title: Sham1

city: Guangzhou

first: Fang

last: Tan

address: Dongfengdong Road 567

institute: Sun Yat-sen University Cancer Center

description: Library name: Sample 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in pair end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -q -L 16 --phred64 -p 6
TPM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample.
Supplementary files format and content: Tab-delimited text files include raw gene counts for each Sample.

source_name: Intestine

extract_protocol:
Total RNA of intestine samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an BGISEQ-500 platform.

value: Intestine

value: CLP


title: DKO RING1B, R70H, GSK3431uM, 48h, IgG, Replicate 1

status: Public on Feb 17 2026

type: SRA

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

country: USA

institute: Sylvester Comprehensive Cancer Center

description: Library name: DKO_RING1B_R70H_GSK3431uM_48h_IgG_REP1

library_source: genomic

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment algainst mm10 using nf-core/cutandrun v3.2.2 (https://github.com/nf-core/cutandrun/tree/3.2.2)  with additional ‘--aligner bowtie2 --read_length 150 --trim_nextseq 20 --blacklist [BED]’
Assembly: mm10, GRCh38
Supplementary files format and content: Bigwig files with average (normalized) signal from replicates and/or alleles (WT/M)
Library strategy: Cut&Run

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: mESCs were cultured in ESC+2i media, while mNPCs were differentiated using a three-stage protocol: 4 days in ESC media, followed by 4 days in EB media, and a final 4 days in EB media supplemented with 5 μM of RA.

extract_protocol:
CUT&RUN assays were performed using the CUTANA kit following the manufacturer's protocol (EpiCypher, 14-1048). Briefly, mESCs Ring1B WT and R70H mutants were trypsinized (0.05%) to obtain a single-cell suspension followed by mild crosslinking with 0.1% formaldehyde for 1 minute. A total of 2 × 10⁵ cells were incubated with ConA beads, followed by overnight incubation with antibodies against HA (EpiCypher, 13-2010), Flag (EpiCypher, 13-2031), H3K27me3 (Active Motif, 39155), H2AK119ub (Cell Signaling D27C4), and IgG (EpiCypher, 13-0042).
E. coli was used as a spike-in control for all samples. Additionally, the SNAP-CUTANA™ K-MetStat Panel (EpiCypher, 19-1002) was included as an additional spike-in control for IgG and H3K27me3. Two biological replicates were used per condition.

treatment_protocol: there was no additional treatments

tag: cell line

tag: cell type

value: Human embryo kidney tissue

tag: antibody

value: IgG, EpiCypher (Cat #13-0042)1ug

tag: genotype

value: RNF2 R70H/WT


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 6C)

city: DALLAS

first: ZHUAN

last: ZHOU

state: TX

address: 7430 W Northwest Hwy APT 1, Dallas, TX 75225, USA

department: Surgery

institute: University if Texas Southwestern Medical Center

description: Library name: MDST8_TG3_6C

library_source: transcriptomic

data_processing:
[ChIP-seq] Raw reads were quality trimmed using Trim Galore, aligned to hg38 using Bowtie 2 (v.2.4.5), and converted to BAM format using samtools (v.1.6).
[ChIP-seq] Sorted BAM files were used as input for MACS2 (v.2.2.7.1) for peak calling (p-value < 0.05). Significant peaks were annotated by CHIPpeakAnno (v.3.30.1).
[RNA-seq] Raw reads were quality trimmed using Trim Galore (v0.6.6) and mapped to hg38 using HISAT2 (v.2.1.0). Mapped reads were converted to BAM format using samtools (v.1.6).
[RNA-seq] Sorted BAM files were used as input for featureCounts (v.2.0.0) to count the mapped reads to the gene coordinates reported in the GTF annotation file (GENCODE v.43).
Assembly: hg38
Supplementary files format and content: [ChIP-seq] MACS2 output files (.narrowPeak) containing genomic coordinates, peak boundaries, and statistical significance. [RNA-seq] Tab-delimited text files containing raw read counts per gene.

molecule: polyA RNA

source_name: colon

growth_protocol: DMEM plus 10% FBS, 37oC, 5% CO2

extract_protocol:
[For ChIP-seq] Cells were cultured, fixed with formaldehyde, lysed, and sonicated. TWIST1 antibody (Abcam ab50887) was used for immunoprecipitation. [For RNA-seq] RNA was isolated using the Qiagen RNeasy Mini Kit. mRNA was purified from total RNA using oligo-dT magnetic beads.
[For ChIP-seq] Paired-end libraries were generated using Illumina protocols. Libraries were sequenced on the Illumina NextSeq 500 platform (150-bp paired-end). [For RNA-seq] After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using dUTP. Libraries were sequenced on the Illumina NovaSeq 6000.

treatment_protocol: WIST1 knockout was generated using CRISPR-Cas9. TWIST1 knockdown was generated using shRNA.

tag: tissue

value: colon

value: TWIST1 knockout


title: Sham2

country: China

description: Library name: Sample 4

molecule: total RNA

organism: Mus musculus

tag: treatment


title: RNA-seq of Control LoVo cells (Rep A)

description: Library name: LoVo_C1_A

value: LoVo

value: wild type

value: shRNA control


title: CLP1

description: Library name: Sample 1


title: R70H mNPC, H3K27me3, MB, Replicate 1

description:
Library name: 112_mNPC_k27me3_MB_REP1
Merged Signal of k27me3 R70H mNPC Reps MB

value: Mouse Neural progenitor cells (mNPCs)

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: R70H mNPC, Histone H2B ubiquitination, MA, Replicate 1

description:
Library name: 112_mNPC_Ub_MA_REP1
Merged Signal of Histone H2B ubiquitination R70H mNPC Reps MA


title: CLP2

description: Library name: Sample 2


title: DKO RING1B, R70H, GSK3431uM, 48h, IgG, Replicate 2

description: Library name: DKO_RING1B_R70H_GSK3431uM_48h_IgG_REP2


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 6B)

description: Library name: MDST8_TG3_6B


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 6A)

description: Library name: MDST8_TG3_6A


title: R70H mNPC, allelM, FL, MB, Replicate 1

description:
Library name: 112_mNPC_allelM_FL_MB_REP1
Merged Signal of all Mutant mNPC R70H allele and replicates

value: Flag(DYKDDDDK-Tag)


title: DKO RING1B, R70H, DMSO, IgG, Replicate 2

description: Library name: DKO_RING1B_R70H_DMSO_IgG_REP2


title: R70H mNPC, H3K27me3, MA, Replicate 1

description:
Library name: 112_mNPC_k27me3_MA_REP1
Merged Signal of k27me3 R70H mNPC Reps MA


title: R70H mESC, Histone H2B ubiquitination, MB, Replicate 1

description:
Library name: 112_mESC_Ub_MB_REP1
Merged Signal of Histone H2B ubiquitination R70H mESC Reps MB

value: Mouse embryonic stem cells (mESCs)


title: DKO RING1B, R70H, GSK3431uM, 48h, H3k27me3, Replicate 2

description: Library name: DKO_RING1B_R70H_GSK3431uM_48h_H3k27me3_REP2


title: DKO RING1B, R70H, DMSO, IgG, Replicate 1

description: Library name: DKO_RING1B_R70H_DMSO_IgG_REP1


title: DKO RING1B, R70H, DMSO, H3K27me3, Replicate 2

description: Library name: DKO_RING1B_R70H_DMSO_H3K27me3_REP2


title: R70H mNPC, allelW, FL, MA, Replicate 1

description:
Library name: 112_mNPC_allelW_FL_MA_REP1
Merged Signal of all Mutant mNPC WT allele and replicates


title: DKO RING1B, R70H, DMSO, H3K27me3, Replicate 1

description: Library name: DKO_RING1B_R70H_DMSO_H3K27me3_REP1


title: HMB9

type: RNA

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

hyb_protocol: GeneChip™ Hybridization, Wash, and Stain Kit Fluidics stations FS450-007

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Data processing and statistical data evaluation was performed in the R environment. The raw data were normalized and summarized using the RMA (robust multi-array average) algorithm from the R package oligo version 1.68.2. The genes were associated with vendor-provided annotation information (Release 36, Thermo Fisher Scientific, https://www.thermofisher.com/order/catalog/product/sec/assets?url=TFS-Assets/LSG/Support-Files/Clariom_S_Human.r1.na36.hg38.a1.transcript.csv.zip) and control genes were removed after background correction. Furthermore, irrelevant genes with low expression were removed so that 21,250 probes corresponding to 19,358 genes remained (intensity > 4 in at least 2 samples). After applying quality metrices to normalized data, it was determined that one biological replicate from control models at timepoint 4 was an outlier. Thus, that sample was further excluded from the microarray data analysis.   Differential gene expression (DGE) analysis was performed by the R package limma version 3.60.2: linear models were fit and moderated t-statistics computed by the eBayes function. The linear models were fitted, and moderated t-statistics were computed using the eBayes function. Subsequently, the Benjamini-Hochberg correction was applied to exclude false-positive results, and the differentially expressed genes were considered significant with an adjusted p-value<0.05 and a log2FC>0.5 as well as log2FC<-0.5.

label: biotin

source_name: tissue inoculated with skin bacteria

label_protocol: Terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: Tissues were cultivated at 37°C and 5% CO2 in antibiotic-free maintenance medium (MLNM-FT-MM-AFAB) obtained from MatTek.

extract_protocol: Total RNA of the epidermis was extracted using Trizol ® reagent (Ambion) following manufacturer´s protocol.

treatment_protocol: Tissues were inoculated with bacteria obtained from a skin swab. As vehicel control, PBS was used.

value: MatTek's:Melanoma-Full Thickness-A375

value: malignant melanoma cells

value: human-derived epidermal keratinocytes

value: NHEK

value: human-derived dermal fibroblasts

value: NHDF

value: inoculated

tag: time point

value: day 12


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 5B)

description: Library name: MDST8_TG3_5B

value: colon


title: HMB15


title: R70H mESC, Histone H2B ubiquitination, MA, Replicate 1

description:
Library name: 112_mESC_Ub_MA_REP1
Merged Signal of Histone H2B ubiquitination R70H mESC Reps MA

value: RNF2 R70H/WT


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 5C)

description: Library name: MDST8_TG3_5C

value: TWIST1 knockout


title: ctrl7

source_name: negative control

value: negative control


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 2C)

description: Library name: MDST8_TG3_2C


title: R70H mESC, H3K27me3, MA, Replicate 1

description:
Library name: 112_mESC_k27me3_MA_REP1
Merged Signal of k27me3 R70H mESC Reps MA


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 5A)

description: Library name: MDST8_TG3_5A


title: DKO RING1B, WT, GSK3431uM, 48h, H3k27me3, Replicate 1

description: Library name: DKO_RING1B_WT_GSK3431uM_48h_H3k27me3_REP1

value: Human embryo kidney tissue

value: WT


title: R70H mESC, H3K27me3, MB, Replicate 1

description:
Library name: 112_mESC_k27me3_MB_REP1
Merged Signal of k27me3 R70H mESC Reps MB

