title: Hepa1-6 siH, ChIP HCFC1

data_processing:
Reads were mapped to the mouse reference genome (mm10) using BWA-MEM v0.7.12 in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1 (https://broadinstitute.github.io/picard/).
HCFC1 peaks (summit +/- 150 bp) were called using MACS2 software suite v2.1.1.20160309 with the default FDR (alpha = 0.05) using sequenced libraries of IgG as control.
Peaks in mitochondrial chromosome and scaffold regions were removed. Peak intersections and annotations were performed using HOMER v4.11.1. Peaks were filtered to retain those ± 20kb of gene TSSs.
Assembly: mm10
Supplementary files format and content: Excel sheet includes the HCFC1 ChIP peaks for all the conditions
Supplementary files format and content: BigWig (.bw) files

growth_protocol: Hepa 1-6 cells, originally sourced from the ATCC (RRID: CVCL_0327), were maintained in DMEM (319-005-CL, Wisent) supplemented with 10% (v/v) fetal bovine serum (FBS, 12483020, Thermo Fisher Scientific) and 100 units/ml penicillin-streptomycin (450-201-EL, Wisent). Cultured cells were maintained at 37°C with 5% CO2.

extract_protocol:
For the ChIP procedure, the ChIP-IT High Sensitivity® kit (53040, Active Motif) was employed according to the manufacturer's instructions with some modifications: 60 strokes were used for homogenization using a loose Dounce homogenizer and sonication was performed with 700 μl of ChIP buffer using an automatic sonicator (Qsonica Shearing System, model Q800R) set for 20 min of continuous operation with a 30-second ON/30-second OFF cycle at 40% amplitude. For each ChIP, 30 μg of chromatin was utilized, along with either 10 μl of HCFC1 antibody (A301-399A, Bethyl; RRID: AB_961012) or 1 μl of non-specific rabbit IgG (10500C, Thermo Fisher; RRID: AB_2532981). At the end of the ChIP procedure, the ChIP DNA was eluted in 100 μl of elution buffer.
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra II DNA Library Prep kit according to manufacturer's recommendations and sequenced as 150bp paired-end reads on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: Hepa 1-6 cells were trypsinized, and 400,000 cells were reseeded in 6 cm plates. Cells were then transfected with 100 nM of either a control pool of scrambled siRNAs (D-001810-01-50, Dharmacon) or siRNAs targeting mouse ERRα (L-040772-00-0050, Dharmacon) or HCFC1 (L-051186-01-0050, Dharmacon). To elaborate, 4 μl of siRNAs were mixed with 37.5 μl of Hiperfect transfection reagent (301707, Qiagen) and enough Optimem Opti-MEM reduced serum medium (31985070, Thermo Fisher) to reach a final volume of 1 ml. This mixture was allowed to incubate at room temperature for 10 min then added to the cells, and media was added to have a final volume of 4 ml, bringing the final siRNA concentration to 100 nM. The siRNA transfection was repeated after 48 h, directly on the attached cells, and the cells were left for another 48h.

value: siHCFC1 (96h, 200nM)

tag: chip antibody


title: Hepa1-6 cells: siC (96h, 200nM) rep3

status: Public on Apr 17 2024

type: SRA

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Hisat2 (version 2.0.5) was employed to align the paired-end clean reads to the mouse reference genome mm10.
FeatureCounts (v1.5.0-p3) was used to count the number of reads per gene during the mapping process.
The Fragments per Kilobase of Transcript Sequence per Million Base Pairs Sequenced (FPKM) for each gene were computed based on the gene's length and the read counts mapped to it. Differential expression analysis between two groups (n=3 per group) was carried out using the DESeq2 R package (version 1.20.0) and genes with an adjusted p-value < 0.05 and log2|fold change| ≥ 0.5 were considered significantly altered.
Assembly: mm10
Supplementary files format and content: Excel sheet includes TPM values for all samples (Scholtes_TPM_annotated.xlsx)
Supplementary files format and content: Excel sheets includes dataset comparisons: DESeq2 differential expression analysis with adjusted p-values and fold changes shown (Scholtes_Dataset comparisons.xlsx)

molecule: total RNA

organism: Mus musculus

growth_protocol: Hepa 1-6 cells, originally sourced from the ATCC (RRID: CVCL_0327), were maintained in DMEM (319-005-CL, Wisent) supplemented with 10% (v/v) fetal bovine serum (FBS, 12483020, Thermo Fisher Scientific) and 100 units/ml penicillin-streptomycin (450-201-EL, Wisent). Cultured cells were maintained at 37°C with 5% CO2,

extract_protocol:
Total RNA was extracted from frozen Hepa 1-6 cell pellets using the RNeasy Mini kit (74106, QIAGEN) following the manufacturer’s instructions with an on-column DNase digestion step (79254, Qiagen).
The RNA underwent quantification and quality assessment before library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) in accordance with the manufacturer's recommendations at Novogene Bioinformatics Technology Co., Ltd.

treatment_protocol: Hepa 1-6 cells were trypsinized, and 400,000 cells were reseeded in 6 cm plates. Cells were then transfected with 100 nM of either a control pool of scrambled siRNAs (D-001810-01-50, Dharmacon) or siRNAs targeting mouse ERRα (L-040772-00-0050, Dharmacon) or HCFC1 (L-051186-01-0050, Dharmacon). To elaborate, 4 μl of siRNAs were mixed with 37.5 μl of Hiperfect transfection reagent (301707, Qiagen) and enough Optimem Opti-MEM reduced serum medium (31985070, Thermo Fisher) to reach a final volume of 1 ml. This mixture was allowed to incubate at room temperature for 10 min then added to the cells, and media was added to have a final volume of 4 ml, bringing the final siRNA concentration to 100 nM. The siRNA transfection was repeated after 48 h, directly on the attached cells, and the cells were left for another 48h (200 nM siRNA total).

