: gene expression


title: NPC43 scONEseq 051

description:
RNA+DNA
NPC single cell 051


title: CD21-Cre Atr+/C_S 24h_3 [SD006]


title: CD21-Cre Atr+/C_G1_10h_3 [SD005]


title: PET_83T

description: gene expression


title: PET_79T

description: gene expression


title: CD21-Cre Atr+/C_S 24h_2 [SD004]


title: NPC43 scONEseq 050

description:
RNA+DNA
NPC single cell 050


title: NPC43 scONEseq 053

description:
RNA+DNA
NPC single cell 053


title: PET_76T

description: gene expression


title: PET_75T

description: gene expression


title: CD21-Cre Atr+/C_G1_10h_2 [SD003]


title: PET_80T

description: gene expression


title: NPC43 scONEseq 049

description:
RNA+DNA
NPC single cell 049


title: NPC43 scONEseq 048

description:
RNA+DNA
NPC single cell 048


title: CD21-Cre Atr+/C_S 24h_1 [SD002]


title: PET_74T

description: gene expression


title: NPC43 scONEseq 047

description:
RNA+DNA
NPC single cell 047


title: NOMO1.1.0µM.GSK3484862.d4.n1

city: Collegeville

first: Shawn

middle: W

last: Foley

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

description:
d4
n1

hyb_protocol: RNA was isolated, labeled, and hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays at Q2 Solutions.

scan_protocol: Standard Affymetrix protocol

data_processing: Differential gene expression analysis was performed using limma with default settings for priors and other parameters on human genome U133 Plus 2.0 Affymetrix microarray .CEL files. Expression changes with adjusted p-values < 0.05 and absolute log2 fold change > 1 were considered significant.

growth_protocol: Cell lines were obtained from the American Type Culture Collection, the Deutsche Sammlung von Mikroorganismen und Zellbulturen, or AddexBio and maintained in the recommended cell culture media at 37°C in 5% CO2.

treatment_protocol: Cells were plated 24 hours before treatment with 0.1% DMSO, 1 µM GSK3484862, 0.4 µM DAC, or 10 µM GSK3510477 then grown for 96 hours before collection.

tag: dose


title: CD21-Cre Atr+/C_G1_10h_1 [SD001]


title: NOMO1.0µM.DMSO.d4.n2

description:
d4
n2

label_protocol: RNA was isolated, labeled, and hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays at Q2 Solutions.

value: DMSO

value: 0 uM


title: NOMO1.1.0µM.GSK3484862.d4.n2

description:
d4
n2

extract_protocol: RNA was isolated, labeled, and hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays at Q2 Solutions.


title: THP1.1.0µM.GSK3484862.d4.n2

description:
d4
n2


title: THP1.1.0µM.GSK3484862.d4.n1

description:
d4
n1


title: THP1.0µM.DMSO.d4.n2

description:
d4
n2


title: NOMO1.0µM.DMSO.d4.n1

description:
d4
n1


title: THP1.0µM.DMSO.d4.n1

description:
d4
n1


title: C57BL/6J mouse, CRS+IMQ, day 29, rep3

city: 杭州市

first: musab

middle: al

last: rudaisat

state: 浙江省

address: 浙江大学，华家池校区

institute: Zhejiang university Affiliated hospital Sir Run Run Shaw hospital

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
CRS_IMQ_3

data_processing:
To measure the expression levels of mRNAs in the different groups, edgeR and StringTie software were used to determine FPKM values.
The limma R software package was used to identify DEGs between two sample groups.
Statistically significant genes were considered at adjusted p-values < 0.05 and absolute log2FC values ≥ 1 (Benjamini and Hochberg, 1995).
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values

source_name: Dorsal skin

extract_protocol:
Total RNA was extracted from mouse dorsal skin tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, United States).
The NanoDrop ND-1000 (NanoDrop, Wilmington, DE, United States) was used for RNA quantification and assessment of sample purity.
RNA-sequencing and library generation was performed by Novaseq™ 6000 (LC-Bio Technology, Hangzhou, China).

value: Dorsal skin

value: CRS+IMQ


title: MV411.10µM.GSK3510477.d4.n2

description:
d4
n2

value: 10 uM


title: PET_72T

description: gene expression


title: NPC43 scONEseq 045

description:
RNA+DNA
NPC single cell 045

tag: method


title: C57BL/6J mouse, CRS+IMQ, day 29, rep2

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
CRS_IMQ_2


title: NPC43 scONEseq 043

description:
RNA+DNA
NPC single cell 043


title: MV411.10µM.GSK3510477.d4.n1

description:
d4
n1


title: NPC43 scONEseq 044

description:
RNA+DNA
NPC single cell 044


title: MV411.1.0µM.GSK3484862.d4.n2

description:
d4
n2


title: C57BL/6J mouse, CRS+IMQ, day 29, rep1

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
CRS_IMQ_1


title: PET_70T

description: gene expression


title: C57BL/6J mouse, Imiquimod (IMQ), day 29, rep3

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
Ctrl_IMQ_3

value: Imiquimod (IMQ)


title: PET_71T

description: gene expression


title: PET_73T

description: gene expression


title: PET_6T

description: gene expression


title: NPC43 scONEseq 042

description:
RNA+DNA
NPC single cell 042


title: NPC43 scONEseq 046

description:
RNA+DNA
NPC single cell 046


title: C57BL/6J mouse, Imiquimod (IMQ), day 29, rep2

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
Ctrl_IMQ_2


title: C57BL/6J mouse, Imiquimod (IMQ), day 29, rep1

description:
CRS_IMQVSCtrl_IMQ_Gene_differential_expression
Ctrl_IMQ_1


title: NPC43 scONEseq 041

description:
RNA+DNA
NPC single cell 041


title: C57BL/6J mouse, Chronic restrain stress (CRS), day 29, rep3

description:
CRSVSCtrl_Gene_differential_expression
CRS_3

value: Chronic restrain stress (CRS)


title: PET_67T

description: gene expression


title: PET_69T

description: gene expression


title: NPC43 scONEseq 040

description:
RNA+DNA
NPC single cell 040


title: NPC43 scONEseq 039

description:
RNA+DNA
NPC single cell 039


title: PET_68T

description: gene expression


title: PET_66T

description: gene expression


title: PET_65T

description: gene expression


title: MV411.0.4µM.DAC.d4.n2

description:
d4
n2

value: DAC


title: NPC43 scONEseq 038

description:
RNA+DNA
NPC single cell 038

value: nasopharyngeal carcinoma


title: MV411.0.4µM.DAC.d4.n1

description:
d4
n1


title: MV411.1.0µM.GSK3484862.d4.n1

description:
d4
n1


title: NPC43 scONEseq 037

description:
RNA+DNA
NPC single cell 037

value: scONE-seq


title: C57BL/6J mouse, no treatment, day 29, rep3

description:
CRSVSCtrl_Gene_differential_expression
Ctrl_3


title: PET_64T

description: gene expression


title: NPC43 scONEseq 036

description:
RNA+DNA
NPC single cell 036


title: C57BL/6J mouse, no treatment, day 29, rep2

description:
CRSVSCtrl_Gene_differential_expression
Ctrl_2


title: PET_63T

description: gene expression


title: MV411.0µM.DMSO.d4.n1

description:
d4
n1


title: MV411.0µM.DMSO.d4.n2

description:
d4
n2


title: C57BL/6J mouse, Chronic restrain stress (CRS), day 29, rep2

description:
CRSVSCtrl_Gene_differential_expression
CRS_2


title: C57BL/6J mouse, no treatment, day 29, rep1

description:
CRSVSCtrl_Gene_differential_expression
Ctrl_1


title: PET_62T

description: gene expression


title: NPC43 scONEseq 034

description:
RNA+DNA
NPC single cell 034


title: PET_61T

description: gene expression


title: C57BL/6J mouse, Chronic restrain stress (CRS), day 29, rep1

description:
CRSVSCtrl_Gene_differential_expression
CRS_1


title: Tumor-infiltrating lymphocytes, IL_27 [IL_27_S4_L003]