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: HMB11


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 2B)

description: Library name: MDST8_TG3_2B


title: ctrl5


title: ctrl6


title: DKO RING1B, WT, GSK3431uM, 48h, IgG, Replicate 1

description: Library name: DKO_RING1B_WT_GSK3431uM_48h_IgG_REP1

value: IgG, EpiCypher (Cat #13-0042)1ug


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG3 (Rep 2A)

description: Library name: MDST8_TG3_2A


title: R70H mESC, allelW, FL, MA, Replicate 1

description:
Library name: 112_mESC_allelW_FL_MA_REP1
Merged Signal of all Mutant mESC WT allele and replicates

value: Mouse embryonic stem cells (mESCs)

value: Flag(DYKDDDDK-Tag)


title: DKO RING1B, WT, GSK3431uM, 48h, H3k27me3, Replicate 2

description: Library name: DKO_RING1B_WT_GSK3431uM_48h_H3k27me3_REP2


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG2 (Rep C)

description: Library name: MDST8_TG2_2C


title: R70H mESC, allelM, HA, MA, Replicate 1

description:
Library name: 112_mESC_allelM_HA_MA_REP1
Merged Signal of all Mutant mESC R70H allele and replicates

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: DKO RING1B, WT, DMSO, H3K27me3, Replicate 2

description: Library name: DKO_RING1B_WT_DMSO_H3K27me3_REP2


title: DKO RING1B, WT, DMSO, H3K27me3, Replicate 1

description: Library name: DKO_RING1B_WT_DMSO_H3K27me3_REP1


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG2 (Rep B)

description: Library name: MDST8_TG2_2B


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG2 (Rep A)

description: Library name: MDST8_TG2_2A


title: DKO RING1B, WT, GSK3431uM, 48h, IgG, Replicate 2

description: Library name: DKO_RING1B_WT_GSK3431uM_48h_IgG_REP2


title: HMB6

value: MatTek's:Melanoma-Full Thickness-A375

value: malignant melanoma cells

value: human-derived epidermal keratinocytes

value: day 4


title: mESC WT, RYBP, Replicate 2

description: Library name: WT_RYBP_REP2

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment. Nf-core/chipseq v2.2.0 ( https://github.com/nf-core/chipseq/tree/2.0.0)
BAM files were used in ENCODE pipeline 2 v2.2.1 to  generate signal over noise bigwigs as well as to call peaks (spp for transcription factors; macs2 for broad markers) and IDR for optimal peak calling consistency between replicates.
Assembly: mm10
Supplementary files format and content: Bigwig files signal from pooled replicates

source_name: Mouse embryonic stem cells (mESCs)

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH(pH 7.5), 100mM Nacl, 0.5M EDTA, 0.5M EGTA for 10 min. 1/20 of the plates volume equivalent of freshly prepared Glycine 2.5M(stock) was added to quench the reaction for 5min . The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers . Cells were pelleted at 2950 x g for 10 min at 4°C, washed 1x with 10 ml cold PBS, and pelleted once more. Cell pellets were flash freeze in liquid nitrogen and store at -80°C until processing day. Cell pellet collected from 6 plates of cells was resuspended in 5 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 5 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then transfer to 15ml sonication tubes (Diagenode cat# C01020031). Cells were sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 50µl of sonicated samples was transferred to a new microtube with 50µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H20. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples. 2ug of Antibody (see Key Resources table for list of antibodies) was bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), previously washed with 1 ml of 0.5% BSA in 1x PBS three times, and rotated end-to-end overnight at 4°C (Eppendorf cat# 0030108051). After binding of the antibodies, beads were washed with 1 ml of 0.5% BSA in 1x PBS three times. 10ug of chromatin was added to 1.5ml LoBind tube (Eppendorf cat# 0030108051) containing pre-bound antibodies beads and brought up to 500µl final volume with Lysis Buffer and rotated end-to-end overnight at 4°C. 5 µl was removed as input material (1%) and placed in a separate microtube at 4°C completing the volume to 50uL with Lysis Buffer 3. Beads were washed 6 times with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and 150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 960xg at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample and input, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H2O and quantified by Qubit
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370L. Lot: 10193454) following the manufacturer’s instructions.

value: RYBP, EMD Milipore  (Cat #AB3637)5ug


title: DKO RING1B, WT, DMSO, IgG, Replicate 2

description: Library name: DKO_RING1B_WT_DMSO_IgG_REP2


title: mESC WT, RYBP, Replicate 1

description:
Library name: WT_RYBP_REP1
RYBP WT Pooled replicates 1 and 2


title: ctrl3

value: NHEK

value: human-derived dermal fibroblasts

value: NHDF


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG1 (Rep C)

description: Library name: MDST8_TG1_1C

value: colon

value: TWIST1 knockout


title: DKO EV H3K27me3, Replicate 2

description: Library name: DKO_H3K27me3_REP2

value: Human embryo kidney tissue


title: mESC WT, MEL18, Replicate 1

description:
Library name: WT_MEL18_REP1
MEL18 WT Pooled replicates 1 and 2

value: MEL18, Santacruz (Cat #sc-390868X)5ug

value: WT


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG1 (Rep B)

description: Library name: MDST8_TG1_1B


title: HMB4

value: inoculated


title: mESC WT, MEL18, Replicate 2

description: Library name: WT_MEL18_REP2

value: Mouse embryonic stem cells (mESCs)


title: DKO RING1B, WT, DMSO, IgG, Replicate 1

description: Library name: DKO_RING1B_WT_DMSO_IgG_REP1

value: IgG, EpiCypher (Cat #13-0042)1ug


title: ctrl1

value: negative control


title: HMB8

value: MatTek's:Melanoma-Full Thickness-A375


title: ctrl2

value: malignant melanoma cells


title: DKO EV  H3K27me3, Replicate 1

description: Library name: DKO_H3K27me3_REP1

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: mESC R70H, RYBP, Replicate 1

description:
Library name: 112_RYBP_REP1
RYBP R70H Pooled replicates 1 and 2


title: DKO IgG, Replicate 2

description: Library name: DKO_IgG_REP2


title: RNA-seq of TWIST1 KO MDST8 cells, clone TG1 (Rep A)

description: Library name: MDST8_TG1_1A


title: mESC R70H, RYBP, Replicate 2

description: Library name: 112_RYBP_REP2


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 10 mM MTX, 2A3-treated

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Library name: Targeted_SHAPE-MaP_MTX_10mM

library_source: other

data_processing:
Paired-end reads were clipped of sequencing adapters using Cutadapt v4.478 (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 100:100 -O 1) and merged using PEAR v0.9.1179 (parameters: -n 50 -q 10 -u 0 -e -y 20G -z). Merged reads were then mapped to a reference containing the target transcripts (ENST00000253788.12, ENST00000352983.7, ENST00000360079.8, ENST00000472174.7, ENST00000544040.7 and ENST00000651894.2) using Bowtie2 v2.5.4 and the rf-map module of the RNA Framework (parameters: -mp "--very-sensitive-local" -ctn -bnr -ba). Mutation counts and coverage (RC files) were obtained from BAM alignments using the rf-count module of the RNA Framework (parameters: -m -ds 100 -rd -me 0.1 -ncl), further providing a mask file containing the sequences of the primers used for targeted analysis. For reactivity normalization, cross-experiment normalization factors were derived using the rf-normfactor utility of the RNA Framework (parameters: -sm 3 -nm 3 -mc 1000) and provided to the rf-norm utility via the -nf parameter.
Supplementary files format and content: Wiggle files of raw SHAPE-MaP mutation frequencies
Library strategy: SHAPE-MaP

molecule: other

growth_protocol: Human MDA-MB-231 cells were cultured in high glucose DMEM medium (cat. L0104, Biowest), supplemented with 10% fetal bovine serum (FBS) (cat. H1138, Merck), 25 U/mL penicillin and 25 μg/mL streptomycin, at 37°C and 5% CO2. Culture plates were pre-coated with 0.001% poly-L-lysine (cat. P8920, Merck) to ensure that cells would remain attached during probing.

extract_protocol: Cells were lysed by direct addition of 2 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific). RNA samples in TRIzol™ were mixed with 0.2 volumes chloroform (cat. 319988, Merck) by vigorous vortexing for 15 sec, after which samples were allowed to sit at room temperature for 2 min, before centrifugation at 12,500g for 15 min (4°C). After phase separation, the upper aqueous phase was transferred to a clean 2 mL tube and mixed with 1 volume 2-propanol (cat. 190764, Merck) by vigorous vortexing for 15 sec. Samples were allowed to sit at room temperature for 10 min, before centrifugation at 17,000g for 10 min (4°C). Supernatant was discarded and the RNA pellet was washed twice in 75% ethanol. The RNA pellet was then allowed to air-dry for 10 min, before resuspension in nuclease-free water, pre-warmed at 70°C. Residual gDNA was removed by digestio I at 37°C for 30 min.

treatment_protocol: For drug treatment, cells were first washed once with PBS, prewarmed at 37°C. Then, Mitoxantrone (MTX) from a 10 mM stock in DMSO was mixed with fresh complete medium, prewarmed at 37°C, to achieve the desired final concentration (0-0.1-0.5-1-5-10-25 μM), and the medium added to the cells. For control experiments, medium was mixed with an equivalent amount of neat DMSO. Cells were then incubated for 30 min at 37°C. For SHAPE probing, cells were washed twice with PBS, prewarmed at 37°C, to remove any traces of serum. 2A3 (or an equivalent volume of neat DMSO, for control experiments) was then mixed with fresh PBS, prewarmed at 37°C, and added to the cells. Cells were incubated at 37°C for 7.5 min. Reactions were then quenched by addition of 1 volume ice-cold 1 M DTT in PBS, after which the supernatant was aspired, cells were washed once in PBS.


title: RNA-seq of WT MDST8 cells (Rep C)

description: Library name: MDST8_WT_C

value: wild type


title: mESC R70H, MEL18, Replicate 1

description:
Library name: 112_MEL18_REP1
MEL18 R70H Pooled replicates 1 and 2


title: RNA-seq of WT MDST8 cells (Rep B)

description: Library name: MDST8_WT_B


title: DKO IgG, Replicate 1

description: Library name: DKO_IgG_REP1


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 1 mM MTX, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_1mM


title: EV-IgG, Replicate 2

description: Library name: EV-IgG_REP2


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 5 mM MTX, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_5mM


title: mESC WT, CBX7, Replicate 2

description: Library name: WT_CBX7_REP2

value: CBX7, Abcam (Cat #ab21873)5ug


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 25 mM MTX, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_25mM


title: mESC R70H, MEL18, Replicate 2

description: Library name: 112_MEL18_REP2


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 0.5 mM MTX, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_0.5mM


title: RNA-seq of WT MDST8 cells (Rep A)

description: Library name: MDST8_WT_A


title: EV-IgG, Replicate 1

description: Library name: EV-IgG_REP1


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, 0.1 mM MTX, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_0.1mM