tag: cell line

tag: cell type

value: Hepatocyte

tag: genotype

value: WT

tag: treatment


title: D010-PJS-059

city: Sejong

first: Sinwoo

last: Park

address: Sejongro

country: South Korea

institute: Korea Universiy

data_processing:
Low qaulity of reads in the raw reads were trimmed using the Trimmomatic (v0.39)
Trimmed reads were align using HISAT2 (v2.2.1)
FeatureCounts (v2.0.3) was used for the quantification of aligned reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Homo sapiens

source_name: blood

extract_protocol:
For Illumina NovaSeq 6000, total RNA was extracted using TruSeq Stranded Total RNA LT Sample Prep Kit (Globin). For MGISEQ-2000RS, total RNA was isolated from tissue using TRI-reagent based method. Total RNA (500 ng) was processed for  preparing whole transcriptome sequencing library.
For Illumina NovaSeq 6000, libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E, For MGISEQ-2000RS,  Enrichment of whole transcriptome RNA by depleting  ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

tag: tissue

value: blood

tag: Sex

value: M

tag: disease

value: COPD


title: D008-ASJ-642


title: Hepa1-6 cells: siC (96h, 200nM) rep2


city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

country: USA

institute: Stanford University

description:
Patient SU353 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

library_source: genomic

data_processing:
ATAC-sea data was processed based on workflows similar to Corces et al. Science 201826. First, read trimming and quality control was performed using trim_galore using default parameters. Reads were aligned to the GRCh38 reference genome using bowtie2 and the --very-sensitive option. Aligned reads were converted to bam format and sorted using SAMtools, and deduplicated using Picard MarkDuplicates. Reads were subsequently indexed and mitochondrial reads were removed using SAMTools. TagAlign bed files from technical replicate libraries were generated using bedtools, shifted to find ATAC-seq cut sites, and pooled. Peaks were called using MACS2 using p-value cut-off of 0.01 and peaks falling within black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed. A consensus peak set was generated using methods from Corces et al. Science 201828. Briefly, called peaks were merged by merging all peak bed files and using an iterative removal process to resolve overlapping peaks. This approach resulted in a consensus set of 115,551 500bp fixed-width peaks covering accessible regions represented in at least 2 or more samples. Count matrices were generated using the consensus peak set, and the number of Tn5 cut sites in each peak were calculated using the CountOverlaps function from the GenomicRanges package in R.
Assembly: Processed data files aligned to hg38 reference genome.
Supplementary files format and content: R data file containing peak counts or gene accessibility scores for each sample.

molecule: genomic DNA

source_name: AML

extract_protocol:
Sorted AML blasts were prepared for ATAC-seq as previously described54. 5,000-50,000 cells were washed in cold FACS buffer and spun at 4°C for 5 minutes at 500 rcf in a fix-angled centrifuge. Cell pellets were then resuspended in 50 uL of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) with 0.1% NP40, 0.01% digitonin, and 0.1% Tween-20 and incubated on ice for three minutes. After lysis, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added and tubes were inverted six times to mix. Isolated nuclei were then spun at 4°C for 10 minutes at 500 rcf in a fix-angled centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (25uL 2xTD buffer, 2.5 uL Tn5 transposase (100 nM final), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, and 5 uL nuclease-free water).
Transposition reactions were incubated at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up using Qiagen MinElute Reaction Cleanup kits and processed as previously described. All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product.
All libraries were sequenced on an Illumina NextSeq with 75 bp paired end reads.

value: AML

tag: individual

value: Patient SU353

tag: timepoint

value: Diagnosis

value: LSC


title: D005-KDD-183


title: SCNd+a, S550

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

library_source: transcriptomic single cell

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to GRCm38.p4  to get gene counts (Data-sce-count.txt)
Cells that passed quality control were normalized (Data-sce-normed.txt, Lab-Sara-sce-log.txt)
Differential gene expression was analyzed using DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: Data-sce-count.txt; raw counts
Supplementary files format and content: Data-sce-normed.txt; normalized counts
Supplementary files format and content: Data-sce-log.txt; log of normalized counts

source_name: interneurons of the suprachiasmatic nucleus

extract_protocol:
single cell extraction via patch pipette
Nextera XT DNA Library Preparation kit

tag: time of_day

value: day

tag: electrophysiology

value: active

tag: cfos expression

value: cFOS+


description:
Patient SU360 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU360

value: Relapse

value: Blast


description:
Patient SU360 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU353 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: D006-YYJ-361


title: Hepa1-6 siE, ChIP HCFC1

value: siERRa (96h, 200nM)


title: SCNn+s, S543

value: interneurons of the suprachiasmatic nucleus

value: night

value: silent


title: Hepa1-6 siH, ChIP IgG

value: Hepatocyte

value: WT

value: siHCFC1 (96h, 200nM)

value: rabbit IgG:10500C, Thermo Fisher; RRID:AB_2532981


description:
Patient SU360 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: D004-BJK-632

value: blood

value: M

value: COPD


title: Hepa1-6 siE, ChIP IgG


description:
Patient SU353 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU353

value: LSC


title: D003-JKJ-487


title: D001-KSM-001


title: Hepa1-6 siC, ChIP HCFC1


title: SCNd-a, S547

value: day

value: active

value: cFOS-


description:
Patient SU353 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: Hepa1-6 siC, ChIP IgG


title: SCNn-a, S537

value: interneurons of the suprachiasmatic nucleus


title: D002-CYK-580


title: SCNn-a, S540

value: night


title: 12778445

value: F


title: SeV control scmultiome ATAC

city: Houston

first: Dalia

last: Hassan

state: TX

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description:
2-wk post Sendai Virus injury
Aggregate_SeV_atac_fragments.tsv.gz
Aggregate_SeV_atac_peak_annotation.tsv
Aggregate_SeV_cloupe.cloupe

library_source: genomic single cell

data_processing:
Raw sequencing data (fastq file) was demultiplexed and analyzed using 10X Genomics Cell Ranger ARC software
Further analysis can be achieved using the Cell Ranger ARC-derived analysis files in 10X Genomics Loupe Browser software.
Assembly: mm10
Supplementary files format and content: Rds, tsv and mtx files can be opened with Seurat&Signac (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.
Supplementary files format and content: filtered_feature_bc_matrix.h5 can be opened with Seurat (R package)

source_name: lung

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
FACS-purified lung epithelial, were processed through the CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_Revf.
scRNA-seq  28 cycles read1, 90 cycles read2, 10 cycles Index1, and 10 cycles Index2
scATAC-seq 50 cycles for read 1, 49 cycles for read2, 8 cycles for index1, and 24 cycles for index2