city: shanghai

first: Moran

last: Yang

address: shenyang road 128

institute: fudan university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Assembly: mm10
Supplementary files format and content: raw-count

source_name: mouse subcutaneous tumor

extract_protocol:
Fresh tissue of vehicle or rmIL-27 treated mouse  tumors was collected in cold RPMI media, cut into small pieces with surgical scissors, digested with Gentle MACS Dissociator (MiltenyiBiotec) for 45 min at 37°C on a shaker, and consequently meshed through a Falcon 70-um cell strainer. After PBS washing, red cells were lysed with an ammonium chloride solution. Tumor infiltrating lymphocytes were sorted using mouse CD45 (TIL) MicroBeads (MiltenyiBiotec)  according to the protocol of MACS® Separation.
Single-cell RNA libraries were prepared using the Chromium Single Cell 5’v2 Reagent (10x Genomics), and Chromium Single Cell V(D)J Reagent kits (10x Genomics) was used to prepare single-cell RNA libraries according to the manufacturer s instructions. Each sequencing library was generated with a unique sample index. Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: mouse subcutaneous tumor

tag: cell line

value: Lymphocytes

value: 6-8 weeks old


title: NPC43 scONEseq 033

description:
RNA+DNA
NPC single cell 033


title: M4-09, SHI1.0uM.DMSO.d4.n1.n1

hyb_protocol: Not provided

scan_protocol: Not provided

source_name: SHI1, DMSO, 0 µM

label_protocol: Not provided

treatment_protocol: Cells were plated 24 hours before treatment with 0.1% DMSO, 1 µM GSK3484862, then grown for 96 hours before collection.

tag: cell type

value: AML


title: NPC43 scONEseq 032

description:
RNA+DNA
NPC single cell 032

source_name: NPC43 cell line


title: PET_59T

description: gene expression

value: liver

tag: disease state

value: HCC


title: NPC43 scONEseq 031

description:
RNA+DNA
NPC single cell 031


title: M4-25, SHI1.0uM.DMSO.d4.n2.n2


title: M4-26, SHI1.1uM.GSK862.d4.n2.n2


title: NPC43 scONEseq 035

description:
RNA+DNA
NPC single cell 035


title: Tumor-infiltrating lymphocytes, control [Control_S1_L001]

description: 10x Genomics


title: PET_58T

description: gene expression


title: Tumor-infiltrating lymphocytes, control [Control_S3_L002]

description: 10x Genomics


title: PET_57T

description: gene expression


title: Tumor-infiltrating lymphocytes, IL_27 [IL_27_S1_L001]

description: 10x Genomics


title: NPC43 scONEseq 030

description:
RNA+DNA
NPC single cell 030


title: NPC43 scONEseq 029

description:
RNA+DNA
NPC single cell 029


title: M4-12, NOMO1.1uM.GSK862.d4.n1.n1


title: M4-10, SHI1.1uM.GSK862.d4.n1.n1


title: HBs-HepR-1-60w [WYW60_6]

city: Hefei

first: Yuwei

last: Wu

address: Huangshan Road #443

institute: the university of science and technology of China

data_processing:
Screening quality was evaluated using FastQC (RRID: SCR_014583)
HiSat2 (RRID: SCR_015530, version 2.1.0) was used to map reads to the mouse genome GRCm38.p6 from ENSEMBL (RRID: SCR_002344).
DESeq2 (RRID: SCR_000154) was used for differential analysis of all expressed genes
Read counts were computed with Rsubread using default settings.
Assembly: mm9
Supplementary files format and content: raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol regent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: Sex

value: male

value: intrasplenically injected HBs-Tg hepatocytes

tag: time


title: HBs-HepR-2-60w [WYW60_10]


title: M4-11, NOMO1.0uM.DMSO.d4.n1.n1

source_name: NOMO1, DMSO, 0 µM


title: M4-27, NOMO1.0uM.DMSO.d4.n2.n2


title: M4-32, SKNO1.1uM.GSK862.d4.n2.n2


title: M4-16, SKNO1.1uM.GSK862.d4.n1.n1


title: PET_56T

description: gene expression


title: PET_60T

description: gene expression


title: B6-HepR-2-60w [WYW60_3]

value: intrasplenically injected B6-WT hepatocytes


title: M4-31, SKNO1.0uM.DMSO.d4.n2.n2

source_name: SKNO1, DMSO, 0 µM


title: PET_55T

description: gene expression


title: NPC43 scONEseq 027

description:
RNA+DNA
NPC single cell 027


title: NPC43 scONEseq 028

description:
RNA+DNA
NPC single cell 028


title: M4-28, NOMO1.1uM.GSK862.d4.n2.n2


title: PET_54T

description: gene expression


title: M4-15, SKNO1.0uM.DMSO.d4.n1.n1


title: B6-HepR-1-60w [WYW60_1]


title: NPC43 scONEseq 026

description:
RNA+DNA
NPC single cell 026


title: HBs-HepR-2-52w [WYW52_12]


title: PET_53T

description: gene expression


title: HBs-HepR-1-52w [WYW52_8]


title: NPC43 scONEseq 025

description:
RNA+DNA
NPC single cell 025


title: NPC43 scONEseq 024

description:
RNA+DNA
NPC single cell 024


title: B6-HepR-2-52w [WYW52_3]


title: M4-23, THP1.0uM.DMSO.d4.n2.n2

source_name: THP1, DMSO, 0 µM


title: PET_50T

description: gene expression


title: B6-HepR-1-52w [WYW52_1]


title: NPC43 scONEseq 023

description:
RNA+DNA
NPC single cell 023


title: M4-08, THP1.1uM.GSK862.d4.n1.n1


title: HBs-HepR-2-40w [WYW40_10]


title: PET_51T

description: gene expression


title: NPC43 scONEseq 021

description:
RNA+DNA
NPC single cell 021


title: PET_4T

description: gene expression


title: NPC43 scONEseq 022

description:
RNA+DNA
NPC single cell 022


title: M4-07, THP1.0uM.DMSO.d4.n1.n1


title: PET_49T

description: gene expression


title: B6-HepR-2-40w [WYW40_2]


title: HBs-HepR-1-40w [WYW40_3]


title: PET_48T

description: gene expression


title: M4-24, THP1.1uM.GSK862.d4.n2.n2


title: PET_52T

description: gene expression


title: B6-HepR-1-40w [WYW40_1]


title: HBs-HepR-3-18w [Tg3]

source_name: hepatocytes

value: hepatocytes


title: NPC43 scONEseq 019

description:
RNA+DNA
NPC single cell 019


title: PET_46T

description: gene expression


title: NPC43 scONEseq 018

description:
RNA+DNA
NPC single cell 018


title: HBs-HepR-2-18w [Tg2]


title: M4-18, SKM1.1uM.GSK862.d4.n2.n2


title: PET_45T

description: gene expression


title: NPC43 scONEseq 016

description:
RNA+DNA
NPC single cell 016


title: M4-17, SKM1.0uM.DMSO.d4.n2.n2

source_name: SKM1, DMSO, 0 µM


title: M4-22, MOLM13.1uM.GSK862.d4.n2.n2


title: NPC43 scONEseq 020

description:
RNA+DNA
NPC single cell 020


title: HBs-HepR-1-18w [Tg1]


title: PET_44T

description: gene expression


title: PET_43T

description: gene expression


title: NPC43 scONEseq 014

description:
RNA+DNA
NPC single cell 014


title: B6-HepR-3-18w [B63]


title: NPC43 scONEseq 015

description:
RNA+DNA
NPC single cell 015


title: PET_47T

description: gene expression


title: PET_42T

description: gene expression


title: M4-06, MOLM13.1uM.GSK862.d4.n1.n1


title: M4-02, SKM1.1uM.GSK862.d4.n1.n1


title: M4-01, SKM1.0uM.DMSO.d4.n1.n1


title: NPC43 scONEseq 017

description:
RNA+DNA
NPC single cell 017


title: NPC43 scONEseq 013

description:
RNA+DNA
NPC single cell 013


title: B6-HepR-1-18w [B61]