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, DMSO, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_MTX_0mM


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR overexpress group, biol repl2

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description:
Library name: HK1LR-2
Column name in gene_count.xls: HK1LR-2

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: xls file includes gene counts for all Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Human nasopharyngeal carcinoma cells


title: TAS19-Hypoxia, replicate 3_Female FXD, Ribosomal RNA depletion

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

description: Library name: TAS719-3

data_processing:
The reads were aligned to GRCh38 reference genome from Ensembl using STAR (v 2.7.3a)2. The gene model retrieved from Ensembl, release 110 was used to generate gene read counts.
The transcript abundance TPM (Transcript per Million) was quantified using RSEM (v 1.3.0).
Assembly: GRCh38
Supplementary files format and content: Gene expression in TPM (Transcripts per Million) : rsem_tpm.txt
Supplementary files format and content: Gene counts : star_counts.txt

source_name: B-Lymphocyte

growth_protocol: LCLs were cultured in Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, 15 % fetal bovine serum (Heat Inactivated) at 37C under 5% CO2.

extract_protocol:
Total RNA was extrcated using TRIzol (Invitrogen).
Total RNA was treated with NEBNext rRNA Depletion Kit (Human/Mouse/Rat), and then mRNA was used for library  construction. Library construction was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 1% Hypoxia for 22 hours

value: B-Lymphocyte

value: lymphoblastoid cell lines

value: B-cells

tag: phenotype

value: affected

value: 1% Hypoxia

tag: Sex

value: Female


title: TAS19-Hypoxia, replicate 2_Female FXD, Ribosomal RNA depletion

description: Library name: TAS719-2


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR overexpress group, biol repl1

description:
Library name: HK1LR-1
Column name in gene_count.xls: HK1LR-1


title: mESC WT, CBX7, Replicate 1

description:
Library name: WT_CBX7_REP1
CBX7 WT Pooled replicates 1 and 2

value: WT


title: mESC R70H, CBX7, Replicate 1

description:
Library name: 112_CBX7_REP1
CBX7 R70H Pooled replicates 1 and 2


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-HR overexpress group , biol repl3

description:
Library name: HK1HR-3
Column name in gene_count.xls: HK1HR-3


title: mESC R70H, CBX7, Replicate 2

description: Library name: 112_CBX7_REP2


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR overexpress group, biol repl3

description:
Library name: HK1LR-3
Column name in gene_count.xls: HK1LR-3


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, non treated

description: Library name: Targeted_SHAPE-MaP_NT


title: Targeted SHAPE-MaP analysis of MTX targets in MDA-MB-231 cells, Control, 2A3-treated

description: Library name: Targeted_SHAPE-MaP_Ctrl


title: mESC WT, POL2, Replicate 2

description: Library name: WT-ESC-POL2_REP2

value: POL2, CST (Cat #14958)5ul


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-HR overexpress group , biol repl2

description:
Library name: HK1HR-2
Column name in gene_count.xls: HK1HR-2


title: mESC WT, POL2, Replicate 1

description:
Library name: WT-ESC-POL2_REP1
POL2 WT Pooled replicates 1 and 2

value: Mouse embryonic stem cells (mESCs)


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-HR overexpress group , biol repl1

description:
Library name: HK1HR-1
Column name in gene_count.xls: HK1HR-1


title: Mouse-heart-chow-Fe-2

city: Charlottesville

first: Caitlin

last: Pavelec

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia School of Medicine

description: Library name: 3D

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Assembly: The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

source_name: heart

extract_protocol:
10 mg frozen tissue submited to
poly A Enrichment, cDNA synthesis, and adapter ligation

value: heart

value: Mixed

value: Chow + IV Iron


title: mESC R70H, POL2, Replicate 1

description:
Library name: 112-ESC-POL2_REP1
POL2 R70H Pooled replicates 1 and 2


title: TAS2-Hypoxia, replicate 1_Female FXD, Ribosomal RNA depletion

description: Library name: TAS702-1

value: No data


title: Mouse-heart-HFHS-Fe-3

description: Library name: 4C

value: High Fat High Sucrose + IV Iron


title: TAS43-Hypoxia, replicate 3_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS743-3

value: Apparently healthy


title: Mouse-heart-HFHS-Fe-2

description: Library name: 3C


title: Human tongue squamous cell carcinoma CAL27, siNSUN2 knock down, biol repl3

description:
Library name: Positive3
Column name in FPKM_anno.xls: Positive3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.22.0 (the default parameters) Trimmed sequence reads were mapped to GrCM38 using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: hg38
Supplementary files format and content: Excel FPKM values of genes for each sample

source_name: Human tongue squamous cell carcinoma CAL32

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.


title: TAS2-Hypoxia, replicate 3_Female FXD, Ribosomal RNA depletion

description: Library name: TAS702-3


title: TAS43-Hypoxia, replicate 2_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS743-2


title: mESC R70H, POL2, Replicate 2

description: Library name: 112-ESC-POL2_REP2


title: mESC R70H, Ring1b, Replicate 2

description: Library name: 112-Ring1b_REP2

value: Ring1b, CST (Cat #5694)10ul


title: TAS2-Hypoxia, replicate 2_Female FXD, Ribosomal RNA depletion

description: Library name: TAS702-2


title: Human tongue squamous cell carcinoma CAL27, siNSUN2 knock down, biol repl2

description:
Library name: Positive2
Column name in FPKM_anno.xls: Positive2

source_name: Human tongue squamous cell carcinoma CAL31


title: Mouse-heart-chow-Fe-1

description: Library name: 2D


title: TAS43-Hypoxia, replicate 1_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS743-1


title: Human tongue squamous cell carcinoma CAL27, siNSUN2 knock down, biol repl1

description:
Library name: Positive1
Column name in FPKM_anno.xls: Positive1

source_name: Human tongue squamous cell carcinoma CAL30


title: TAS11-Hypoxia, replicate 3_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS711-3


title: Human tongue squamous cell carcinoma CAL27, control, biol repl3

description:
Library name: Negative3
Column name in FPKM_anno.xls: Negative3

source_name: Human tongue squamous cell carcinoma CAL29


title: Human tongue squamous cell carcinoma CAL27, control, biol repl2

description:
Library name: Negative2
Column name in FPKM_anno.xls: Negative2

source_name: Human tongue squamous cell carcinoma CAL28


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, MTX-treated, 5 mM GTP, Replicate #2

description: Library name: DMS-MaPseq_MTX_GTP_T4_td_intron_rep2

data_processing:
Paired-end reads were clipped of sequencing adapters using Cutadapt v4.478 (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 200:200 -O 1) and merged using PEAR v0.9.1179 (parameters: -n 200 -q 20 -u 0 -e -y 15G -z). Merged reads were then mapped to the T4 td intron sequence using the rf-map module of the RNA Framework v2.9.3 and Bowtie2 v2.3.5.1 (parameters: -b2 -ctn -cmn 0 -mp "--very-sensitive-local --norc" -cl 200). Bulk (ensemble average) mutation counts and coverage (RC files) and MM files (necessary for ensemble deconvolution analysis) were obtained from BAM alignments files using the rf-count module of the RNA Framework (parameters: -m -ds 250 -ncl -es -ni -na -me 0.1 -dc 3 -mm). Reads harboring more than 10% mutated bases, as well as reads spanning less than 250 nt, were discarded. Insertions, ambiguous deletions and consecutive mutations falling within 3 nt from each other were discarded. Furthermore, a mask file (parameter: -mf) was provided to mask the RT primer binding site (TAACGACCTTATCTGAACATAATG). Prior to ensemble deconvolution analysis, MM files were further polished by removing non-A/C mutations and by discarding reads carrying fewer than 2 A/C mutations, by using the extract function of the rf-mmtools tool of the RNA Framework (parameters: -mpr 2 -kb AC). For the analysis of bulk (ensemble average) data, cross-experiment normalization factors were derived using the rf-normfactor utility of the RNA Framework (parameters: -sm 4 -nm 3 -rb AC -mc 1000) and provided to the rf-norm utility via the -nf parameter. Reactivities from independent replicates were combined using the rf-combine tool of the RNA Framework. Areas under the Receiver Operator Characteristic (ROC) curve were calculated using the T4 td intron reference structure, combined reactivities and the rf-eval tool of the RNA Framework, by ignoring terminal base-pairs (parameters: -kl -kp -it).
Supplementary files format and content: Wiggle files of normalized DMS-MaPseq mutation frequencies
Library strategy: DMS-MaPseq

organism: Escherichia phage T4

source_name: none (IVT RNA)

growth_protocol: As group I introns efficiently splice co-transcriptionally, in vitro transcription reactions typically yield very low amounts of full-length unspliced precursor. However, we found that addition of Urea at a final concentration of 1 M during transcription can efficiently inhibit co-transcriptional splicing, while preserving high transcription efficiency. Synthesis of the unspliced T4 td group I intron was performed in a reaction volume of 20 μl, using 200 ng dsDNA template, 2 μl 100 mM each NTP, 2 μl 10X T7 Reaction Buffer, 1 μl T7 RNA Polymerase Mix and 2.5 μl 8 M Urea, and by incubating at 37°C for 3 h. Template DNA was removed by digestion with TURBO DNase I at 37°C for 30 min and RNA was purified on Monarch® Spin RNA Cleanup columns (10 μg) (cat. T2030L, New England Biolabs) as per manufacturer instructions. RNA was mixed with 1 volume 2X RNA Gel Loading Dye (cat. R0641, ThermoFisher Scientific), denatured at 70°C for 5 min, snap-cooled on ice and resolved on a 5% TBE-Urea polyacrylamide gel. The product corresponding to the full-length unspliced RNA (50 nt exon 1 + 265 nt intron + 50 nt exon 2) was excised and recovered by passive diffusion at 4°C for 16 h in 300 μl 0.05% SDS, supplemented with 60 U SUPERase•In™ RNase Inhibitor.

extract_protocol: Reactions were quenched by addition of 1 volume 1 M DTT, and RNA was purified on Monarch® Spin RNA Cleanup columns (10 μg) as per manufacturer instructions. To prevent carryover of other species that might have formed during the folding/splicing process, the probed RNA was further resolved on a 5% TBE-Urea polyacrylamide gel. The product corresponding to the full-length unspliced RNA was excised and recovered by passive diffusion at 4°C for 16 h in 300 μl 0.05% SDS, supplemented with 60 U SUPERase•In™ RNase Inhibitor.