value: lung

value: epithelial cells

value: CebpaCKO/+; SftpcCreER;SUN1GFP

tag: age

value: 3 doses of Tamoxifen each 3mg at 7-wk , Sendai Virus treatment at 10-wk, lung harvest at 12-wk

value: pooled male and female


title: SCNn+s, S542

value: silent

value: cFOS+


title: SCNn+s, S534


description:
Patient SU353 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Relapse

value: Bulk


title: SeV control scmultiome GE

description:
2-wk post Sendai Virus injury
Aggregate_SeV_filtered_feature_bc_matrix.h5
Aggregate_SeV.rds
Aggregate_SeV_cloupe.cloupe

molecule: nuclear RNA


description:
Patient SU353 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU353

value: Blast


title: SCNn-s, S544

value: cFOS-


title: 12778438

value: blood

value: COPD


title: SCNn-a, S533

value: interneurons of the suprachiasmatic nucleus

value: night

value: active


title: SeV mutant scmultiome ATAC

value: lung

value: epithelial cells

value: CebpaCKO/CKO; SftpcCreER;Sun1GFP


description:
Patient SU353 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 12492431

value: F


title: SCNn+s, S532

value: silent


title: 12255702

value: M


title: SCNn+s, S531

value: cFOS+


title: 7-wk control scmultiome ATAC

description:
Deletion of cebpa in mature AT2 cells
Aggregate7-wk_atac_fragments.tsv.gz
Aggregate7-wk.rds
Aggregate7-wk_cloupe.cloupe

value: CebpaCKO/+; SftpcCreER;SUN1GFP

value: 2 doses of Tamoxifen each 3mg at 5-wk

value: pooled male and female


description:
Patient SU353 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU353

value: Relapse

value: Bulk


title: 7-wk control scmultiome GE

description:
Deletion of cebpa in mature AT2 cells
Aggregate7-wk_filtered_feature_bc_matrix.h5
Aggregate7-wk_raw_feature_bc_matrix.h5
Aggregate7-wk_cloupe.cloupe


title: 12255579

value: blood

value: COPD


description:
Patient SU353 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: Blast


title: SCNn+a, S530

value: interneurons of the suprachiasmatic nucleus

value: night

value: active


description:
Patient SU353 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: SCNn-a, S529

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: cFOS-


title: 12255517

value: M


title: 7 wk mutant scmultiome GE

description:
Deletion of cebpa in mature AT2 cells
Aggregate7wk_filtered_feature_bc_matrix.h5
Aggregate7wk_raw_feature_bc_matrix.h5
Aggregate7-wk_cloupe.cloupe

value: lung

value: epithelial cells

value: CebpaCKO/CKO; SftpcCreER;Sun1GFP


title: 7-wk mutant scmultiome ATAC

value: 2 doses of Tamoxifen each 3mg at 5-wk

value: pooled male and female


title: SCNn-s, S528

value: silent


title: 12255461


title: SCNn+a, S527

value: cFOS+


description:
Patient SU332 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU332

value: LSC


title: 12255447

value: blood

value: COPD


title: control P9 scmultiome ATAC

description:
Deletion of cebpa from neonatal AT2 cells
Aggregate.P9_atac_fragments.tsv.gz
Aggregate.P9.atac_peak_annotation.tsv
Aggregate7-wk_cloupe.cloupe

value: CebpaCKO/+; SftpcCreER;SUN1GFP

value: postnatal day 9

value: 250ug-Tamoxifen at at postnatal day 2


title: SCNn+s, S525

value: interneurons of the suprachiasmatic nucleus

value: night


title: control P9 scmultiome GE

description:
Deletion of cebpa from neonatal AT2 cells
Aggregate.P9_filtered_feature_bc_matrix.h5
Aggregate.P9.rds
Aggregate.P9_cloupe.cloupe

value: lung


title: 12255391

value: M


description:
Patient SU353 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU353

value: Diagnosis

value: Bulk


title: SCNn+s, S524

value: silent


description:
Patient SU332 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: SeV mutant scmultiome GE

value: epithelial cells

value: CebpaCKO/CKO; SftpcCreER;Sun1GFP

value: 3 doses of Tamoxifen each 3mg (last dose at 7-wk) , Sendai Virus treatment at 10-wk, lung harvest at 12-wk

value: pooled male and female


title: mutant P9 scmultiome ATAC

description:
Deletion of cebpa from neonatal AT2 cells
Aggregate.P9_atac_fragments.tsv.gz
Aggregate.P9.atac_peak_annotation.tsv
Aggregate.P9_cloupe.cloupe


description:
Patient SU353 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: 12255656

value: blood

value: COPD


description:
Patient SU332 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU332


title: 12255384


title: SCNn+a, S523

value: active

value: cFOS+


title: mutant P9 scmultiome GE

value: postnatal day 9

value: 250ug-Tamoxifen at at postnatal day 2


description:
Patient SU332 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse

value: LSC


title: 12255360

value: M


description:
Patient SU332 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


description:
Patient SU332 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 12255322


description:
Patient SU332 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: 12255308


title: SCNn-a, S522

value: interneurons of the suprachiasmatic nucleus

value: night

value: cFOS-


title: MEFS, female, Sirt3 knock-out, rep3

city: Zagreb

first: Robert

last: Beluzic

address: Bijenicka 54

department: Department of Molecular Medicine

country: Croatia

institute: Rudjer Boskovic Institute

data_processing:
Adapter and low-quality base trimming was performed by Novogene.
TPM (transcripts per million) values were obtained by Salmon 1.10.1. pseudoaligner with fastq files as inputs
Assembly: Mouse, Mus musculus (GRCm38)
Supplementary files format and content: Sirt3_RNASeq_TPMs_all_samples.tsv file contains a TPM matrix of all 12 samples

molecule: polyA RNA

source_name: embryo; fibroblasts

growth_protocol: MEFs were maintained in a 37°C incubator with 5% CO2. Passage 6 cells (4E5 per well) were seeded into 6 wells and RNA was extracted after 48h.