title: M4-21, MOLM13.0uM.DMSO.d4.n2.n2

source_name: MOLM13, DMSO, 0 µM


title: M4-04, GDM1.1uM.GSK862.d4.n1.n1


title: M4-05, MOLM13.0uM.DMSO.d4.n1.n1


title: PET_41T

description: gene expression

source_name: liver cancer


title: NPC43 scONEseq 012

description:
RNA+DNA
NPC single cell 012


title: PET_40T

description: gene expression


title: hypoxic Vegfr2Y949F B set, sample 4, scRNAseq

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Preprocessing of the FASTQ sequencing data was performed using the fastp preprocessor tool with default parameters. To improve quantification accuracy, sequencing errors in the UMI sequence were modeled using the UMI-Tools method. Thereafter, the clean reads were mapped to the mouse genome (Ensembl100) and analyzed using a Seurat package (Version 4.1.0).
Quality control steps were performed to filter out rare reads/genes that were found in less than 10 cells, low-quality cells with less than 250 detected genes, cells with low gene expression complexity (threshold: log10GenesPerUMI<0.8), cells with more than 20% reads mapping to the mitochondrial genome and cell doublets (doubletThresholding=0.25) identified by the scDblFinder (v1.6.0) function
Subsequently, the Seurat SCTransform function was applied to normalize the retained data and found the most variable genes from each sample. The Seurat FindIntegrationAnchors function was then conducted using the 3,000 most variable genes to identify shared sources of variation and the correct anchors for integration of all data across different batches
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Fresh lungs were dissected from mice following 6-week hypoxia exposure, minced and subjected to collagenase/DNase digestion as described above. The dissociated cell suspension was filtered through a 70-μm strainer and then a 40-μm strainer. Thereafter, red blood cells were lysed and removed from the cell suspension and the remaining pulmonary cells were centrifuged at 1,500 rpm for 5 minutes, rinsed with 0.04% BSA/PBS for 3 times, and re-suspended in 0.04% BSA/PBS
A 10X Genomics analysis system was used to prepare single-cell whole transcriptome. Single cell capture was achieved by nanodroplet (single-Poisson distribution loading)-based encapsulation of 10X barcoded gel beads with the cells. The resulting gel beads in emulsion (GEMs) containing the captured cells were then retrieved, dissolved and subjected to reverse transcription of polyadenylated mRNAs.
Single-cell transcriptomic sequencing libraries were generated from 10X barcoded cDNAs and feature barcode DNAs and sequenced on a NovaSeq System (Illumina) with a 150 bp paired-end run according to the manufacture’s instruction

treatment_protocol: 6-8 week old WT and Vegfr2Y949F mice were exposed to hypoxia for 6 weeks

value: Lung

tag: strain background

tag: age

value: 6-8 week old

value: 6-week hypoxia exposure


title: NPC43 scONEseq 011

description:
RNA+DNA
NPC single cell 011


title: M4-20, GDM1.1uM.GSK862.d4.n2.n2


title: hypoxic WT B set, sample 3, scRNAseq

value: WT


title: M4-19, GDM1.0uM.DMSO.d4.n2.n2

source_name: GDM1, DMSO, 0 µM


title: PET_3T

description: gene expression


title: M4-03, GDM1.0uM.DMSO.d4.n1.n1


title: YE3-1

city: Ningbo

first: Weiwei

last: Ma

state: Zhejiang

address: #19 Dehou Stress

institute: Ningbo Academy of Agricultural Sciences

data_processing:
Illumina/BGI platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using perl scripts.
Trimmed sequence reads were mapped toIRGSP-1.0 using HISAT2 software
Read count extraction and normalization were performed using FeatureCounts
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: NIP

growth_protocol: grown in nutrient solution for 2 weeks

extract_protocol:
total RNAs were extracted with RNAprep Pure Plant Kit (TIANGEN, Beijing, China) and quantified by NanoDrop 2000C spectrophotometer (Thermo Fisher Scientific)
For cDNA synthesis, a total 1 μg RNA for each sample was treated with DNase I to eradicate the genomic DNA and then used as a template for reverse transcription (QuantiTect Reverse Transcription Kit, Qiagen, China). We added fragment buffer to break into short segments using short segment RNA as template. Sequencing libraries was created using NEB Next Ultra RNA Library Prep Kit following manufacturer′s instructions. The index codes were added to each sample. Paired-end cDNA libraries with an insert size of 300 bp were constructed for transcriptome sequencing.

value: NIP

value: 2 week old young seedlings

value: grown in nutrient solution for 2 weeks

value: 2 weeks


title: YE3-2


title: YE3-3


title: PET_39T

description: gene expression


title: NPC43 scONEseq 010

description:
RNA+DNA
NPC single cell 010

value: nasopharyngeal carcinoma

value: scONE-seq


title: NPC43 scONEseq 009

description:
RNA+DNA
NPC single cell 009


title: B6-HepR-2-18w [B62]

tag: strain


title: YC12-3


title: hypoxic Vegfr2Y949F A set, sample 2, scRNAseq


title: YC12-2


title: PET_38T

description: gene expression


title: hypoxic WT A set, sample 1, scRNAseq


title: YC12-1


title: NPC43 scONEseq 007

description:
RNA+DNA
NPC single cell 007


title: PET_37T

description: gene expression


title: NPC43 scONEseq 008

description:
RNA+DNA
NPC single cell 008


title: PET_36T

description: gene expression


title: YC11-2


title: YC11-3


title: PET_35T

description: gene expression


title: OGE-1

first: XIANWEI

last: SU

address: Shatin

institute: The Chinese University of Hong Kong

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HT22 murine hippocampal cells were seeded into a 100 cm dish and maintained  in DMEM high glucose supplemented with 10% FBS at 37 ℃/5% CO2 in an incubator

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: The cells were then placed in a hypoxia chamber , which was flushed with 95 % N2 and 5 % CO2 for 10 min and then sealed for the OGD treatment. HT22 cells were exposed to the mixture gas in the hypoxic box for 2 hr. After the deprivation period, the cells were changed to the standard medium and re-oxygenated for 24 hr.

value: murine hippocampal cells

value: with OGD and reoxygenation with hiPS-MSC-Evs


title: OGE-3


title: NPC43 scONEseq 006

description:
RNA+DNA
NPC single cell 006

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics


title: OGP-3

value: with OGD and reoxygenation with PBS


title: NPC43 scONEseq 005

description:
RNA+DNA
NPC single cell 005


title: YC11-1


title: PET_33T

description: gene expression

value: liver

value: HCC


title: YC10-3

source_name: DJ

value: DJ


title: NPC43 scONEseq 003

description:
RNA+DNA
NPC single cell 003


title: OGP-2


title: YC10-2


title: C3

value: without treatment


title: OGP-1


title: NPC43 scONEseq 002

description:
RNA+DNA
NPC single cell 002


title: OGE-2


title: C2


title: YR9-3


title: HUVEC+H9 scONEseq 067

description:
RNA+DNA
Normal single cell 067

source_name: HUVEC+H9 cell line co-culture

value: Human umbilical vein endothelial cell and human embryonic stem cell


title: PET_30T

description: gene expression


title: C1


title: NPC43 scONEseq 004

description:
RNA+DNA
NPC single cell 004


title: HUVEC+H9 scONEseq 066

description:
RNA+DNA
Normal single cell 066


title: NPC43 scONEseq 001

description:
RNA+DNA
NPC single cell 001


title: Macrophage, ischemic brain of Foxp3Egfp mice, rep2, scRNAseq

first: Mengyan

last: Hu

address: Tianhe Road

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
Demultiplexing, alignment to the GRCh38 reference with the Mus musculus genome (GRCm38) by the STAR aligner v2.5.1b with default settings, and quantification of sequencing reads for each sample were performed using Cell Ranger (Version 4.0.0) with the default parameter. The filtered gene-barcode matrices for single cells were analyzed using Seurat (V4) following the tutorial at https://satijalab.org/seurat/.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Brain

extract_protocol:
Foxp3Egfp mice were flushed with PBS and single cell suspensions were prepared after flow sorting of CD45+CD11b+CD3-F4/80+ cells using a BD FACSAria cell-sorting system (BD Biosciences, San Jose, CA).
Cells were droplet separated using Chromium™ Single Cell 3’ v3 Reagent Kit with the 10x Genomics microfluidic system creating cDNA library with individual barcodes for individual cells. Barcoded cDNA transcripts from stroke mice were pooled and sequenced using the novaseq 6000 Sequencing System.