treatment_protocol: For in vitro probing of the refolded T4 td intron, 50 ng of full-length unspliced precursor in 41.5 μl nuclease-free water were denatured at 55°C for 5 min and snap-cooled on ice for 1 min. Refolding was initiated by addition of 5 μl ice-cold 10X RNA Folding Buffer [400 mM Tris-HCl pH 7.5; 100 mM MgCl2; 4 mM Spermidine], followed by incubation at 32°C for 5 min. For experiments involving MTX (10 μM final) and/or excess GTP (5 mM final), these were added together with the folding buffer. DMS (from a 1:4 dilution in 100% ethanol) wad added at a final concentration of 100 mM, followed by incubation at 32°C for 2 min.

value: none (IVT RNA)


title: mESC R70H, H2A, Lys119, Replicate 2

description: Library name: 112-H2A_Lys119_REP2

value: H2AK119ub, CST (Cat #8240)5ul


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, MTX-treated, 5 mM GTP, Replicate #1

description: Library name: DMS-MaPseq_MTX_GTP_T4_td_intron_rep1


title: Mouse-heart-HFHS-Fe-1

description: Library name: 1C


title: mESC R70H, Ring1b, Replicate 1

description: Library name: 112-Ring1b_REP1


title: TAS11-Normoxia, replicate 3_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS11re.3

value: B-Lymphocyte

value: lymphoblastoid cell lines

value: Normoxia


title: mESC R70H, H2A, Lys119, Replicate 1

description: Library name: 112-H2A_Lys119_REP1


title: RNA-seq-shKDM5C-MCF7

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

description:
Library name: Sample 3
RS_HS_MCF7_shKDM5C

data_processing:
The raw reads were processed to obtain clean data, which were then mapped to the reference genome using Hisat2 v2.2.1. Gene expression levels were quantified as FPKM values by cuffdiff v2.2.1.
Assembly: Homo sapiens genome Ensembl GRCh37 (hg19)
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: MCF7 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA-easy Isolation Reagent (Vazyme Biotech). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using the NEBNext® UltraTM Directional RNA Library Prep Kit following manufacturer's protocols.

value: breast cancer cells

value: KDM5C knockdown


title: TAS11-Normoxia, replicate 2_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS11re.2

value: B-cells

value: Female


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, MTX-treated, Replicate #2

description: Library name: DMS-MaPseq_MTX_T4_td_intron_rep2


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, MTX-treated, Replicate #3

description: Library name: DMS-MaPseq_MTX_T4_td_intron_rep3


title: Human tongue squamous cell carcinoma CAL27, control, biol repl1

description:
Library name: Negative1
Column name in FPKM_anno.xls: Negative1


title: mESC R70H, H3K27me3, Replicate 1

description: Library name: 112-H3K27me3_REP1

value: Mouse embryonic stem cells (mESCs)

value: H3K27me3, Activemotif (Cat #39155)5ug


title: RNA-seq-shESRRA-MCF7

description:
Library name: Sample 2
RS_HS_MCF7_shESRRA

value: ESRRA knockdown


title: TAS11-Hypoxia, replicate 1_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS711-1

value: 1% Hypoxia


title: mESC R70H, H3K27me3, Replicate 2

description: Library name: 112-H3K27me3_REP2


title: TAS20-Hypoxia, replicate 2_Male FXD, Ribosomal RNA depletion

description: Library name: TAS720-2

value: affected

value: Male


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, Control, Replicate #3

description: Library name: DMS-MaPseq_Control_T4_td_intron_rep3


title: TAS11-Normoxia, replicate 1_Female Healthy, Ribosomal RNA depletion

description: Library name: TAS11re.1

value: Apparently healthy


title: RNA-seq-shCTL-MCF7

description:
Library name: Sample 1
RS_HS_MCF7_shCTL

value: WT


title: TAS20-Hypoxia, replicate 1_Male FXD, Ribosomal RNA depletion

description: Library name: TAS720-1


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, MTX-treated, Replicate #1

description: Library name: DMS-MaPseq_MTX_T4_td_intron_rep1

value: none (IVT RNA)


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, Control, Replicate #2

description: Library name: DMS-MaPseq_Control_T4_td_intron_rep2


title: Tumor 14, spatial proteomics

city: Urbana

first: Zeynep

last: Madak-Erdogan

address: 1201 W Gregory Dr

institute: University of Illinois Urbana-Champaign

description:
Library name: 8714_PEX
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing
8714_GEX_PEX_tissue_positions.csv
8714_GEX_PEX_aligned_fiducials.jpg
8714_GEX_PEX_detected_tissue_image.jpg
8714_GEX_PEX_scalefactors_json.json
8714_GEX_PEX_tissue_hires_image.png
8714_GEX_PEX_tissue_lowres_image.png
8714_GEX_PEX_matrix.mtx.gz
8714_GEX_PEX_barcodes.tsv.gz
8714_GEX_PEX_features.tsv.gz

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to hg38 genome to gene expresison count using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

molecule: protein

source_name: Primary breast tumor

extract_protocol:
Tissue is initially placed in formalin for fixation. Once fixed, the specimen is then placed in a processor for approximately twelve hours. After processing, the tissue is embedded into a block, cut on a microtome and placed on a glass slide to be submitted as a formalin-fixed paraffin-embedded (FFPE) sample
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. Spatial transcriptome and proteome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene and Protein Expression Slides & Reagent kit according to manufacturer's construction.

value: Primary breast tumor


title: TAS18-Hypoxia, replicate 3_Male FXD, Ribosomal RNA depletion

description: Library name: TAS718-3

value: B-Lymphocyte


title: Tumor 14, spatial transcriptomics

description:
Library name: 8714_GEX
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing
8714_GEX_PEX_tissue_positions.csv
8714_GEX_PEX_aligned_fiducials.jpg
8714_GEX_PEX_detected_tissue_image.jpg
8714_GEX_PEX_scalefactors_json.json
8714_GEX_PEX_tissue_hires_image.png
8714_GEX_PEX_tissue_lowres_image.png
8714_GEX_PEX_matrix.mtx.gz
8714_GEX_PEX_barcodes.tsv.gz
8714_GEX_PEX_features.tsv.gz

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to hg38 genome to gene expresison count using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics


title: mESC R70H, Input, Replicate 2

description: Library name: 112-Input_REP2


title: mESC R70H, Input, Replicate 1

description: Library name: 112-Input_REP1


title: DMS-MaPseq analysis of in vitro refolded T4 td intron, Control, Replicate #1

description: Library name: DMS-MaPseq_Control_T4_td_intron_rep1


title: mESC WT, Ring1b, Replicate 2

description: Library name: WT-Ring1b_REP2

value: Ring1b, CST (Cat #5694)10ul


title: mESC WT, Ring1b, Replicate 1

description: Library name: WT-Ring1b_REP1


title: TAS18-Hypoxia, replicate 2_Male FXD, Ribosomal RNA depletion

description: Library name: TAS718-2

value: lymphoblastoid cell lines


title: Plasmid Pool

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

description: Library name: plasmid_pool

data_processing:
mageck count -l  grna_library.tsv --fastq Plasmid_Pool.fastq.gz  <remaining fastq.gz> --sample-label Plasmid_Pool  <remaining samples>--unmapped-to-file --trim-5 1 --sgrna-len 19
Assembly: mm39
Supplementary files format and content: gRNA_counts.tsv: tab delimted, raw counts for each guideRNA x sample
Supplementary files format and content: grna_library.tsv: tab delimted, gRNA library sequences
Library strategy: CRISPR Screen

organism: synthetic construct

source_name: marrow

growth_protocol: Cells were maintained at 60-70% confluence in DMEM supplemented with 10% Fetal Calf Serum and Penicillin/Streptomycin.

extract_protocol:
Flow cytometry and PCR amplification of genomic sgRNA sequences were conducted as previously described in detail in https://doi.org/10.1016/j.celrep.2020.108541.
Up to 10 gRNAs were designed for each noncanocial coding sequence (CDS) with CRISPRware. Six gRNAs were chosen against canonical CDSs with CRISPick. 1,500 non-targeting were also included, and up to 8 gRNAs targeting long noncoding RNA regions outside of targeted ORF. GRNAs wer cloned into pU6 lentivirus and transduced at multiplicity of infection <0.3

treatment_protocol: Library infected and puromycin selected iBMDM, +NFkB-EGFP +CRISPR-sgRNA cells were expanded to 2000X coverage. Cells were stimulated with PAM3CSK4 (200 ng/mL) for 24 h to induce expression of NFkB-EGFP.

value: marrow

value: Immortalized bone marrow derived macrophage

value: Bone marrow derived macrophage

value: No treatment


title: TAS42-Hypoxia, replicate 2_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS742-2

value: B-cells


title: mESC WT, H2A, Lys119, Replicate 2

description: Library name: WT-H2A_Lys119_REP2

value: Mouse embryonic stem cells (mESCs)

value: H2AK119ub, CST (Cat #8240)5ul


title: Tumor 13, spatial transcriptomics

description:
Library name: 6814_GEX
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing
6814_GEX_PEX_tissue_positions.csv
6814_GEX_PEX_aligned_fiducials.jpg
6814_GEX_PEX_detected_tissue_image.jpg
6814_GEX_PEX_scalefactors_json.json
6814_GEX_PEX_tissue_hires_image.png
6814_GEX_PEX_tissue_lowres_image.png
6814_GEX_PEX_matrix.mtx.gz
6814_GEX_PEX_barcodes.tsv.gz
6814_GEX_PEX_features.tsv.gz

source_name: Bone metastatic breast tumor

value: Bone metastatic breast tumor


title: Tumor 13, spatial proteomics

description:
Library name: 6814_PEX
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing
6814_GEX_PEX_tissue_positions.csv
6814_GEX_PEX_aligned_fiducials.jpg
6814_GEX_PEX_detected_tissue_image.jpg
6814_GEX_PEX_scalefactors_json.json
6814_GEX_PEX_tissue_hires_image.png
6814_GEX_PEX_tissue_lowres_image.png
6814_GEX_PEX_matrix.mtx.gz
6814_GEX_PEX_barcodes.tsv.gz
6814_GEX_PEX_features.tsv.gz


title: mESC WT, H2A, Lys119, Replicate 1

description: Library name: WT-H2A_Lys119_REP1


title: TAS18-Hypoxia, replicate 1_Male FXD, Ribosomal RNA depletion

description: Library name: TAS718-1

value: affected

value: 1% Hypoxia


title: mESC WT, H3K27me3, Replicate 2

description: Library name: WT-H3K27me3_REP2

value: H3K27me3, Activemotif (Cat #39155)5ug


title: DDC D5 mouse liver

city: Würzburg

first: Stefan

last: Thomann

address: Versbacher Strasse 9

institute: Würzburg Systems Immunology

description: FFPE in situ sequencing

hyb_protocol: The Xenium Mouse Tissue Atlassing panel (379 genes) was used in combination with an add-on panel containing another 100 genes. Hybridization, ligation and rolling circle amplication was conducted according to the manufacturer's recommendations. Xenium slide containing the DDC tissue section was placed in an imaging cassette to conduct image acquisition in the Xenium Analyzer.  Sequential image acquisition of specific fluorescently-conjugated secondary probes complementary to rolling circle amplified regions enabled hybridization and signal detection.