extract_protocol:
RNA was extracted using Qiagen RNEasy Mini kit.
Sample QC, library preparation and sequencing were performed by external NGS service provider (Novogen)
After RNA fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: embryo; fibroblasts

value: immortalized fibroblast cell line

value: female

value: Sirtuin 3 knock-out


title: SCNn+s, S520

value: silent


title: MEFS, female, Sirt3 knock-out, rep2


title: SCNn-a, S519

value: active


title: MEFS, female, Sirt3 knock-out, rep1


description:
Patient SU332 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU332


title: MEFS, male, Sirt3 knock-out, rep3

value: male


title: MEFS, male, Sirt3 knock-out, rep2


title: 12255276

value: blood

value: COPD


title: 12255182

value: F


description:
Patient SU332 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse

value: Blast


description:
Patient SU332 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: SCNn-a, S518

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: interneurons of the suprachiasmatic nucleus

value: night


title: 12255269

value: M


title: MEFS, male, Sirt3 knock-out, rep1

value: embryo; fibroblasts

value: immortalized fibroblast cell line


title: SCNn+a, S517

value: cFOS+


title: SCNn-a, S5162

value: cFOS-


title: MEFs, female, wild-type, rep3

value: female

value: Sirtuin 3 wild-type


title: 12248463


description:
Patient SU332 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU332


title: SCNn+a, S521

value: active


title: MEFs, female, wild-type, rep2


title: 12247857

value: blood

value: COPD


description:
Patient SU320 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU320

value: Relapse


title: 12247833


title: MEFs, female, wild-type, rep1


title: SCNn-s, S511

value: silent


title: SCNn-s, S510

value: interneurons of the suprachiasmatic nucleus


title: 12247686


title: MEFs, male, wild-type, rep3

value: male


description:
Patient SU332 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


description:
Patient SU320 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: SCNn-a, S509

value: night


title: 12247600

value: F


title: MEFs, male, wild-type, rep2

value: embryo; fibroblasts

value: immortalized fibroblast cell line


title: 12247530

value: M


description:
Patient SU303 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU303


title: Mutant Cerebellum E16.5

city: Hamburg

first: Ulrich

last: Schüller

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Raw sequencing reads were aligned against a murine reference genome (mm10-2020-A, provided by 10x Genomics) and were simultaneously counted with the Cell Ranger pipeline (v7.0.1) (Zheng et al., 2017) employing the count command.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebellum

extract_protocol:
Total cerebella were digested in Papain/DNase solution (Papain 20 U/ml (Worthington, NJ, USA); DNase 400 µg/ml) at 37°C for 30 to 60min. Dead cells were excluded from the single-cell suspension by FACS sorting after labelling with 7-AAD. Three samples for each genotype were pooled to generate one control and one mutant sample.
Preparation of single-cell gene expression libraries was performed at the Single Cell Core Facility of the University Medical Center Hamburg using the Chromium Next GEM Single Cell 3ʹ v3.1 kit (10x Genomics, CA, USA) with 40,000 cells of each pooled sample. Sufficient quality of the generated library was confirmed on a TapeStation with the High Sensitivity D5000 ScreenTape® (Agilent, CA, USA).

value: cerebellum

value: total cerebellar cells


title: 12017443

value: blood

value: COPD


title: SCNn+s, S508

value: cFOS+


title: SCNn+a, S507

value: active


title: 12017412


description:
Patient SU303 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: SCNn+a, S513

value: interneurons of the suprachiasmatic nucleus


title: Control Cerebellum E16.5

value: cre-negative


title: SCNn+s, S506

value: silent


title: 12017405


title: SCNn+a, S505


title: Sperm, TT genotype, FASD6

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

data_processing:
Raw fastq files were trimmed of adaporter sequences with trimmoatic (version 0.36)
Trimmed reads were aligned to the mm10 genome using bismark aligner (version 0.18.1)
Duplicate aligned reads (if they have the same 5' alignment positions for bother paired in paired-end reads) are removed with picard tools (version 2.9.0).  All duplicated reads are removed and only the best pair, based on alignment score, is kept
Methylation information was extracted from the bisulfite read aligment files for indivudial cytosines using bismark (version 0.18.1)
Assembly: mm10
Supplementary files format and content: CpG methylation profiles for individual samples as a txt file.  Files contains the following columns: chrBase, chr, base, strand, coverage, freqC, freqT

source_name: Sperm

extract_protocol:
Frozen sperm was thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Canada) according to the manufacturer’s guide, with modifications. For sample  were incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
Using 1-2ug of DNA from each sample, whole genome bisulfite sequencing (WGBS) library preparation was performed as described previously. Briefly, DNA was sonicated to obtain 300-400bp fragments, proceeded by DNA-end repair, 3’-end adenylation, adaptor ligation and clean up, according to the KAPA High Throughput Library Preparation kit protocol (Roche/KAPA Biosystems). Samples were then bisulfite converted using the EpiTect Fast DNA bisulfite kit (Qiagen) followed by 9-12 cycles of PCR amplification. The final WGBS libraries were purified using Agencourt AMPure Beads (Beckman Coulter)

treatment_protocol: Mthfr TT mice and wild-type mice as control (Mthfr CC) at four weeks of age were given one of 3 different diets:  control (CD, 2mg folic acid/kg diet), folate-deficient (FD, 0.3mg folic acid/kg diet) and moderate dose folic acid-supplemented (FASD, 5-fold supplemented: 10 mg folic acid/kg diet) diets. They were maintained on these diets for four months.  At the end of diet treatments mice were sacrificed and tissues and organs were collected.  Mature spermatozoa from paired cauda epididymides were collected and kept frozen at -80oC until use.