value: Macrophage

value: ischemic brain

value: 6-8 weeks old


title: YR9-1

value: NIP


title: PET_28T

description: gene expression


title: PET_32T

description: gene expression


title: YR9-2

value: 2 week old young seedlings


title: Macrophage, ischemic brain of Foxp3Egfp mice, rep1, scRNAseq

description: 10x Genomics


title: HUVEC+H9 scONEseq 065

description:
RNA+DNA
Normal single cell 065


title: YC10-1

value: grown in nutrient solution for 2 weeks


title: PET_31T

description: gene expression


title: BMDM, IgG isotype, Invitrogen

data_processing:
Basecalls performed using CASAVA version 1.4
DNA product sequencing reads of CUT & RUN were aligned to the mm10 genome assembly using EasyAlign version 3.2 with the following configurations.
Data were filtered using the following specifications:
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: peaks file
Library strategy: CUT&RUN

source_name: BMDM

growth_protocol: MCSF-conditioned RPMI1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with Cells were fixed with  at room temperature for 2 min. DNA product was obtained using CST's Cut&Run kit and Foxp3 antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 0.1% formaldehyde

value: BMDM

tag: chip antibody

value: IgG isotype (Invitrogen, #MA5-14447)


title: PET_2T

description: gene expression


title: HUVEC+H9 scONEseq 063

description:
RNA+DNA
Normal single cell 063

value: scONE-seq


title: BMDM, FOXP3, Invitrogen, rep2

value: Foxp3 (Invitrogen, #FJK-16s)


title: YC8-1

value: 2 weeks


title: PET_34T

description: gene expression


title: PET_27T

description: gene expression


title: PET_29T

description: gene expression


title: YC8-2


title: PET_26T

description: gene expression


title: YC8-3


title: YC7-3


title: PET_25T

description: gene expression


title: HUVEC+H9 scONEseq 061

description:
RNA+DNA
Normal single cell 061


title: HUVEC+H9 scONEseq 062

description:
RNA+DNA
Normal single cell 062


title: BMDM, FOXP3, Invitrogen, rep1


title: DHFR 3

city: Toulouse

first: Alice

last: Davy

address: 118 route de Narbonne

department: MCD, CBI

country: France

institute: CNRS

description:
E12.5 neocortical tissues were extracted from two different embryos and divided into sample pools based on genotype.
DHFR+/Δ
Read counts: 35M

data_processing:
All files were aligned to the reference mouse genome (Ensembl Mus musculus GRCm39; gtf(mm10)) using RNA STAR (Version Galaxy Tool: v2.7.2b) with parameters --alignIntronMin 20 --alignIntronMax 1000000 --outFilterMismatchNmax 10.
Assembly: mm10
Supplementary files format and content: Wig files were generated using an in-house script (reads were elongated to 100b).

source_name: E12.5 neocortical tissues

extract_protocol:
RNA was isolated from the cell pellet using Trizol reagent.
400 ng of total RNA (RIN>7) was used for the construction of sequencing libraries using NEBNext Ultra II following manufacturer's protocols.

value: Neocortical tissues

value: DHFR+/delta


title: PET_24T

description: gene expression

value: liver

value: HCC


title: YC7-1


title: DHFR 2


title: PET_23T

description: gene expression


title: YC7-2


title: HUVEC+H9 scONEseq 059

first: Angela

last: WU

address: Clear water bay street

institute: HKUST

description:
RNA+DNA
Normal single cell 059


title: DHFR 1


title: YC6-3


title: HUVEC+H9 scONEseq 058

description:
RNA+DNA
Normal single cell 058


title: PET_20T

description: gene expression


title: WT 3

description:
E12.5 neocortical tissues were extracted from two different embryos and divided into sample pools based on genotype.
Read counts: 35M

value: WT


title: HUVEC+H9 scONEseq 057

description:
RNA+DNA
Normal single cell 057

value: Human umbilical vein endothelial cell and human embryonic stem cell


title: YC6-2


title: YC6-1


title: WT 2


title: HUVEC+H9 scONEseq 060

description:
RNA+DNA
Normal single cell 060


title: WT 1


title: YC5-3

value: DJ


title: PET_1T

description: gene expression


title: PET_22T

description: gene expression


title: Nnmt LKO6

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nnmt LKO


title: Nnmt LKO5


title: PET_18T

description: gene expression


title: YR4-3


title: HUVEC+H9 scONEseq 054

description:
RNA+DNA
Normal single cell 054


title: HUVEC+H9 scONEseq 056

description:
RNA+DNA
Normal single cell 056


title: PET_17T

description: gene expression


title: HUVEC+H9 scONEseq 053

description:
RNA+DNA
Normal single cell 053


title: Nnmt LKO4


title: HUVEC+H9 scONEseq 052

description:
RNA+DNA
Normal single cell 052


title: PET_21T

description: gene expression


title: YR4-1


title: PET_15T

description: gene expression


title: HUVEC+H9 scONEseq 051

description:
RNA+DNA
Normal single cell 051


title: WT5


title: PET_13T

description: gene expression


title: YC3-3


title: WT4


title: HUVEC+H9 scONEseq 050

description:
RNA+DNA
Normal single cell 050


title: PET_12T

description: gene expression


title: HUVEC+H9 scONEseq 049

description:
RNA+DNA
Normal single cell 049


title: HUVEC+H9 scONEseq 055

description:
RNA+DNA
Normal single cell 055


title: WT3


title: YC3-2


title: YC5-1


title: PET_19T

description: gene expression


title: PET_10T

description: gene expression


title: HUVEC+H9 scONEseq 048

description:
RNA+DNA
Normal single cell 048


title: YC3-1


title: YR4-2


title: Nnmt LKO1


title: YC2-3


title: PSC27-F-03

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
F3_S42_L003
processed data file: F.deseq2.annot

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Transcripts Per Million fragments mapped (TPM) were calculated using a protocol from Tajnik et al. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Research. 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample

source_name: PSC27_treated with bleomycin and RU.521

growth_protocol: Prostate stromal cells were routinely cultured and passaged (typically 0.5–1 × 106 cells in a T75 flask) in stroma-specific media supplemented with 10% FBS.

extract_protocol:
At the end of cell culture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon 80% confluency, cells were treated with 50 μg/ml bleomycin, or 50 μg/ml bleomycin plus 20 μM ML324 in culture for consecutive 7-10 days, with the media changed every 2-3 days.

tag: cell line source

value: Derived from the prostate tisue of a human patient

value: Primary normal human prostate stromal cells

value: treated with bleomycin and RU.521


title: intestinal epithelial cells, Kdm6a/b ablation, rep4

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Basecalls were performed using NovaSeq Control Software 1.7.5, RTA v3.4.4
ChIP-Seq data quality was assessed using FastQC (v0.10.1) and raw read alignment was completed using Bowtie (v0.12.7).
Aligned reads were filtered using samtools (v1.11) and picard (v1.141) to remove reads that were unmapped, reads in which the next segment was unmapped, reads that were not properly aligned, reads not passing platform quality, secondary alignments, and PCR or optical duplicates.
Deduplication was performed using picard (v1.141), peak calling was completed using SICER2 (v1.0.3), and wig files were produced to visualize coverage generated by peak calling
Differential methylation analysis was performed using csaw. Reads overlapping the ENCODE blacklisted regions were removed. Reads were then counted using 2 different sliding window resolutions (2000 bp with 500 bp spacing and 1000 bp with 250 bp spacing), and windows having at least 2-fold more coverage than the average background were retained. Normalization factors were computed using the composition bias method
edgeR was used for statistical modeling of differential H3K27me3, and combined p-values for the 2 window resolutions were calculated by csaw using the Simes’ method for region-level FDR control
All regions with an FDR less than 0.05 were called as differentially methylated. Differentially methylated regions were annotated to all neighboring genes within 5000 base pairs of the region.
Assembly: mm10
Supplementary files format and content: wig files
Supplementary files format and content: db_csaw is a comma-separated values (CSV) file containing the final output of the csaw analysis. Listed in this file are the differential H3K27me3 genomic regions identified through this analysis.