scan_protocol: Xenium slide containing the DDC tissue section was placed in an imaging cassette to conduct image acquisition in the Xenium Analyzer and sequential image acquisition conducted after each round of probe hybridisation. Image  acquisition of DAPI-stained nuclei was conducted in parallel.

data_processing:
Pre-processed data of the Xenium Analyzer workflow was used,  For visualization a Q-score cutoff of 0.2 was applied, removing low quality transcripts. For NiCo analysis, count filtering of the spatial data ("min_counts=5") resulted in an AnnData object containing 100330 cells and 479 genes. To enable NiCo label transfer of cell type labels derived from scRNA-seq data.  A merged scRNA-seq seurat object containing the data of Fig. 1J/L and Fig 4A was generated ("merged_matrix.csv.gz"). Cluster 11 from the DDC atlas (Fig 1) was removed due to low quality. The merged dataset gave rise to an object that was further cleaned for doublets and low quality cells yielding in an annotated seurat object containing 81168 cells. The count matrix of this data was then saved  (merged_matrix.csv.gz) for the NiCo pipeline. Cell type labels were saved as .csv.gz in a separate data file ("ref_cluster_tag.csv.gz").
"merged_matrix.csv.gz" contains  the merged and cleaned DDC scRNA-seq atlas data combined with the gdT cell data. "Ref_cluster_tag.csv.gz" contains the cell type annotation of the scRNA-seq data.  The file "1_nico_annotationct_name.csv.gz" contains the cellnames and spatial cluster annotation. The file "1_nico_annotation_cluster.csv.gz" contains information regarding cell type annotation after label transfer and cell frequency. All other files are standard output files derived from the Xenium experiment.

label: RCA and detection based on Xenium codebook

source_name: male mouse liver receiving DDC diet for 5 days

label_protocol: The Xenium cell segmenetation kit from 10x Genomics was used containing oligonucleotide-conjugated antibodies (ATP1A1, E-Cadherin, CD45, ASMA, Vimentin and 18S rRNA) to label cellular compartments for cell segmentation.

extract_protocol: Tissue section was deparrafinized and permeabilized enabling access to tissue RNA.

treatment_protocol: Male C57Bl/6 male mouse received DDC diet for 5 days. Liver was resected and liver lobes  cut into slices of 5 mm thickness. Slices were immediately fixed in 4% PFA. Fixed tissues were then paraffin embedded using a standard protocol.

tag: strain

value: male

value: liver

value: DDC diet


title: TAS42-Hypoxia, replicate 1_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS742-1

value: B-Lymphocyte

value: Apparently healthy

value: Male


title: Tumor 12

description:
Library name: Breast_8714
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing

value: Primary breast tumor


title: CD1D-/+ s4

city: Columbia

first: John

last: Driver

address: 1201 Rollins Street

institute: University of Missouri

description: Library name: pig 92

library_source: transcriptomic single cell

data_processing:
The Sscrofa 11.1 genome assembly was used to align sequencing reads to generate gene matrix data by Cell Ranger (v8.0.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix files and fasta files

organism: Sus scrofa

source_name: lung

extract_protocol:
Cryopreserved cells were thawed
Gene expression libraries were prepared using the Chromium Next GEM Single Cell 5′ Kit v2 (10× Genomics, Pleasanton, CA) according to the manufacturer’s instructions. V(D)J libraries were enriched for TCR and BCR transcripts with pig-specific primers.

value: lung

value: primary cells

value: lung cells


title: TAS10-Hypoxia, replicate 1_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS710-1

value: lymphoblastoid cell lines

value: B-cells


title: Tumor 11

description:
Library name: Breast_6997
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: mESC WT, H3K27me3, Replicate 1

description: Library name: WT-H3K27me3_REP1

value: Mouse embryonic stem cells (mESCs)

value: WT


title: mESC WT, Input, Replicate 2

description: Library name: WT-Input_REP2


title: CD1D-/- s4

description: Library name: pig 86


title: CD1D-/+ s3

description: Library name: pig 87


title: TAS10-Hypoxia, replicate 3_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS710-3


title: CD1D-/- s3

description: Library name: pig 82


title: Tumor 9

description:
Library name: Breast_6995
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: Tumor 10

description:
Library name: Breast_6996
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: mESC WT, Input, Replicate 1

description: Library name: WT-Input_REP1


title: CD1D-/- s2

description: Library name: pig 81


title: TAS10-Normoxia, replicate2_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS10re.2

value: Normoxia


title: NPC, R70H, Replicate 2

description: Library name: NPC_112M_rep2

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment algainst mm10 using nf-core/atacseq v2.1.2 (https://github.com/nf-core/atacseq/tree/2.1.2) with additional ‘--aligner bowtie2 --read_length 150 --trim_nextseq 20 --blacklist [BED]’
Assembly: mm10
Supplementary files format and content: Merged replicates bigwigs

source_name: Mouse Neural progenitor cells (mNPCs)

extract_protocol:
The ATAC-seq of the mESCs and mNPCs WT and RNF2 R70H was performed according to manufacturer’s protocols (Active Motif 53150). Briefly, 1 × 10⁵ cells were resuspended in ATAC Lysis Buffer to extract nuclei. The nuclei were then resuspended in the Tagmentation Master Mix, and incubated for 30 minutes at 37°C in a Thermomixer (Eppendorf). Subsequently, the DNA was purified using the DNA purification columns provided in the kit.
The library was prepared using the indexing reagents and Q5 polymerase provided in the ATAC-seq kit, following the manufacturer's protocol (Active Motif, 53150).

value: Mouse Neural progenitor cells (mNPCs)


title: Tumor 8

description:
Library name: Breast_6994
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: TAS10-Normoxia, replicate 3_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS10re.3


title: Tumor 7

description:
Library name: Bone_8715
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing

value: Bone metastatic breast tumor


title: NPC, R70H, Replicate 1

description: Library name: NPC_112M_rep1


title: NPC, WT, Replicate 2

description: Library name: NPC_WT_rep2


title: CD1D-/+ s2

description: Library name: pig 80


title: TAS10-Normoxia, replicate 1_Male Healthy, Ribosomal RNA depletion

description: Library name: TAS10re.1


title: CD1D-/- s1

description: Library name: pig 78


title: NPC, WT, Replicate 1

description: Library name: NPC_WT_rep1


title: human liver, ctrl, P6

data_processing:
Data was mapped and processed using cellranger-6.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Barcodes, features, matrix files

source_name: liver

growth_protocol: human far distant liver tissue from oncologic resections was used for scRNA-seq

extract_protocol:
Pseudonormal and far distant human liver tissue was used for cell isolation from 6 patients (4 female, 2 male, age range 45-76 yrs, receiving a lobectomy or hemihepatectomy for oncologic resection) and the following cell populations were FACS enriched at equal distribution: 1) alive, 2) CD45+ CD3E-, 3) CD45+ CD3E+ 4)CD45+ CD11C+ 5) CLEC4G+ 6) CLEC4G- CD31+, 7) EPCAM+.
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index)

treatment_protocol: Human liver tissue was minced and digested using Collagenase D (Roche, Grenzach-Whlyen, Germany) and liver cells isolated using a FACS Aria III cell sorter. Sorted cell populations were then mixed at equal ratios and cell suspensions then loaded on 10x chromium controller.


title: Tumor 6

description:
Library name: Bone_8713
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: ESC, R70H, Replicate 2

description: Library name: ESC_112M_rep2


title: ESC, R70H, Replicate 1

description: Library name: ESC_112M_rep1


title: NK cells, Hif1a KO, 7 days hypoxia, biological replicate 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Library name: H_K3

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCm39
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

source_name: spleen

growth_protocol: NK cells were cultured in RPMI-1640 supplemented with 10% fetal calf serum, 1% Penicillin/Streptomycin, 1% L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate, 50 μM β-mercaptoethanol, and 1700 U/ml of recombinant human IL-2. NK cells under hypoxic conditions (1% O2), with 5% CO2 at 37C for 7 days

extract_protocol:
RNA extraction was performed using the RNeasy® Mini Kit (Qiagen). Concentration of isolated RNA was measured using the Qubit™ RNA High Sensitivity (HS) kit and Qubit™ 4 Fluorometer. RNA quality was determined  on a 2100 Bioanalyzer (Agilent).
RNA libraries were prepared for sequencing using standard BGI DNBSEQ Eukaryotic Strand-specific mRNA library

value: spleen

value: NK cells

value: Ncr1 iCre, Hif1a fl/fl

value: Hypoxia


title: human liver, ctrl, P4

value: liver


title: Tumor 4

description:
Library name: Bone_6816
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: Tumor 5

description:
Library name: Bone_8712
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: human liver, ctrl, P5


title: NK cells, Hif1a KO, 7 days hypoxia, biological replicate 2

description: Library name: H_K2


title: CD1D-/+ s1

description: Library name: pig 79


title: human liver, ctrl, P3


title: ESC, WT, Replicate 2

description: Library name: ESC_WT_rep2

source_name: Mouse embryonic stem cells (mESCs)


title: NK cells, Hif1a KO, 7 days hypoxia, biological replicate 1

description: Library name: H_K1


title: human liver, ctrl, P1


title: Tumor 3

description:
Library name: Bone_6815
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: NK cells, Hif1a-flox, 7 days hypoxia, biological replicate 3

description: Library name: H_F3

value: Hif1a fl/fl


title: ESC, WT, Replicate licate 1

description: Library name: ESC_WT_rep1


title: Tumor 1

description:
Library name: Bone_6813
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: human liver, ctrl, P2


title: NK cells, Hif1a-flox, 7 days hypoxia, biological replicate 2

description: Library name: H_F2


title: Tumor 2

description:
Library name: Bone_6814
Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing


title: mNeuronDiff ,WT ,Replicate 2

description: Library name: NeuronDiff_WT_REP2

data_processing:
Data was processed using nf-core/rnaseq v3.10.1 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020).  The pipeline was executed with Nextflow v22.10.7 (Di Tommaso et al., 2017)
trimGalore! 0.6.7
salmon  1.9.0
STAR 2.7.9a
Assembly: mm10
Supplementary files format and content: tab-delimited text files inclues raw counts for each sample