value: Sperm

value: male

tag: strain

value: TT

value: FASD


description:
Patient SU303 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: Blast


description:
Patient SU320 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU320

value: Relapse


title: SCNn-s, S503

value: night

value: cFOS-


title: SCNn-a, S501


description:
Patient SU302 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU302

value: LSC


description:
Patient SU302 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 11996815

value: blood

value: M

value: COPD


description:
Patient SU320 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: MEFs, male, wild-type, rep1

value: embryo; fibroblasts

value: immortalized fibroblast cell line

value: Sirtuin 3 wild-type


title: 11996808


title: SCNn-s, S499

value: interneurons of the suprachiasmatic nucleus

value: silent


title: 11996776


title: Sperm, TT genotype, FASD3

value: Sperm

value: male

value: TT

value: FASD


title: SCNd-s, S498

value: day


title: 11996721


title: SCNd-s, S497


title: Sperm, TT genotype, FASD4


description:
Patient SU303 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU303

value: Relapse

value: Blast


title: Sperm, TT genotype, FASD1


title: Sperm, TT genotype, FASD2


description:
Patient SU302 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU302

value: LSC


description:
Patient SU302 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


description:
Patient SU302 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 11996699

value: blood

value: F

value: COPD


title: Sperm, TT genotype, CD6

value: CD


title: 12001936

value: M


title: SCNd-s, S493

value: interneurons of the suprachiasmatic nucleus

value: silent

value: cFOS-


title: 11996675


title: SCNd+a, S492

value: active

value: cFOS+


title: Sperm, TT genotype, FASD5

value: Sperm

value: male

value: TT

value: FASD


description:
Patient SU302 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU302

value: Relapse

value: Blast


description:
Patient SU302 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: Sperm, TT genotype, CD5


title: Sperm, TT genotype, CD4


title: SCNd-a, S491

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: day


title: 11996644

value: blood

value: COPD


title: 11996598

value: M


title: Sperm, TT genotype, CD3

value: CD


title: SCNd+a, S490

value: interneurons of the suprachiasmatic nucleus


description:
Patient SU302 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Sperm, TT genotype, CD2


description:
Patient SU302 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


description:
Patient SU302 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: SCNd+s, S488

value: silent

value: cFOS+


description:
Patient SU302 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Sperm, TT genotype, CD1

value: Sperm

value: male


title: SCNd-s, S489

value: cFOS-


title: 11981402


title: SCNd+s, S487


description:
Patient SU302 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: Sperm, CC genotype, FASD5

value: CC

value: FASD


title: SCNd-a, S486

value: active


title: 11981318


title: 11981394


title: 11981200

value: F


description:
Patient SU291 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU291

value: Relapse

value: Blast


title: Sperm, CC genotype, FASD6


title: 11789790

value: blood

value: COPD


title: 11780003


title: SCNd+s, S483

value: interneurons of the suprachiasmatic nucleus

value: day


title: SCNd+a, S482


description:
Patient SU291 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: Sperm, CC genotype, FASD4


title: SCNd-a, S485


description:
Patient SU291 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 11789745

value: M


description:
Patient SU277 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU277


title: Sperm, CC genotype, FASD1

value: Sperm

value: male


title: SCNd-s, S481

value: silent

value: cFOS-


title: Sperm, CC genotype, FASD3

value: CC

value: FASD


title: Sperm, CC genotype, FASD2


title: SCNd-s, S477


title: 11779919

value: F


title: Sperm, CC genotype, CD5

value: CD


title: 11779793


title: SCNd-s, S480


title: SCNd+a, S476

value: active

value: cFOS+


description:
Patient SU277 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Blast


title: Sperm, CC genotype, CD6


title: Sperm, CC genotype, CD3


title: 11779818

value: blood

value: COPD


description:
Patient SU277 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


description:
Patient SU277 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: 11775258


title: SCNd+a, S475

value: interneurons of the suprachiasmatic nucleus

value: day


title: SCNd-a, S472


description:
Patient SU291 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU291


description:
Patient SU142 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU142

value: LSC


title: 11779988

value: M


title: 11775188


title: Sperm, CC genotype, CD2

value: Sperm

value: male

value: CC


title: Sperm, CC genotype, CD1

value: CD


description:
Patient SU142 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


description:
Patient SU142 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: 11772019

value: F


title: Sperm, CC genotype, CD4


title: 11771395

value: blood


title: SCNd-s, S469

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: silent

value: cFOS-


title: Renca VHL KO.1 TAM1 F480lo M8

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
For scRNAseq/snRNAseq, demultiplex, barcode processing, and gene counting were done using cellranger.
matrix got from cellranger were further processed using Seurat
For RNAseq, raw reads were first aligned to the genome (mm10), and the gene count were done using featurecount
The differentially expressed genes were captured using edgeR
Assembly: mm10 or GRCh38
Supplementary files format and content: Tab delimited txt for RNAseq gene counts
Supplementary files format and content: Matrix files for sc/RNAseq/snRNAseq

source_name: Tumor

growth_protocol: Prior to injection into mouse for sub-cutaneous growth, Renca cell lines were maintained in RPMI supplemented with 10% FBS, 1% pen/strep, 1% L-glutamine, 1% hepes, 1% sodium pyruvate, and 1% MEM amino acid.

extract_protocol:
For single cell experiments, 10-week-old Balb/c mice were injected s.c. with 1 × 106 Vhl WT or Vhl KO cells. Tumors were harvested at 16 days post injection and then enzymatically digested. CD45+ and CD45- live cells were flow sorted and counted using trypan blue and a TC20 counter. For single nucleus RNA seq experiment, nuclei was isolated from human patient ccRCC tumors as previously described [Wu., H. et al., J Am Soc Nephrol, 2019]. For bulk RNA-seq, CD11b+ fractions from experimentally matched tumors were bead isolated prior to staining of indicated surface markers and viability dye. The fractions were then sorted on a BD FACSAria III cell sorter and stored in 5 parts RNA cell protect to 1 part FACS solution. RNA was isolated, and low-input RNA sequencing was performed using the SMART-Seq v4 Ultra Low Input RNA Kit.
Libraries were made according to manufacturers's protocol (10X genomics or Truseq stranded library kit)
scRNAseq, snRNAseq, RNAseq

value: Tumor

value: Renca

value: Tumor TAM1

value: VHL KO.1


title: SCNd-a, S467

value: interneurons of the suprachiasmatic nucleus

value: day

value: active


description:
Patient SU142 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU142

value: Diagnosis


description:
Patient SU142 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse

value: LSC


title: SCNn+a, S466

value: night

value: cFOS+


title: Renca VHL KO.1 PMN MDSC LY6G M8

value: Tumor PMN MDSC


title: 11779786

value: blood

value: F

value: COPD


title: 11771388

value: M


title: 11771326


description:
Patient SU142 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


description:
Patient SU142 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: SCNn-a, S464