source_name: jejunum

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Chromatin was digested into fragments using 10 U/mL and 5 U/mL MNase.
ChIP-Seq libraries were prepared using the protocol reported in the following publication: Sadeh R, Launer-Wachs R, Wandel H, Rahat A & Friedman N. Elucidating combinatorial chromatin states at single-nucleosome resolution. Molecular Cell 2016; 63: 1080–1088.

value: jejunum

value: intestinal epithelial cells

value: Kdm6a/Kdm6b knockout

value: H3K27me3 (Millipore Sigma, 07-449)

value: acute (7 days post ablation)

value: Female


title: HUVEC+H9 scONEseq 046

description:
RNA+DNA
Normal single cell 046

value: scONE-seq


title: HUVEC+H9 scONEseq 047

description:
RNA+DNA
Normal single cell 047


title: YC1-3

value: NIP

value: 2 week old young seedlings

value: grown in nutrient solution for 2 weeks

value: 2 weeks


title: PSC27-F-01

city: Shanghai

description:
F1_S40_L003
processed data file: F.deseq2.annot


title: intestinal epithelial cells, Kdm6a/b ablation, rep3


title: HUVEC+H9 scONEseq 044

city: Hong Kong

description:
RNA+DNA
Normal single cell 044

value: Human umbilical vein endothelial cell and human embryonic stem cell


title: PSC27-E-03

description:
E3_S39_L003
processed data file: E.deseq2.annot

source_name: PSC27_treated with bleomycin and STING deficiency


title: intestinal epithelial cells, Kdm6a/b ablation, rep2


title: HUVEC+H9 scONEseq 045

description:
RNA+DNA
Normal single cell 045


title: intestinal epithelial cells, Kdm6a/b ablation, rep1


title: YC1-2


title: HUVEC+H9 scONEseq 043

description:
RNA+DNA
Normal single cell 043


title: intestinal epithelial cells, control, rep4

value: Control/WT


title: YC1-1


title: PSC27-E-01

description:
E1_S37_L003
processed data file: E.deseq2.annot

value: treated with bleomycin and STING deficiency


title: HUVEC+H9 scONEseq 042

description:
RNA+DNA
Normal single cell 042


title: WT2

source_name: liver

value: liver

value: WT


title: NIP-3


title: intestinal epithelial cells, control, rep3


title: PSC27-D-03

description:
D3_S36_L003
processed data file: D.deseq2.annot

source_name: PSC27_treated with bleomycin and CCCP

value: Derived from the prostate tisue of a human patient

value: Primary normal human prostate stromal cells

value: treated with bleomycin and CCCP


title: NIP-2


title: PSC27-F-02

description:
F2_S41_L003
processed data file: F.deseq2.annot

value: treated with bleomycin and RU.521


title: HUVEC+H9 scONEseq 041

description:
RNA+DNA
Normal single cell 041


title: YC2-2


title: intestinal epithelial cells, control, rep2

value: jejunum

value: intestinal epithelial cells

value: H3K27me3 (Millipore Sigma, 07-449)


title: HUVEC+H9 scONEseq 040

description:
RNA+DNA
Normal single cell 040

value: scONE-seq


title: YC2-1

value: NIP


title: PSC27-D-02

description:
D2_S35_L003
processed data file: D.deseq2.annot


title: NIP-1

value: 2 week old young seedlings


title: intestinal epithelial cells, control, rep1

value: acute (7 days post ablation)

value: Female


title: PSC27-D-01

description:
D1_S34_L003
processed data file: D.deseq2.annot


title: DJ-3

value: DJ

value: grown in nutrient solution for 2 weeks

value: 2 weeks


title: HUVEC+H9 scONEseq 039

description:
RNA+DNA
Normal single cell 039

value: Human umbilical vein endothelial cell and human embryonic stem cell


title: intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep5 [KO.TATAAT]

data_processing:
Basecalls performed using NovaSeq Control Software 1.7.0, RTA v3.4.4
RNA-Seq data quality was assessed using FastQC (v.0.11.5)
Alignment was performed using the STAR method (v2.4.0) (default parameters with a maximum fragment size of 2 kb)
Samtools (v1.9) was used to filter for properly paired primary alignments
Bedtools (v2.27.1) was used to remove mitochondrial reads and reads on non-chromosome contigs
Read counts on RefSeq genes were computed using featureCounts (v1.6.2).
Differential gene expression analysis was performed using the DESeq2 R package with normalizaiton to correct for library sizes
Genes with an FDR value of 0.05 or less were defined as differentially expressed
Assembly: mm9
Supplementary files format and content: comma-separated values (CSV) text files containing DESeq2 normalized read counts for each sample
Supplementary files format and content: bigwig files

extract_protocol:
RNA was extracted using the Rneasy Micro Kit (74004, QIAGEN). 250 ng of RNA per sample was used as input for library generation.
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina (E7530, NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). Manufacturer protocols were followed.

value: Kdm6a/Kdm6b knockout

value: prolonged (5 months post ablation)


title: PSC27-E-02

description:
E2_S38_L003
processed data file: E.deseq2.annot

value: Derived from the prostate tisue of a human patient

value: Primary normal human prostate stromal cells

value: treated with bleomycin and STING deficiency


title: HUVEC+H9 scONEseq 038

description:
RNA+DNA
Normal single cell 038


title: intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep4 [KO.GACGAC]

value: jejunum


title: intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep3 [KO.GTGATC]

value: intestinal epithelial cells


title: PSC27-C-01

description:
C1_S31_L003
processed data file: C.deseq2.annot

source_name: PSC27_treated with bleomycin and SB203580

value: treated with bleomycin and SB203580


title: HUVEC+H9 scONEseq 037

description:
RNA+DNA
Normal single cell 037

value: scONE-seq


title: HUVEC+H9 scONEseq 036

description:
RNA+DNA
Normal single cell 036


title: intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep2 [KO.CTAGCT]


title: PSC27-G-03

description:
G3_S45_L003
processed data file: G.deseq2.annot

source_name: PSC27_treated with bleomycin in culture

value: treated with bleomycin in culture


title: PSC27-C-02

description:
C2_S32_L003
processed data file: C.deseq2.annot


title: PSC27-C-03

description:
C3_S33_L003
processed data file: C.deseq2.annot


title: DJ-1

value: 2 week old young seedlings

value: WT


title: HUVEC+H9 scONEseq 064

description:
RNA+DNA
Normal single cell 064


title: PSC27-G-02

description:
G2_S44_L003
processed data file: G.deseq2.annot


title: HUVEC+H9 scONEseq 035

description:
RNA+DNA
Normal single cell 035


title: intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep1 [KO.CACCGG]

value: Female


title: HUVEC+H9 scONEseq 034

description:
RNA+DNA
Normal single cell 034


title: php1,2,3 5 uM Rep 3

city: Chapel Hill

first: Charles

last: Hodgens

state: North Carolina (NC)

address: 250 Bell Tower Drive

department: GMB

institute: UNC Chapel Hill

data_processing:
alignment: star, overhang of 49 bases, SA index N bases parameter of 13
quantification: salmon, flags used: --gcBias, --seqBias
data analysis: DESeq2
Genome_build: IRGSP 1.0

organism: Oryza sativa Japonica Group

source_name: whole root tissue

extract_protocol: polyA-enriched, cDNA generated with random primers, PCR amplified