source_name: Differentiated cell

extract_protocol: Please check manuscript

treatment_protocol: NPCs and differentiated NPCs were generated following the protocol from Bibel and colleagues (https://www.nature.com/articles/nprot.2007.147). Rescue experiments were performed by adding 3µg of CHIR99021 at day 6 of ESC differentiation with retinoic acid and 10%

value: Differentiated cell


title: H1299_scramble_control_siRNA_biolrep_3

city: London

first: Pradeep

last: Ramagiri

state: Greater London

address: 15 Cotswold Rd

department: Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

description: Library name: H1299_SCRM_3

data_processing:
Raw FastQ files were processed using nf-core/rnaseq pipeline (version 21.04.3) which comprises the following software:  1. Read QC (FastQC v0.11.9 and MultiQC v1.12) 2. Alignment to the reference genome (GRCh38) using STAR aligner (v.2.7.6a) 3. Sort and index alignments (SAMtools) 4. Duplicate read marking (picard MarkDuplicates)
Once the reads were aligned, HTSeq-count (HTSeq v0.12.4) was used to count the number of reads mapping unambiguously to genomic features in each sample.
Differential expression analysis of the count data was performed in R using the Bioconductor package DESeq2 (v1.20.0). For differential splicing analysis, 1st pass and 2nd pass BAM files were created by mapping raw reads to reference genome (GRCh38) using STAR (v.2.7.6a). Differential local splicing variations (LSV) were detected and quantified using MAJIQ (v2.2-e25c4ac). Pathway and Gene Set Enrichment Analysis was carried out in R using package fgsea (v1.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Lung

growth_protocol: Human cell lines were obtained from ATCC and identity confirmed by short tandem repeat profiling. Cells were cultured in DMEM supplemented with 10% FCS, 2 mM glutamine and non-essential amino acids. All cell lines were maintained at 37 °C, 5% CO2 and tested negative for mycoplasma.

extract_protocol:
RNA extracted using an automated Magnapure (Roche) workstation according to the manufacturer’s instructions and RNA quality assessed using an Agilent bioanalyzer (Agilent)
RNA libraries for RNA-seq were prepared using Novogene NGS Stranded RNA Library Prep Set (PT044)* and sequenced in NovaSeq X Plus.

treatment_protocol: H1299 dTAG cells were treated for 6 hours with 250 nM dTAG-V1. U2OS, HCT116 and H1229 cells were reverse transfected with DHX8 or negative control siRNA using Hiperfect cationic lipid for 72 hours. HCT116 cells transfected with DHX8 or scramble control siRNA were treated +/- doxycyline to induce exogenous wild-type or mutant DHX8. U2OS cells were transfected with DHX8-O5 (GCAGUGGGUUCUUCCGUAA), DHX8-O2 (GGAAUAAAGUGAAGUCUAG) or AllStars negative control siRNA (Quagen).

value: Lung

value: Non-small cell lung cancer

value: Scramble negative control siRNA

tag: time

value: 72 hours


title: KO Raldh2+ATRA

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

description:
Library name: X970-E95KO-Atra
Illumina

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software version 8.0.1.
Assembly: Mouse GRCm39; annotation version M33
Supplementary files format and content: HDF5 file format for the raw and filtered feature-barcode matrices from the Cell Ranger output

source_name: E9.5 placenta

extract_protocol:
Placentas from E9.5 embryos for each experimental condition were pooled and enzymatically digested into a single cell suspension with 1mL of 10% Collagenase type I from Clostridium histolyticum with agitation at 37°C for 1hour. Cells were passed through a 70μm cell strainer and rinsed with 1 mL ice-cold HBSS. Placentas were passed through a 70μm cell strainer into 1X red cell lysis buffer and incubated for 10 minutes at room temperature. The sample was depleted of CD45+ cells and enriched for CD31+ cells to increase the number of ECs using microbeads. 5% of all other cells were spiked back to the final sample.
Single-cell suspensions were loaded into a multi-channel microfluidic chip within the Chromium Controller (10x Genomics) to generate GEMs, targeting a recovery of 5,000–10,000 cells. The 10x Genomics Chromium Single Cell System was used to process the suspension. Gene expression libraries were prepared with the Chromium™ Next GEM Single Cell GEM-X 3’ kit. Sequencing was performed on the Illumina NextSeq 2000 instrument using Illumina P2-100 kit (WT and KO samples) and P4-100 kit (WT + ATRA and KO + ATRA samples).

value: E9.5 placenta


title: H1299_scramble_control_siRNA_biolrep_2

description: Library name: H1299_SCRM_2


title: mNeuronDiff ,WT ,Replicate 1

description: Library name: NeuronDiff_WT_REP1


title: WT Raldh2+ATRA

description:
Library name: X969-E95WT-Atra
Illumina


title: NK cells, Ahr KO, 7 days hypoxia, biological replicate 3

description: Library name: A_K3

value: primary cells

value: Ncr1 iCre, Ahr fl/fl


title: mNeuronDiff ,Clone R70H 282 ,Replicate 2

description: Library name: NeuronDiff_Clone_282_REP2


title: mNeuronDiff ,Clone R70H 282 ,Replicate 1

description: Library name: NeuronDiff_Clone_282_REP1


title: H1299_scramble_control_siRNA_biolrep_1

description: Library name: H1299_SCRM_1

value: WT


title: NK cells, Ahr KO, 7 days hypoxia, biological replicate 2

description: Library name: A_K2


title: H1299_scramble_control_siRNA_biolrep_4

description: Library name: H1299_SCRM_4


title: H1299_DHX8_siRNA_biolrep_4

description: Library name: H1299_DHX8kd_4

value: DHX8 siRNA


title: KO Raldh2 rep1

description:
Library name: X968-E95KO
Illumina


title: WT Raldh2 rep2

description:
Library name: AC5362WTr
Illumina


title: KO Raldh2 rep2

description:
Library name: AC5362KOr
Illumina


title: NK cells, Ahr KO, 7 days hypoxia, biological replicate 1

description: Library name: A_K1


title: NK cells, Ahr-flox, 7 days hypoxia, biological replicate 3

description: Library name: A_F3

value: Ahr fl/f


title: NK cells, Hif1a-flox, 7 days hypoxia, biological replicate 1

description: Library name: H_F1

value: spleen


title: mNeuronDiff ,Clone R70H 112 ,Replicate 1

description: Library name: NeuronDiff_Clone_112_REP1


title: mNeuronDiff ,Clone R70H 112 ,Replicate 2

description: Library name: NeuronDiff_Clone_112_REP2


title: mNPC ,WT ,Replicate 2

description: Library name: NPC_WT_REP2

source_name: Mouse neural progenitor cells (mNPCs)

value: Mouse neural progenitor cells (mNPCs)


title: NK cells, Ahr-flox, 7 days hypoxia, biological replicate 2

description: Library name: A_F2

value: NK cells


title: H1299_DHX8_siRNA_biolrep_2

description: Library name: H1299_DHX8kd_2


title: mouse, liver LN, gdT, D19 and STOP [ADT]

data_processing:
Data was mapped and processed using cellranger, the feature table for the CITE-seq antibodies (TotalSeqB) or for Multiplexing are listed as additional files in each experiment.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Matrix, gene/ADT and barcode files

source_name: liver draining lymph node

growth_protocol: All animal experiments were authorized by the German Regional Council of Baden-Württemberg and Bavaria (Regierungspräsidium Freiburg and Würzburg, Regierung Unterfranken. C57BL/6J mice were bred in a 12 hour light/dark cycle with free access to water and food and kept under defined pathogen free conditions, while tolerating commensal and non-pathogenic opportunistic bacteria. Treatment and termination criteria were defined based on the ATBW criteria and reevaluated at defined time intervals based on the severity of burden.

extract_protocol:
Gamma delta T cells were isolated from liver or liver draining lymph node (Zheng et al. Cell Mol Immunol (2013). Alive Cd45+ Cd3e+ TCRβ- TCRγδ+ cells were FACS-sorted. For LN-derived CITE seq data, the following cell populations of interest were FACS-sorted at equal ratios: alive singlet, Cd45+ Itgax-, Cd45+ Itgax+, Pdpn+, Cd45- Pdpn-.
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) with Feature Barcoding technology for Cell Surface Protein.

treatment_protocol: Mice were fed with chow supplemented with 0.1% 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) for time periods of 0 - 25 days or a combination of prolonged diet (DDC D18) in combination with a subsequent recovery period of 7 days. For Mgl2-DTR depletion experiments, Mgl2-DTR mice were used (Kumamoto et al. Immunity (2013)). For depletion, mice were injected DT at day -1 and day 2 and mice were fed DDC for 5 days. Depending of the cells of interest, either liver or cells derived from liver draining lymph nodes were further processed.

value: liver draining lymph node

value: gdT, D19 and STOP


title: H1299_DHX8_siRNA_biolrep_1

description: Library name: H1299_DHX8kd_1


title: H1299_DHX8_siRNA_biolrep_3

description: Library name: H1299_DHX8kd_3


title: NK cells, Ahr-flox, 7 days hypoxia, biological replicate 1

description: Library name: A_F1

value: Hypoxia


title: mNPC ,WT ,Replicate 1

description: Library name: NPC_WT_REP1


title: WT Raldh2 rep1

description:
Library name: X967-E95WT
Illumina


title: mouse, liver LN, gdT, D19 and STOP [GEX]


title: mNPC ,Clone R70H 282 ,Replicate 1

description: Library name: NPC_Clone_282_REP1


title: WT_IFN-γ_R2

city: New York

first: Falak

last: Sher

state: New York

address: 630 W 168th street

institute: Columbia University

description:
Library name: FIH005
FIH005

data_processing:
bases2fastq version 1.5.0.962525890 for converting BCL to fastq, coupled with adaptor trimming
perform a pseudoalignment to a kallisto index created from transcriptomes
Assembly: Ensembl v96, Human:GRCh38.p12 using kallisto (0.44.0)
Supplementary files format and content: .txt

source_name: iPSC-derived cells

growth_protocol: iPSC-derived microglia were cultured in homoestatic media described in PMID: 38600587