value: cFOS-


title: Renca VHL WT.1 TAM2 F480lhi M7

value: Tumor

value: Renca

value: Tumor TAM2

value: VHL WT.1


title: 11771319


description:
Patient SU142 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU142


title: SCNd+a, S471

value: interneurons of the suprachiasmatic nucleus

value: day

value: active


title: Renca VHL KO.1 TAM2 F480lhi M8

value: VHL KO.1


title: SCNn-a, S463

value: night


title: Renca VHL WT.1 TAM1 F480lo M7

value: Tumor TAM1


description:
Patient SU142 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse

value: Blast


title: Renca VHL WT.1 PMN MDSC LY6G M7

value: Tumor PMN MDSC


title: 11766898

value: blood

value: F

value: COPD


title: SCNn+a, S461

value: cFOS+


description:
Patient SU142 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


description:
Patient SU142 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: 11766843

value: M


title: 11766850


title: SCNn-a, S465

value: cFOS-


title: SCNn-a, S457

value: interneurons of the suprachiasmatic nucleus


title: Renca VHL WT.1 M MDSC LY6C M7

value: Tumor

value: Renca

value: Tumor MDSC

value: VHL WT.1


title: 11766603


title: SCNn+a, S453

value: night

value: active


title: 11766829


title: Renca VHL KO.1 TAM2 F480lhi M6

value: Tumor TAM2

value: VHL KO.1


title: Renca VHL KO.1 M MDSC LY6C M8


description:
Patient SU067 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU067

value: Blast


title: 11766571

value: blood

value: COPD


title: 11766906

value: F


title: SCNn-s, S455

value: silent


title: Renca VHL KO.1 M MDSC LY6C M6


title: SCNn-a, S454


description:
Patient SU142 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU142

value: Diagnosis


description:
Patient SU067 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: SCNn+s, S451

value: interneurons of the suprachiasmatic nucleus

value: cFOS+


title: SCNn-s, S456

value: cFOS-


title: Renca VHL KO.1 PMN MDSC LY6G M6

value: Tumor

value: Renca

value: Tumor PMN MDSC


title: 11766502

value: M


description:
Patient SU042 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU042


description:
Patient SU067 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU067

value: Blast


title: SCNn+s, S449

value: night


title: SCNn-a, S452

value: active


title: Renca VHL WT.1 TAM2 F480lhi M5

value: Tumor TAM2

value: VHL WT.1


description:
Patient SU067 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: 11766487

value: blood

value: COPD


title: Renca VHL KO.1 TAM1 F480lo M6

value: Tumor TAM1

value: VHL KO.1


title: Renca VHL WT.1 PMN MDSC LY6G M5


title: SCNd+s, S447

value: interneurons of the suprachiasmatic nucleus

value: day

value: silent

value: cFOS+


title: 11766463

value: F


title: Renca VHL WT.1 TAM1 F480lo M5

value: Tumor

value: Renca


title: 11766595

value: M


title: Renca VHL KO.1 TAM2 F480lhi M4


title: 11766393


description:
Patient SU042 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU042

value: Diagnosis

value: Blast


title: SCNd-s, S445

value: cFOS-


title: Renca VHL KO.1 TAM1 F480lo M4


title: fsN2_OE_EdUseq_R90

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
Assembly: Human GRCh37/hg19

source_name: Human cell line

growth_protocol: Cyclin E-inducible (tet-off system) U2OS (U2OS CycE) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, penicillin/streptomycin/glutamine and with puromycin, G418 in presence or absence of tetracycline to suppress or induce, respectively, expression of an ectopic Cyclin E gene

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina Hi-Seq 4000 sequencer.

treatment_protocol: EdU-seq samples were treated with nocodazole for 8hrs and mitotic cells were obtained with mitotic shake-off. They were then released in medium containing HU and EdU for 6 (OE samples) or 14hrs (NE samples). Fork progression studies were performed with same setup: nocodazole, MSO, 14hr with HU (both NE and OE), 30 or 90min release, with EdU pulse at the last 30min before collection. Corresponding EdU-seq samples were used as time 0. MiDAS-seq was performed as described in https://doi.org/10.1038/s41422-020-0358-x

value: Human cell line

value: U2OS (Tet-Off CCNE overexpression)

value: Human Bone Osteosarcoma Epithelial Cells

tag: genetic modification

value: KO – CRISPR frameshift mutation in the N-terminal domain of the RECQL4 gene


title: 13024716

value: blood

value: COPD


title: Renca VHL WT.1 M MDSC LY6C M5

value: Tumor MDSC

value: VHL WT.1


title: 11766456


title: fsN2_OE_EdUseq_R30


title: SCNd-a, S446

value: interneurons of the suprachiasmatic nucleus

value: day

value: active


title: Renca VHL KO.1 M MDSC LY6C M4

value: Tumor

value: Renca

value: VHL KO.1


title: 13023946

value: F


title: Renca VHL KO.1 PMN MDSC lY6G M4

value: Tumor PMN MDSC


title: SCNd+a, S443

value: cFOS+


title: fsN2_NE_EdUseq_R90

value: Human cell line


title: 13024615


title: Renca VHL WT.1 TAM2 F480lhi M3

value: Tumor TAM2


title: fsN2_NE_EdUseq_R30

value: U2OS (Tet-Off CCNE overexpression)

value: Human Bone Osteosarcoma Epithelial Cells


description:
Patient SU042 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU042

value: Diagnosis

value: Blast


title: 13005094

value: blood

value: M

value: COPD


title: Renca VHL WT.1 TAM1 F480lo M3

value: Tumor

value: Tumor TAM1

value: VHL WT.1


title: 12785056

value: F


description:
Patient SU042 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: fsH2_OE_EdUseq_R90

value: KO - CRISPR frameshift mutation in the helicase domain of the RECQL4 gene


title: Renca VHL WT.1 PMN MDSC lY6G M3

value: Renca

value: Tumor PMN MDSC


title: SCNd-s, S440

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: interneurons of the suprachiasmatic nucleus