value: 5 uM benzyl adenine

tag: replicate


title: intestinal epithelial cells, control, prolonged model, rep3 [Control.TACAGC]

tag: tissue

value: Control/WT


title: php1,2,3 5 uM Rep 2

tag: genotype


title: php1,2,3 5 uM Rep 1


title: PSC27-G-01

description:
G1_S43_L003
processed data file: G.deseq2.annot


title: HUVEC+H9 scONEseq 033

description:
RNA+DNA
Normal single cell 033


title: intestinal epithelial cells, control, prolonged model, rep2 [Control.CTATAC]


title: php1,2,3 100 nM Rep 3

value: 100 nM benzyl adenine


title: DJ-2

value: DJ

value: grown in nutrient solution for 2 weeks

value: 2 weeks


title: PSC27-A-03

description:
A3_S30_L003
processed data file: A.deseq2.annot

source_name: PSC27_untreated in culture

value: Derived from the prostate tisue of a human patient

value: untreated in culture


title: PSC27-A-02

description:
A2_S29_L003
processed data file: A.deseq2.annot

value: Primary normal human prostate stromal cells


title: PSC27-A-01

description:
A1_S28_L003
processed data file: A.deseq2.annot


title: php1,2,3 control Rep 1

value: control


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep6 [DKO.mouse10796_TCCCGA]

data_processing:
Basecalls performed using NovaSeq Control Software 1.6.0, RTA v3.4.4
RNA-Seq data quality was assessed using FastQC (v.0.11.5)
Alignment was performed using the STAR method (v2.4.0) (default parameters with a maximum fragment size of 2 kb)
Samtools (v1.9) was used to filter for properly paired primary alignments
Bedtools (v2.27.1) was used to remove mitochondrial reads and reads on non-chromosome contigs
Read counts on RefSeq genes were computed using featureCounts (v1.6.2).
Differential gene expression analysis was performed using the DESeq2 R package with normalizaiton to correct for library sizes
Genes with an FDR value of 0.05 or less were defined as differentially expressed
Assembly: mm9
Supplementary files format and content: comma-separated values (CSV) text files containing DESeq2 normalized read counts for each sample
Supplementary files format and content: bigwig files

value: jejunum

value: intestinal epithelial cells

value: Kdm6a/Kdm6b knockout

value: acute (7 days post ablation)


title: WT 5 uM Rep 3

value: Kitaake


title: HUVEC+H9 scONEseq 031

description:
RNA+DNA
Normal single cell 031

value: Human umbilical vein endothelial cell and human embryonic stem cell

value: scONE-seq


title: HUVEC+H9 scONEseq 027

description:
RNA+DNA
Normal single cell 027


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep7 [DKO.mouse10979_TCGGCA]

value: Female


title: HUVEC+H9 scONEseq 028

description:
RNA+DNA
Normal single cell 028


title: HUVEC+H9 scONEseq 025

description:
RNA+DNA
Normal single cell 025


title: HUVEC+H9 scONEseq 030

description:
RNA+DNA
Normal single cell 030


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep3 [DKO.mouse11133_CTATAC]


title: php1,2,3 100 nM Rep 2


title: HUVEC+H9 scONEseq 029

description:
RNA+DNA
Normal single cell 029


title: HUVEC+H9 scONEseq 026

description:
RNA+DNA
Normal single cell 026


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep1 [DKO.mouse10981_CGGAAT]


title: intestinal epithelial cells, control, prolonged model, rep1 [Control.CGGAAT]

value: Control/WT

value: prolonged (5 months post ablation)


title: php1,2,3 100 nM Rep 1

value: 100 nM benzyl adenine


title: FA19 cells, Lactate 10 mM rep2

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

data_processing:
Base call (BCL) files generated by the sequencing platform were converted to fastqsanger.gz using the Illumina cloud service BaseSpace Sequence Hub.
Single-end sequencing fastqsanger.gz files were aligned to the N. gonorrhoeae FA19 genome by using the Tophat2 algorithm (available at the public ABIMS Galaxy tool shed from the Station Biologique de Roscoff-CNRS-Sorbonne University) to generate BAM files. The following changes were made to the default parameters: Use a built in reference genome or own from your history-use a genome from history (FA19 genome .fna file); TopHat settings to use-use full parameter list; Use Gene Annotation Model-use gene annotation from history (FA19 genome .gff annotation file)
Cuffdiff algorithm (available at the ABIMS Galaxy server) was used to determine transcript differential expression reports between the conditions analyzed: Glucose 1 vs 10 mM or Lactate 1 vs 10 mM. Each condition was analyzed in replicates. The following changes were made to the default parameters: Library normalization method- classic fpkm; Perform Bias Correction-yes; Reference sequence data-History (FA19 genome .fna file); apply length correction- standard length correction
Genome_build: N. gonorrhoeae FA19 strain with GenBank assembly accession number GCA_000273665.1
Supplementary_files_format_and_content: The .xlsx files consist of the transcript differential expression report generated by Cuffdiff for each comparison tested. These files contain the locus tag number, the gene chromosome coordinates, FPKM expression values for each gene within each condition, the 10 mM to 1 mM fold-change ratios and the statistical significance p and q values. Tab 1 contains the list of differentially expressed genes at fold changes higher than or equal to 2. Tab 2 contains the list of differentially expressed genes. Tab 3 contains the list of above parameters for all chromosomal genes. The txt. files contain Tophat2 statistics consisting of the alignment rates for the reads in fastqsanger.gz files to the provided genome build.

organism: Neisseria gonorrhoeae

source_name: FA19 cells, Lactate 10 mM

growth_protocol: N. gonorrhoeae strain FA19StrR was plated from a -80oC frozen glycerol stock into gonococcal base (GCB) agar plates supplemented with Kellogg’s supplements I and II and incubated over night at 37°C under 5% (v/v) CO2. Five mL of GCB broth with Kellogg’s supplements I (without D-glucose added) and II and 0.042% (w/v) NaHCO3 were inoculated with the cell biomass at an initial OD600 of 0.1 and incubated at 37°C with agitation (225 rpm). Two concentrations of D-glucose in the medium were compared, 1 and 10 mM with a fix concentration of 3 mM L-lactate for both glucose concentrations. Similarly, two concentrations of L-lactate were compared, 1 and 10 mM with a fix concentration of 1.5 mM glucose for both lactate concentrations. Two mL samples were collected after 4h incubation (cultures had OD600 values of 0.6-0.8) and placed on ice for further RNA processing. Each condition was analyzed in duplicate having 8 samples in total.

extract_protocol:
Total RNA extraction was conducted using the RNeasy mini kit (Qiagen), following the manufacturer’s protocol. One hundred µL of 200 ng/µL total isolated RNA were treated to remove genomic DNA contamination using the Turbo DNA-free Kit (Invitrogen, Thermo Fisher Scientific) as per the manufacturer’s instructions. One hundred µL of DNase I-digested total RNA samples were concentrated and cleaned-up using the RNeasy MinElute Cleanup Kit (QIAGEN). Finally, samples were eluted from the RNeasy MinElute spin columns with 26 µL of Nuclease-Free water (Ambion, Thermo Fisher Scientific) and stored at -80 °C until library preparation.
Library construction and sequencing was done at the UAB Heflin Center for Genomic Sciences, Birmingham, AL. RNA-sequencing was performed on the Illumina NextSeq 500 as described by the manufacturer (Illumina Inc., San Diego, CA). The quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer. RNA with a RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation. Library preparation was done using the Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent, Santa Clara, CA). Library construction began with ribosome reduction using the RiboMinus rRNA depletion kit for bacteria (Invitrogen). The resulting RNA was randomly fragmented with cations and heat, which was followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4ng/µL final concentration). Second strand cDNA production was done with standard techniques, the ends of the resulting cDNA were made blunt, A-tailed and adaptors ligated for amplification and indexing to allow for multiplexing during sequencing. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturer’s recommendations for onboard clustering (Illumina).