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
standard poly(A) selection

treatment_protocol: WT and SORL1 KO iPSC-derived microglia were treated with 10 ng/ml of IFN-γ for 48 hours

value: iPSC-derived cells

value: Human Episomal iPSC Line

value: Microglia

value: 10 ng/ml of IFN-γ

tag: batch


title: WT_IFN-γ_R3

description:
Library name: FIH006
FIH006


title: WT_IFN-γ_R1

description:
Library name: FIH004
FIH004


title: mNPC ,Clone R70H 282 ,Replicate 2

description: Library name: NPC_Clone_282_REP2


title: mouse, liver LN, gdT, D0 AND d5 [GEX]

value: gdT, D0 AND d5


title: mNPC ,Clone R70H 112 ,Replicate 2

description: Library name: NPC_Clone_112_REP2


title: NK cells, Hif1a and Ahr KO, 7 days hypoxia, biological replicate 2

description: Library name: AH_K2

value: Ncr1 iCre, Hif1a fl/fl, Ahr fl/fl


title: mouse, liver LN, gdT, D0 AND d5 [ADT]


title: NK cells, Hif1a-flox Ahr-flox, 7 days hypoxia, biological replicate 2

description: Library name: AH_F2

value: primary cells

value: Hif1a fl/fl , Ahr fl/f


title: IgG, β3-AR-stimulated BAs-rep3

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: IgG_stimulated_rep3

data_processing:
The raw reads of CUT&RUN data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the mouse genome (mm10), read level quality control, and peak level quality control.
The BigWig files were generated by deepTools bamCoverage software (version 3.3.1) with --normalizeUsing CPM --binSize 10 --ignoreDuplicates --extendReads based on uniquely mapped reads in BAM files produced by CHIPs pipeline
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Run

source_name: Primary murine brown adipocytes

growth_protocol: Primary brown adipocytes were isolated from BAT of mice housed either at thermoneutrality or 5°C for 4 hours, conditions that with or without activation of β3-AR signaling, respectively.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature, then washed three times with 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and 1X protease inhibitor cocktail). The cell pellet was resuspended in 1 ml wash buffer containing 10 μl ConA-coated magnetic bead slurry, incubated at room temperature for 5 minutes, and placed on a magnetic rack to remove the solution. Beads were then resuspended in 150 μl antibody solution (wash buffer supplemented with 0.05% digitonin, 0.6 μl of 0.5 M EDTA, and 0.5 μg of H2A.Z antibody (Abcam, ab4174) or 0.5 μg Rabbit IgG and rotated overnight at 4°C. The following day, beads were washed twice with Dig-wash buffer (wash buffer supplemented with 0.05% digitonin), resuspended in 150 μl Protein A/G-MNase (700 ng/μl), and rotated at 4°C for 1 hour. After two additional washes with Dig-wash buffer, beads were resuspended in 100 μl Dig-wash buffer supplemented with 2 μl of 100 mM CaCl₂ and incubated at 0°C for 30 minutes. The reaction was stopped by adding 100 μl of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 μg/ml RNase A, and 50 μg/ml glycogen), followed by incubation at 37°C for 30 minutes. The released genomic fragments were collected and purified.
CUT&RUN  libraries were prepared by BGI.

treatment_protocol: Mice were housed either at thermoneutrality or 5°C for 4 hours.

value: Primary murine brown adipocytes

value: brown adipocytes

value: WT

value: stimulated


title: mouse, liver LN D19 [GEX]


title: NK cells, Hif1a and Ahr KO, 7 days hypoxia, biological replicate 3

description: Library name: AH_K3

value: spleen


title: NK cells, Hif1a-flox Ahr-flox, 7 days hypoxia, biological replicate 3

description: Library name: AH_F3

value: NK cells


title: SORL1-KO_IFN-γ_R3

description:
Library name: FIH003
FIH003

value: SORL1 knockout


title: mNPC ,Clone R70H 112 ,Replicate 1

first: Rodrigo

last: Lucena Borges

institute: Sylvester Comprehensive Cancer Center

description: Library name: NPC_Clone_112_REP1

value: Mouse neural progenitor cells (mNPCs)


title: mouse, liver LN D5 [CSL]

value: liver draining lymph node


title: NK cells, Hif1a-flox Ahr-flox, 7 days hypoxia, biological replicate 1

description: Library name: AH_F1

value: Hypoxia


title: NK cells, Hif1a and Ahr KO, 7 days hypoxia, biological replicate 1

description: Library name: AH_K1


title: IgG, β3-AR-stimulated BAs-rep2

description: Library name: IgG_stimulated_rep1


title: SORL1-KO_IFN-γ_R2

description:
Library name: FIH002
FIH002

value: iPSC-derived cells

value: Human Episomal iPSC Line


title: mouse, liver LN D5 [GEX]


title: SORL1-KO_IFN-γ_R1

description:
Library name: FIH001
FIH001

value: Microglia

value: 10 ng/ml of IFN-γ


title: Kedah-Kelantan whole blood under heat stress, biological replicate 2

city: Zuru

first: Akeem

middle: Babatunde

last: Sikiru

state: Kebbi

address: Department of Animal Science, College of Agriculture, FUAZ, Zuru, Nigeria.

department: Animal Science

country: Nigeria

institute: Federal University of Agriculture Zuru

description:
Library name: Kedah-Kelantan2_L1_1.fq.gz
Female, non-pregnant, non-lactating, age 4.5±1.2 years, body weight 450±15 kg. Sample collected from jugular vein during peak heat load.

data_processing:
Libraries constructed using Illumina Stranded mRNA Prep kit. mRNA enriched by poly-A selection, fragmented, reverse-transcribed. Libraries end-repaired, A-tailed, ligated with indexed adapters, amplified by PCR. Quality assessed using Agilent 2100 Bioanalyzer. Sequenced on Illumina NovaSeq 6000 (paired-end, 2 × 150 bp).
Raw reads quality assessed with FastQC v0.11.9. Adapter trimming and quality filtering with Trimmomatic v0.39.
Reads aligned to Bos taurus reference genome (ARS-UCD1.2) using HISAT2 v2.2.1.
Gene counts quantified using featureCounts v2.0.1. Expression normalized as FPKM.
Assembly: Differential expression analysis using DESeq2 v1.38.0. Genes with adjusted p < 0.05 and log2FC > 1 considered differentially expressed.
Supplementary files format and content: ARS-UCD1.2
Supplementary files format and content: raw_counts.txt: Tab-delimited gene count matrix. FPKM_normalized_expression.txt: FPKM-normalized values. differential_expression_results.txt: DESeq2 results with gene symbols, log2FC, p-values, adjusted p-values.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Bos indicus

source_name: whole blood

growth_protocol: Clinically healthy, non-pregnant, non-lactating adult female cows (mean age: 4.50 ± 1.20 years; mean body weight: 450.00 ± 15.00 kg) were maintained at Universiti Putra Malaysia Teaching and Research Farm, Serdang, Selangor, Malaysia (2°59'24"N, 101°42'32"E, elevation 68 m). The farm is characterized by a humid tropical climate with minimal seasonal temperature variation, mean annual temperature of 27.5°C, and relative humidity of 70-90%.

extract_protocol:
Animals were sampled during peak heat load conditions with Temperature-Humidity Index (THI) of 44.68. All experimental procedures were approved by IACUC (UPM/IACUC/AUP-R055/2025) and conducted in accordance with Malaysian Codes of Practice for Care and Use of Animals for Scientific Purposes and ARRIVE guidelines.
Total RNA was extracted from whole blood using PrimeZOL reagent (Canvax Biotech, Spain). RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water. RNA concentration and purity assessed by NanoDrop. RNA integrity evaluated with RIN > 7.0 required.

treatment_protocol: Heat stress (Temperature-Humidity Index: 44.68)

value: whole blood

value: Kedah-Kelantan (heat-tolerant indigenous tropical breed)

value: heat stress (Temperature-Humidity Index:44.68)


title: H2A.Z, β3-AR-stimulated BAs-rep3

description: Library name: H2AZ_stimulated_rep3

value: Primary murine brown adipocytes


title: mouse, liver LN D0 [CSL]


title: NK cells, 7 days normoxia, biological replicate 3

description: Library name: R3N1

growth_protocol: NK cells were cultured in RPMI-1640 supplemented with 10% fetal calf serum, 1% Penicillin/Streptomycin, 1% L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate, 50 μM β-mercaptoethanol, and 1700 U/ml of recombinant human IL-2. NK cells under normoxic (20% O2) or hypoxic conditions (1% O2), with 5% CO2 at 37C for 7 days

value: primary cells

value: Normoxia


title: mouse, liver LN D19 [ADT]


title: Kedah-Kelantan whole blood under heat stress, biological replicate 1

description:
Library name: Kedah-Kelantan1_L1_1.fq.gz
Female, non-pregnant, non-lactating, age 4.5±1.2 years, body weight 450±15 kg. Sample collected from jugular vein during peak heat load.


title: NK cells, 7 days normoxia, biological replicate 2

description: Library name: R2N1

value: WT


title: mouse, liver LN D0 [GEX]


title: H2A.Z, β3-AR-stimulated BAs-rep2

description: Library name: H2AZ_stimulated_rep2

value: brown adipocytes

value: stimulated


title: H2A.Z, β3-AR-stimulated BAs-rep1

description: Library name: H2AZ_stimulated_rep1


title: Multiome, KO Cerebral organoids, 74 day, Rep 2, ATAC

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Library name: 19312R_X4

library_source: genomic single cell

data_processing:
Multiome data was demultiplexd using cellranger mkfastq
Demuliplex fastq files were processed using cellranger arc
Processed files were futher analysis using Seurat
Assembly: GRCh 38
Supplementary files format and content: cellranger output: filtered_peak_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

source_name: hiPSC-derived cerebral organoid

extract_protocol:
Nuclei were isolated from fresh hiPSC-derived brain organoid tissues (51 days and 74 days) following the 10X Genomics demonstrated protocol for Single Cell Multiome ATAC + Gene Expression sequencing (CG000338). Organoids were triturated in N2/B27 media, filtered through a 70 μm strainer, lysed, and washed. After resuspension in chilled diluted nuclei buffer, nuclei concentrations were determined using a Countess II FL automated cell counter.
The sequencing libraries were constructed using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338). Nnuclei were processed using the 10X Genomics Next GEM Single Cell 3' Gene Expression Library Preparation v3.1 kit with unique dual indexing (UDI), suitable for generating dual modality libraries (gene expression and chromatin accessibility) for sequencing on the Illumina NovaSeq platform

value: hiPSC-derived cerebral organoid

value: KMT2D KO

value: Batch 05 July 2021


title: mouse liver and LN, D5-DT, gdT [ADT]

source_name: liver and LN

value: liver and LN

value: D5-DT, gdT


title: Multiome, KO Cerebral organoids, 74 day, Rep1,  ATAC

description: Library name: 19312R_X3


title: NK cells, 7 days hypoxia, biological replicate 3

description: Library name: R3H1

value: spleen

value: NK cells

value: Hypoxia


title: mouse liver and LN, D5-DT, gdT [GEX]


title: Multiome, WT Cerebral organoids, 74 day, Rep 2, ATAC

description: Library name: 19312R_X2


title: NK cells, 7 days hypoxia, biological replicate 2

description: Library name: R2H1


title: IgG, unstimuated BAs_rep1

description: Library name: IgG_unstimulated_rep1

value: unstimulated


title: NK cells, 7 days normoxia, biological replicate 1

description: Library name: R1N1


title: NK cells, 7 days hypoxia, biological replicate 1

description: Library name: R1H1


title: mouse liver, gdT, D19 and STOP [GEX]