value: day

value: silent

value: cFOS-


title: SCNd-s, S444


title: Renca VHL WT.1 M MDSC LY6C M3

value: Tumor MDSC


title: SCNd-a, S438

value: active


title: SCNd+a, S442

value: cFOS+


title: Renca VHL KO.1 TAM2 F480lhi M2

value: Tumor TAM2

value: VHL KO.1


title: fsH2_NE_EdUseq_R30

value: Human cell line

value: U2OS (Tet-Off CCNE overexpression)

value: Human Bone Osteosarcoma Epithelial Cells


title: 12778647

value: blood

value: F

value: COPD


title: SCNn+a, S432

value: night


title: 12785049

value: M


title: SCNd-a, S439

value: interneurons of the suprachiasmatic nucleus


title: fsH2_OE_EdUseq_R30

value: KO - CRISPR frameshift mutation in the helicase domain of the RECQL4 gene


title: SCNd+a, S437

value: day


title: fsH2_NE_EdUseq_R90


title: SCNd-a, S435

value: cFOS-


title: Renca VHL KO.1 TAM1 F480lo M2

value: Tumor

value: Renca

value: Tumor TAM1


title: SCNn+a, S431

value: active

value: cFOS+


title: Renca VHL KO.1 PMN MDSC LY6G M2

value: Tumor PMN MDSC

value: VHL KO.1


title: Renca VHL KO.1 M MDSC LY6C M2

value: Tumor MDSC


title: Patient 29, scRNAseq

city: Duarte

first: Haiqing

last: Li

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
scRNA seq data was processed using Cell Ranger 3.1 with standard barcode filter. The low quality cells are further filtered based on Mitochondrial reads, the percentage of read the largest gene,  and with low  and high detected features. scRNA seq was analyzed using standard Seurat v4.1 integration workflow to identify shared cell states. Top 2000 variated features were selected to find the anchors between pairs of datasets. The integrated dataset was reduced dimension and visualized on the UMAP spaces using top 30 principal components. All cells are clustered using original Louvain algorithm. The cell type of each cell cluster was identified and annotated using known maker genes. The different expressed gene between two groups was analyzed using Wilcoxon Rank Sum test implemented in Seurat’s FindMaker feature with FDR<0.05 and 1.5 foldchange cutoff.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peritoneal Cells

extract_protocol:
Peritoneal fluid was gently inverted to create an even suspension, passed through a 70μm cell strainer (Fisherbrand™, FisherScientific, Hampton, NH, USA) into 50 mL tubes (Corning Inc, Corning, NY, USA) and entrifuged for 5 min at 300 x g to obtain cell pellets. Visible erythrocytes in the pellets were removed using BD Pham Lyse™ Lysing Buffer. Single cells were maintained in RPMI medium 1640 (Corning Inc, Corning, NY, USA) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic solution. Cell count was determined using Dual-Chamber Cellometer. Single-cell whole transcriptome profiling of the cells collected from the ascites fluid or peritoneal washings was carried out using the Chromium Single Cell Gene Expression Solution system by 10x Genomics (Pleasanton, CA, US)
Library was performed according to the manufacter’s instructions (single cell 3’ v1 protocol, 10x Genomics). Briefly, Peritoneal Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Peritoneal Cells