treatment_protocol: Drawn samples were centrifuged for 2 min at 10000 g and 4°C, resuspended in 200 µL RNAlater solution (Ambion, Life Technologies) and incubated 10 min on ice. Then, samples were centrifuged 3 min at 6500 g and 4°C and the pellets were stored at -80 °C for RNA extraction.

value: FA19 StrR

value: WT

value: GC broth-grown planktonic cells

value: Lactate

value: 10 mM


title: php1,2,3 control Rep 3

value: control


title: WT 5 uM Rep 2

value: 5 uM benzyl adenine


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep2 [DKO.mouse10982_CTAGCT]

value: jejunum

value: intestinal epithelial cells


title: FA19 cells, Lactate 10 mM rep1


title: FA19 cells, Lactate 1 mM rep1

source_name: FA19 cells, Lactate 1 mM

value: 1 mM


title: FA19 cells, Lactate 1 mM rep2


title: HUVEC+H9 scONEseq 032

description:
RNA+DNA
Normal single cell 032


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep5 [DKO.mouse10763_TACAGC]

value: Kdm6a/Kdm6b knockout

value: acute (7 days post ablation)


title: FA19 cells, Glucose 10 mM rep2

description: Table-1_D-Glucose-1_vs_10_mM-CuffDiff.xlsx

source_name: FA19 cells, Glucose 10 mM

value: Glucose


title: intestinal epithelial cells, Kdm6a/b ablation, acute model, rep4 [DKO.mouse11134_GTGATC]

value: Female


title: php1,2,3 control Rep 2


title: FA19 cells, Glucose 10 mM rep1


title: WT 5 uM Rep 1

value: Kitaake


title: WT 100 nM Rep 3


title: HUVEC+H9 scONEseq 024

description:
RNA+DNA
Normal single cell 024

value: Human umbilical vein endothelial cell and human embryonic stem cell

value: scONE-seq


title: intestinal epithelial cells, control, acute model, rep5 [Control.mouse10856_TCGAAG]

value: Control/WT


title: FA19 cells, Glucose 1 mM rep1

source_name: FA19 cells, Glucose 1 mM

value: FA19 StrR

value: WT


title: HUVEC+H9 scONEseq 022

description:
RNA+DNA
Normal single cell 022

source_name: HUVEC+H9 cell line co-culture


title: HUVEC+H9 scONEseq 023

description:
RNA+DNA
Normal single cell 023


title: WT 100 nM Rep 1

value: 100 nM benzyl adenine


title: HUVEC+H9 scONEseq 021

description:
RNA+DNA
Normal single cell 021


title: intestinal epithelial cells, control, acute model, rep3 [Control.mouse10765_TATAAT]


title: FA19 cells, Glucose 1 mM rep2

value: GC broth-grown planktonic cells


title: intestinal epithelial cells, control, acute model, rep4 [Control.mouse10789_TCATTC]


title: WT control Rep 3

value: control


title: intestinal epithelial cells, control, acute model, rep1 [Control.mouse10980_CACCGG]


title: WT control Rep 2


title: intestinal epithelial cells, control, acute model, rep2 [Control.mouse10762_GACGAC]


title: WT 100 nM Rep 2


title: WT control Rep 1


title: HUVEC+H9 scONEseq 020

description:
RNA+DNA
Normal single cell 020


title: HUVEC+H9 scONEseq 019

description:
RNA+DNA
Normal single cell 019


title: M12_1 ovary

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing: fastq data were processed with Cellranger  to obtain filtered data

source_name: ovary cells from 12-month-old mouse

extract_protocol:
Ovaries were digested in HBSS supplemented with 0.25% Trypsin, 1mM EDTA and 0.01% Dnase I and incubated at 37°C to obtain single cell suspensions.
Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number.Interrupt, end repair and add A base. Finally the SPRIselect beads was used to purify the product.Adaptor ligation and SPRIselect purification.Index PCR and SPRIselect purification.Qubit® 3.0 Flurometer (Life Technologies, CA, USA) was used to determine the library concentration.Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA) was used to determine the distribution of library product fragments.

value: ovary


title: HUVEC+H9 scONEseq 018

description:
RNA+DNA
Normal single cell 018


title: M12_2 ovary


title: HUVEC+H9 scONEseq 017

description:
RNA+DNA
Normal single cell 017


title: M8_2 ovary

source_name: ovary cells from 8-month-old mouse


title: 34w

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-trimming set to 20, quality set to 20 and a minimum read length of 20 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The aligned to the horse reference genome (EquCab3.0) using BSMAP (Yuanxin and Wei, 2009) with default options recommended for RRBS data, specifying the enzyme cleavage site (MspI) and mapping only to two forward strands.
The percentage of methylation of individual CpG sites with coverage higher than 5 reads was determined using Methylation Caller software.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: Files containing the percentage of methylation of individual CpG sites determined using Methylation Caller software.

organism: Equus caballus

extract_protocol:
DNA was isolated from tissue using a Sherlock AX (A&A Biotechnology) kit
To quantify DNA methylation levels across the genome RRBS methodology was used following the Ovation RRBS Methyl-Seq System (NuGEN) protocol. 12 DNA libraries were pooled in one pool and sequenced on the NexSeq 500 platform (Illumina) using a 75-bp single-end read and High-Output Flow Cell. The sequencing was performed along with a balanced control library obtained from the viral DNA (PhiX, Illumina).

treatment_protocol: The collected material was transferred into tubes and stored at -20°C.

tag: individual

value: horse 4

value: liver


title: HUVEC+H9 scONEseq 016

description:
RNA+DNA
Normal single cell 016


title: 34p

source_name: lung

value: lung


title: M8_1 ovary


title: HUVEC+H9 scONEseq 015

description:
RNA+DNA
Normal single cell 015


title: 34s

source_name: heart

value: heart


title: W8_2 ovary

source_name: ovary cells from 8-week-old mouse


title: 32p

value: horse 3


title: W8_1 ovary


title: 32s


title: D14_2 ovary

source_name: ovary cells from 14-day-old mouse


title: 30w

source_name: liver

value: horse 2


title: HUVEC+H9 scONEseq 012

description:
RNA+DNA
Normal single cell 012


title: D14_1 ovary


title: H1299 cells transfected with NC siRNA

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

description: Gene expression after NC siRNA transfection in H1299 cell

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

source_name: Cultured cell

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)

growth_protocol: Cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cultures were maintained at 37°C in a 5% CO2 incubator.

extract_protocol: The total RNA was extracted from cells using TRIzol® Reagent (Invitrogen life technologies)

treatment_protocol: H1703, H1299, and H358T cells treated with or without si-ETV4 for 48 hours

value: NSCLC cell line

value: Non-Small Cell Lung Cancer


title: H1703 cells transfected with NC siRNA

description: Gene expression after NC siRNA transfection in H1703 cell

data_processing: Agilent Microarray Scanner (Agilent p/n G2565BA)


title: 30p


title: H358 TGF-β treated cells transfected with NC siRNA

description: Gene expression after NC siRNA transfection in H358Tcell


title: H1703 cells transfected with ETV4 siRNA

description: Gene expression after ETV4 siRNA transfection in H1703 cell


title: H358 TGF-β treated cells transfected with ETV4 siRNA

description: Gene expression after ETV4 siRNA transfection in H358T cell


title: H1299 cells transfected with ETV4 siRNA

description: Gene expression after ETV4 siRNA transfection in H1299 cell


title: 30s


title: P1 ovary

source_name: ovary cells from postnatal 1 day mouse

value: Postnatal day 1


title: HUVEC+H9 scONEseq 010

description:
RNA+DNA
Normal single cell 010

value: Human umbilical vein endothelial cell and human embryonic stem cell

value: scONE-seq


title: HUVEC+H9 scONEseq 011

description:
RNA+DNA
Normal single cell 011


title: 27p

value: horse 1


title: 8719R2_CIA9-60_IndexUDI0044_GGAGCGTC+GTCCGTGC_L004_001

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

data_processing:
Bioinformatics analyses of RNA-seq raw data were performed using the OmicSoft studio software package version 10.1.2.9 (Qiagen)
Mapping of RNA-seq reads (fastq files) to the mouse genome was done using OmicSoftGenCode V19 as gene model with B.38 as reference genome and OSA4 as aligner
Genes with FPKM <1 were filtered out according to a 50% fraction rule for each sample group to exclude minimally expressed genes. Differentially expressed genes were detected by applying the DESeq2 statistical test and P-values were adjusted by the Benjamini-Hochberg procedure to control FDR
Supplementary files format and content: Tab-delimited text file include FPKM values for each sample