value: liver

value: gdT, D19 and STOP


title: mouse liver, gdT, D19 and STOP [ADT]


title: Multiome, WT Cerebral organoids, 74 day, Rep 1, ATAC

description: Library name: 19312R_X1


title: H2A.Z, unstimulated BAs-rep3

description: Library name: H2AZ_unstimulated_rep3

value: Primary murine brown adipocytes


title: Multiome, KO Cerebral organoids, 51 day, Rep 2, ATAC

description: Library name: 19236R_X4


title: IgG, unstimuated BAs_rep3

description: Library name: IgG_unstimulated_rep3


title: Multiome, WT Cerebral organoids, 51 day, Rep 2, ATAC

description: Library name: 19236R_X2


title: ADRB2-KO mice,neutrophil+NE+LPS,rep1

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: ADRB2_NE_LPS_1A

data_processing:
1. Readscontainingadapters(adaptercontamination); 2. Readswithanunknownbase'N'contentexceeding0.1%;3. Low-qualityreads(readswithaproportionofbaseswithaqualityvaluebelow15exceeding20% of the total bases in the read), resulting in clean data.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: The table contains information about the RNA modification sites identified for each sample as well as RNA counts and standardized values

source_name: neutrophil

extract_protocol:
1. Sample Lysis For cultured cells:  Remove the culture medium and wash the cells with cold PBS. Add 1 mL of TRIzol reagent per 1 × 10⁶ cells. Pipette up and down to lyse the cells completely. For tissue samples:  Quickly freeze the tissue in liquid nitrogen and grind it into powder using a mortar and pestle. Transfer the tissue powder into a tube containing 1 mL of TRIzol reagent. Homogenize the sample thoroughly until no visible tissue fragments remain. 2. Phase Separation Incubate the lysate at room temperature for 5 minutes. Add 200 µL of chloroform per 1 mL of TRIzol reagent. Vortex vigorously for 15 seconds and incubate at room temperature for 3 minutes. Centrifuge at 12,000 × g for 15 minutes at 4°C. After centrifugation, three layers should appear: Upper aqueous phase (RNA) Middle interphase (proteins) Lower organic phase (DNA and lipids) Carefully transfer the upper aqueous phase to a new RNase-free tube without disturbing the interphase. 3. RNA Precipitation Add an equal volume of isopropanol to the transferred aqueous phase. Mix gently by inverting the tube several times. Incubate at -20°C for at least 10 minutes (or overnight for better yield). Centrifuge at 12,000 × g for 10 minutes at 4°C. Discard the supernatant, leaving the RNA pellet at the bottom. 4. RNA Washing Add 1 mL of 75% ethanol to wash the pellet. Vortex briefly and centrifuge at 7,500 × g for 5 minutes at 4°C. Remove the supernatant carefully and air-dry the pellet for ~5 minutes (avoid over-drying). 5. RNA Resuspension Dissolve the RNA pellet in 20–50 µL of RNase-free water. Incubate at 55°C for 5–10 minutes to fully dissolve the RNA. Store the RNA at -80°C for long-term use.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

value: neutrophil

value: NE+LPS


title: Multiome, KO Cerebral organoids, 51 day, Rep1,  ATAC

description: Library name: 19236R_X3


title: mouse liver, D0 D5 D9 gdT [ADT]

value: D0 D5 D9 gdT


title: H2A.Z, unstimulated BAs-rep2

description: Library name: H2AZ_unstimulated_rep2

value: brown adipocytes

value: WT


title: ADRB2-KO mice,neutrophil+NE+LPS,rep3

description: Library name: ADRB2_NE_LPS_3A


title: ADRB2-KO mice,neutrophil+LPS,rep3

description: Library name: ADRB2_LPS_3A

value: LPS


title: mouse liver, D5, ATAC, Multiome

data_processing:
cellranger-arc-2.0.2
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Matrix, gene and barcode files

extract_protocol:
Combined scRNA- and scATAC-seq (10x Multiome) was performed as described in the demonstrated protocol for nuclei isolation for single cell Multiome ATAC + Gene Expression Sequencing (CG000365.Rev C). For this, liver cell suspensions were FACS-sorted for alive, Cd45+, Cd64- Cd11c+ cells. Sorted cells were then used for nuclei extraction. Digitonin treatment was performed for 210 s, nuclei suspensions washed, quantified and loaded at a concentration between 3000 – 8000 nuclei/µl to target a recovery of 10.000 nuclei.
10x Multiome preparation according to demonstrated protocol CG000365.Rev C
Combined scRNA- and scATAC-seq (10x Multiome), Single Cell Multiome ATAC + Gene Expression v1

treatment_protocol: Mice were fed with chow supplemented with 0.1% 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) for either 0 or 5 days (DDC D0/D5).

value: fed with chow supplemented with DDC for 5 days


title: ADRB2-KO mice,neutrophil+NE+LPS,rep2

description: Library name: ADRB2_NE_LPS_2A


title: H2A.Z, unstimulated BAs-rep1

description: Library name: H2AZ_unstimulated_rep1


title: mouse liver, D0 D5 D9 gdT [GEX]


title: Multiome, WT Cerebral organoids, 51 day, Rep 1, ATAC

description: Library name: 19236R_X1

value: hiPSC-derived cerebral organoid

value: Batch 05 July 2021


title: ADRB2-KO mice,neutrophil+LPS,rep2

description: Library name: ADRB2_LPS_2A


title: Multiome, KO Cerebral organoids, 74 day, Rep 2, RNA

description: Library name: 19311R_X4

value: KMT2D KO


title: mouse liver, D5, RNA, Multiome


title: mouse liver, D0, ATAC, Multiome

value: fed with chow supplemented with DDC for 0 days


title: Multiome, KO Cerebral organoids, 74 day, Rep1,  RNA

description: Library name: 19311R_X3


title: ADRB2-KO mice,neutrophil+LPS,rep1

description: Library name: ADRB2_LPS_1A


title: mouse liver, D0, RNA, Multiome


title: Multiome, WT Cerebral organoids, 74 day, Rep 2, RNA

description: Library name: 19311R_X2


title: inguinal WAT, Sham_28

city: Ulm

first: Pamela

last: Fischer-Posovszky

address: Eythstr. 24, Haus 16, Forschungslabor KiKli

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

description: miRNA expression data from inguinal white adipose tissue of mice undergoing sham-treatment

hyb_protocol: miRNAs were hybridized to AffymetrixTM miRNA 4.0 arrays

scan_protocol: Arrays were stained and washed on a GeneChip Fluidics Station 450 (Affymetrix)

data_processing: The arrays were analyzed by the Affymetrix GeneChip Scanner 3000 and the Affymetrix Expression ConsoleTM software. As only mouse miRNAs were used, the raw feature data were normalized using the RMA + DBAG algorithm and log2 intensity expression. A miRNA-transcriptome analysis was performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team. Only murine miRNAs were considered for further analysis.

source_name: Male C57BL/6 with Sham-treatment

label_protocol: 200 ng of total RNA were labelled using the FlashTagTM Biotin HSR RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Male C57BL/6 mice aged 10-12 weeks were randomly assigned to sham treatment or PT + HS (n=5 animals per group)

extract_protocol: Whole tissues were minced in liquid nitrogen and afterwards resolved in Tri-Reagent. Total RNA was isolated with Direct-zol RNA mini Prep Kit (Zymo Research) according to the manufacturer’s protocol.

treatment_protocol: Mice were anesthetized with 2.5% sevoflurane in oxygen throughout the experiment before they were subjected to thoracic trauma, closed head injury, and femur fracture including soft tissue injury. Pressure-controlled hemorrhage was induced and monitored by a microcatheter in the femoral artery. A mean arterial pressure of around 30 ± 5 mmHg was maintained for 60 minutes. After resuscitation of the animals with a balanced electrolyte solution, inguinal WAT depots were removed 4 hours after trauma.

value: inguinal white adipose tissue


title: WT mice,neutrophil+NE+LPS,rep3

description: Library name: WT_NE_LPS_3A


title: inguinal WAT, Sham_42


title: inguinal WAT, Sham_37


title: Adjacent normal kidney tissue from ICI non-responder (Case 2)

city: Ube

first: Hiroshi

last: Hirata

address: 1-1-1 Minami-Kogushi

department: Urology

country: Japan

institute: Yamaguchi University

hyb_protocol: Labeled cRNAs were hybridized onto the Arraystar Human LncRNA Microarray v5.0 according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using an Agilent Scanner G2505C.

data_processing: Raw intensity data were extracted using Agilent Feature Extraction software (version 11.0.1.1). Quantile normalization and log2 transformation were performed using GeneSpring GX v12.1 (Agilent Technologies). Normalized log2 expression values were used for downstream analyses.

source_name: disease: normal kidney; matched case: CDC2

label_protocol: RNA samples were amplified and labeled with Cy3 using the Arraystar RNA labeling kit following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor and matched normal kidney tissues using a commercially available RNA extraction kit according to the manufacturer's instructions.

value: adjacent normal kidney FFPE


title: Multiome, WT Cerebral organoids, 74 day, Rep 1, RNA

description: Library name: 19311R_X1


title: Adjacent normal kidney tissue from ICI responder (Case 1)

source_name: disease: normal kidney; matched case: CDC1


title: Collecting duct carcinoma tumor tissue from ICI non-responder (Case 2)

source_name: disease: collecting duct carcinoma; treatment response: non-responder

value: kidney tumor FFPE


title: Multiome, KO Cerebral organoids, 51 day, Rep1,  RNA

description: Library name: 19235R_X3


title: WT mice,neutrophil+NE+LPS,rep1

description: Library name: WT_NE_LPS_1A


title: Collecting duct carcinoma tumor tissue from ICI responder (Case 1)

source_name: disease: collecting duct carcinoma; treatment response: responder


title: inguinal WAT, PT_HS_36

description: miRNA expression data from inguinal white adipose tissue of mice undergoing PT+HS

source_name: Male C57BL/6 with PT+HS


title: WT mice,neutrophil+NE+LPS,rep2

description: Library name: WT_NE_LPS_2A


title: inguinal WAT, Sham_7


title: inguinal WAT, Sham_17


title: WT mice,neutrophil+LPS,rep2

description: Library name: WT_LPS_2A


title: Multiome, KO Cerebral organoids, 51 day, Rep 2, RNA

description: Library name: 19235R_X4


title: inguinal WAT, PT_HS_40


title: Multiome, WT Cerebral organoids, 51 day, Rep 1, RNA

description: Library name: 19235R_X1


title: Multiome, WT Cerebral organoids, 51 day, Rep 2, RNA

description: Library name: 19235R_X2


title: inguinal WAT, PT_HS_27


title: WT mice,neutrophil+LPS,rep3

description: Library name: WT_LPS_3A


title: inguinal WAT, PT_HS_14b