source_name: front paws

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy Mini Kit for animal tissues according to the manufacturer´s instructions
For RNA-seq library preparation the Illumina TruSeq Stranded mRNA Library Preparation Kit was used. RNA libraries were subjected to paired-end sequencing on a Novaseq 6000 system with a reading depth of 80 million raw reads per sample

treatment_protocol: Groups of  mice were treated with antibodies directed against murine TNF (clone XT3.11, BioXcell), murine IL-6 (clone MP5-20F3, BioXcell), or both twice per week by intraperitoneal injection of the indicated doses

value: front paws

value: male

tag: treatment

value: no CIA


title: 8719R2_CIA9-57_IndexUDI0042_GCGCAAGC+TCACGCCG_L004_001


title: HUVEC+H9 scONEseq 014

description:
RNA+DNA
Normal single cell 014


title: Kidney at T3,biological rep 3

first: Guanghai

last: Wang

address: Shatainan Road 1023

department: School of Public Health

institute: Southern Medical University

description: Gene expression data from kidney at 12 weeks treated with CdCl2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RTA 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Command Console Software 4.0(Affymetrix,Santa Clara,CA,US) using Affymetrix default analysis settings and gobal scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Rattus norvegicus

source_name: Rattus norvegicus kidney of cadmium expose for 12 weeks

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

growth_protocol: The rat kidney was harvested and stored at liquid nitrogen without delay with RNA inhibitor protection.

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

treatment_protocol: After grinding at the present of liquid nitrogen,kidney tissue was collected for futher total RNA extraction.

value: 12 weeks


title: Kidney at T3,biological rep 2


title: Kidney at T3,biological rep 1


title: Kidney at T2,biological rep 3

description: Gene expression data from kidney at 6 weeks treated with CdCl2

source_name: Rattus norvegicus kidney of cadmium expose for 6 weeks

value: 6 weeks


title: Kidney at T2,biological rep 2


title: 27w


title: v-abl transformed B cells, Chk1i LY2603618, run2, rep3

city: New York

first: Shan

last: Zha

address: 1130 Saint Nicholas Ave.

institute: Columbia University

description:
20220118_LY2603618_3
gRNA PCR from genomic DNA
labeled: Chk1iLY2603618-1and2

data_processing:
The results were analyzed via the MAGeCK FluteMLE pipeline as previously described (Wang B, et al., Nat Protoc, 2019) using the DMSO samples as the baseline.
Genes with positive z-score and FDR<0.2 identified in the CRISPR screen were analyzed for Gene Ontology (GO) using R studio.
Assembly: Mouse Improved Genome-wide Knockout CRISPR Library v2 developed by Kosuke Yusa was used. A list of gRNAs and genes included can be found on the Addgene listing (67988).
Supplementary files format and content: *.raw_count.xlsx: Processed data files are Excel files of raw gRNA counts generated by the MAGeCK software for all gRNAs represented in the gRNA library used. Each file contains treatments and replicates that were done together in the same experiment.

source_name: bone marrow

growth_protocol: v-abl transformed B-cells were grown in DMEM media with 15% FBS.

extract_protocol:
At least 30 million cells were collected in triplicate for each treatment before dox-induction, after dox-induction but before drug treatment, and after 6 days of drug treatment. Cells were lysed and genomic DNA was extracted.
gRNA from extracted genomic DNA was amplified according to (Joung J, et al., Nat Protoc, 2017) using 2.5ug DNA x 96 reactions per treatment, NEBNext High Fidelity Master Mix (2x) (New England Biolabs) and NGS-Lib-Fwd and NGS-Lib-KO-Rev primers. PCR reactions were purified using Zymospin columns (Zymo Research) and cleaned up using AMPureXP beads (Beckman Coulter).
Amplicon-seq of gRNAs harvested from cells.

treatment_protocol: Cells were infected with a tetracycline inducible Cas9 (Addgene 50661), and a single clone was picked for high inducibility and low leakiness. Cells were then infected with a BFP-tagged whole genome mouse gRNA library (Addgene 67988) with an MOI ~1 and then FACS-sorted for BFP+ cells. At least 30 million cells were then treated with 3ug/ml doxycycline (Sigma-Aldrich) for 5 days, refreshing media every other day. Induced cells were then treated with the IC90 dose of drug (as measured by MTT assay (Roche) at 6 days) or DMSO for 6 days, with at least 30 million cells for each treatment to start, refreshing media as necessary. The IC90 doses used were VE821 (Selleckchem): 1.8uM, AZD6738 (Selleckchem): 0.4uM, LY2603618 (Selleckchem): 0.4uM, DMSO: 0.02%.

value: bone marrow

value: v-abl transformed B cells


title: HUVEC+H9 scONEseq 005

description:
RNA+DNA
Normal single cell 005

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.


title: Kidney at T2,biological rep 1


title: HUVEC+H9 scONEseq 009

description:
RNA+DNA
Normal single cell 009


title: Kidney at T1,biological rep 2

description: Gene expression data from kidney at 1 day treated with CdCl2

source_name: Rattus norvegicus kidney of cadmium expose for 1 day

value: 1 day


title: HUVEC+H9 scONEseq 013

description:
RNA+DNA
Normal single cell 013


title: HUVEC+H9 scONEseq 008

description:
RNA+DNA
Normal single cell 008


title: 8719R2_CIA9-58_IndexUDI0043_AAGATACT+ACTTACAT_L004_001


title: 27s

value: heart


title: Kidney at T1,biological rep 3


title: 8719R2_CIA9-53_IndexUDI0057_TGCGGCGT+CCTCGGTA_L004_001

value: IgG1 isotype ctrl. 30 mg/kg

value: isotype


title: HUVEC+H9 scONEseq 004

description:
RNA+DNA
Normal single cell 004


title: Kidney at N3,biological rep 2

description: Gene expression data from kidney at 12 weeks treated with normal saline

source_name: Rattus norvegicus normal kidney

value: Normal saline


title: HUVEC+H9 scONEseq 007

description:
RNA+DNA
Normal single cell 007


title: 8719R2_CIA9-56_IndexUDI0041_ATATGGAT+CTGTATTA_L004_001


title: 8719R2_CIA9-55_IndexUDI0096_CTAGCGCT+GTGTAGAC_L004_001


title: Kidney at T1,biological rep 1


title: 8719R2_CIA9-54_IndexUDI0083_CTGCTTCC+GATAGATC_L004_001


title: HUVEC+H9 scONEseq 006

description:
RNA+DNA
Normal single cell 006


title: HUVEC+H9 scONEseq 002

description:
RNA+DNA
Normal single cell 002


title: v-abl transformed B cells, Chk1i LY2603618, run2, rep2

description:
20220118_LY2603618_2
gRNA PCR from genomic DNA
labeled: Chk1iLY2603618-2


title: v-abl transformed B cells, Chk1i LY2603618, run2, rep1

description:
20220118_LY2603618_1
gRNA PCR from genomic DNA
labeled: Chk1iLY2603618-1


title: Kidney at N3,biological rep 1


title: v-abl transformed B cells, ATRi AZD6738, run2, rep3

description:
20220118_AZD6738_3
gRNA PCR from genomic DNA
labeled: ATRiAZD6738-1and2

value: ATRi AZD6738


title: 8719R2_CIA9-49_IndexUDI0040_CGGACAAC+TCCGGATT_L004_001


title: HCT116 scONEseq 098

description:
RNA+DNA
HCT116 single cell 194

source_name: HCT116 cell line

value: Colon