tag: sample type

value: Malignant Ascites Fluid


title: SCNn+s, S430

value: silent


title: 12763575

value: blood

value: F

value: COPD


title: Renca VHL WT.1 TAM2 F480lhi M1

value: Tumor TAM2

value: VHL WT.1


title: 12768222

value: M


title: 12763607


title: Patient 27, scRNAseq

description: 10x Genomics


title: Patient 28, scRNAseq

description: 10x Genomics


title: 12784200


title: Patient 26, scRNAseq

description: 10x Genomics


title: SCNn-s, S428

value: interneurons of the suprachiasmatic nucleus

value: night

value: cFOS-


title: Patient 25, scRNAseq

description: 10x Genomics


title: Renca VHL WT.1 TAM1 F480lo M1

value: Tumor

value: Renca

value: Tumor TAM1


title: Renca VHL WT.1 PMN MDSC LY6G M1

value: Tumor PMN MDSC


title: 12768323


title: 12763568


title: Patient 24, scRNAseq

description: 10x Genomics


title: SCNn-s, S427


title: Patient 23, scRNAseq

description: 10x Genomics


title: SCNn+a, S425

value: active

value: cFOS+


title: Renca VHL WT.1 M MDSC LY6C M1

value: Tumor MDSC


title: 12763537


title: 12763241


title: SCNn-s, S426

value: silent


title: Renca VHL WT.1 whole tumor M7

value: Whole tumor


title: 12298329

value: blood

value: F


title: Renca VHL KO.1 whole tumor M8

value: VHL KO.1


title: Patient 21, scRNAseq

description: 10x Genomics

value: Peritoneal Cells

value: Peritoneal Washings


title: SCNn-a, S424

value: interneurons of the suprachiasmatic nucleus


title: Patient 22, scRNAseq

description: 10x Genomics

value: Malignant Ascites Fluid


title: 12298312

value: COPD


title: Renca VHL KO.1 whole tumor M6

value: Tumor


title: SCNn+a, S422

value: night


title: Renca VHL WT.1 whole tumor M5

value: Renca

value: VHL WT.1


title: 12032480


title: 12298297


title: Renca VHL KO.1 whole tumor M4


title: SCNd+a, S421

value: day

value: active


title: Patient 18, scRNAseq

description: 10x Genomics


title: SCNd+a, S415

value: cFOS+


title: SCNn-a, S423

value: cFOS-


title: Renca VHL WT.1 whole tumor M1

value: Whole tumor


title: 12032714

value: blood

value: M


title: 12031975

value: F


title: Renca cells VHL KO.7 CD45 pos primary tumor

value: Immune cells

value: VHL KO.7


title: 12031944


title: SCNd+a, S419

value: interneurons of the suprachiasmatic nucleus


title: Renca VHL WT.1 whole tumor M3


title: SCNd-d, S412

value: depolarized


title: Patient 17, scRNAseq

description: 10x Genomics

value: Peritoneal Cells

value: Malignant Ascites Fluid


title: 12763227

value: COPD


title: SCNd+a, S417


title: Renca VHL KO.1 whole tumor M2

value: Tumor

value: Renca

value: VHL KO.1


title: 12031982


title: SCNd+a, S413

value: day

value: active


title: Patient 11, scRNAseq

description: 10x Genomics

value: Peritoneal Washings


title: 12001967


title: Renca cells VHL WT.2 CD45 neg primary tumor

value: Cancer cell

value: VHL WT.2


title: SCNd-s, S410

value: silent

value: cFOS-


title: Patient 20, scRNAseq

description: 10x Genomics


title: Patient 13, scRNAseq

description: 10x Genomics


title: Renca cells VHL WT.2 CD45 pos primary tumor

value: Immune cells


title: SCNd+a, S409

value: cFOS+


title: Patient 12, scRNAseq

description: 10x Genomics


title: SCNd-a, S411

value: interneurons of the suprachiasmatic nucleus


title: 11986685

value: blood

value: M


title: 11986762

value: F


title: Patient 16, scRNAseq

description: 10x Genomics

value: Peritoneal Cells


title: Patient 8, scRNAseq

description: 10x Genomics

value: Malignant Ascites Fluid


title: Patient 14, scRNAseq

description: 10x Genomics


title: 12031920

value: COPD


title: Renca cells VHL KO.1 CD45 neg primary tumor

value: Tumor

value: Renca

value: VHL KO.1


title: 11985651


title: SCNd+s, S406

value: day


title: Patient 10, scRNAseq

description: 10x Genomics


title: Renca cells VHL KO.7 CD45 neg primary tumor

value: Cancer cell

value: VHL KO.7


title: Renca cells VHL WT.1 CD45 neg primary tumor

value: VHL WT.1


title: SCNd+s, S408

value: silent


title: SCNd+a, S405

value: active


title: 11985637


title: Renca cells VHL KO.1 CD45 pos primary tumor

value: Immune cells


title: Patient 6, scRNAseq

description: 10x Genomics


title: 11996923


title: RPE/choroid complex, INK-ATTAC 8

city: St. Louis

first: Ryo

last: Terao

state: MO

address: 517 S. Euclid Ave

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.  RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA. Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data. An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler. Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: Mouse Ensembl GRCm38.76
Supplementary files format and content: all.gene_counts.tsv: Raw counts.
Supplementary files format and content: group_knockout_Differential_Expression.tsv: Differential gene expression performed comparing control and knockout

source_name: RPE/choroid complex

extract_protocol:
Samples were collected in TRIzol reagent. mRNA was obtained using NucleoSpin RNA columns (Takara, 740955) according to the manufacturer’s instructions.
cDNA amplification for mRNA-Seq was performed by SMARTer

value: RPE/choroid complex

value: Abca1/Abcg1 flox/flox LysM-Cre; INK-ATTAC


title: Patient 9, scRNAseq

description: 10x Genomics

value: Peritoneal Washings


title: 11985606

value: blood

value: M


title: SCNd-s, S404

value: interneurons of the suprachiasmatic nucleus

value: cFOS-


title: Renca cells VHL WT.1 CD45 pos primary tumor

value: Tumor


title: SCNd-a, S403


title: 11981534

value: F

value: COPD


title: SCNd+a, S402

value: day

value: cFOS+


title: Patient 3, scRNAseq

description: 10x Genomics

value: Peritoneal Cells


title: Patient 4, scRNAseq

description: 10x Genomics


title: RPE/choroid complex, INK-ATTAC 5


title: Patient 19, scRNAseq

description: 10x Genomics


title: SCNd-s, S407


title: Patient 7, scRNAseq

description: 10x Genomics


title: Patient 1, scRNAseq

description: 10x Genomics

value: Malignant Ascites Fluid


title: Patient 5, scRNAseq

description: 10x Genomics


title: 11800154


title: SCNd-d, S400

value: depolarized


title: RPE/choroid complex, INK-ATTAC 7


title: SCNd-a, S398

value: active


title: WT_OE_EdUseq_rep2

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
Assembly: Human GRCh37/hg19
Supplementary files format and content:
Library strategy: EdU-seq

value: Human cell line

value: U2OS (Tet-Off CCNE overexpression)

value: Human Bone Osteosarcoma Epithelial Cells

value: Wild Type cells


title: RPE/choroid complex, INK-ATTAC 2

value: RPE/choroid complex

value: Abca1/Abcg1 flox/flox LysM-Cre; INK-ATTAC


title: RPE/choroid complex, INK-ATTAC 6


title: Patient 2, scRNAseq

description: 10x Genomics

value: Peritoneal Washings


title: 11795632

value: blood


title: SCNd+a, S396

value: interneurons of the suprachiasmatic nucleus


title: 11981178

value: M


title: RPE/choroid complex, control 7

value: Abca1/Abcg1 flox/flox LysM-Cre


title: SCNd-d, S401

value: day

value: cFOS-


title: SCNd+d, S395

value: cFOS+


title: RPE/choroid complex, control 6


title: RPE/choroid complex, INK-ATTAC 4


title: RPE/choroid complex, INK-ATTAC 3


title: 11985529

value: COPD


title: WT_OE_EdUseq_rep1


title: 11799999


title: RPE/choroid complex, control 5


title: WT_NE_MiDASseq_rep1

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
Assembly: Human GRCh37/hg19
Supplementary files format and content:
Library strategy: MiDAS-seq


title: WT_OE_EdUseq_R90


title: WT_OE_EdUseq_R30


title: SCNd+a, S394


title: 11799519

value: F


title: SCNd-a, S390

value: active


title: RPE/choroid complex, control 2


title: WT_NE_EdUseq_R30

value: Human cell line


title: WT_NE_MiDASseq_rep2

value: U2OS (Tet-Off CCNE overexpression)


title: 11795579


title: SCNd+a, S393


title: SCNd-a, S392


title: SCNd+a, S389


title: RPE/choroid complex, control 4


title: RPE/choroid complex, control 1


title: 11795562


title: BMDM from KO 4

description: knockout 4

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.  RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA. Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data. An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler. Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: all.gene_counts.tsv: Raw counts.
Supplementary files format and content: group_knockout_Differential_Expression.tsv: Differential gene expression performed comparing control and knockout

source_name: Bone marrow derived macrophage

value: Bone marrow derived macrophage


title: 11795517


title: RPE/choroid complex, INK-ATTAC 1


title: SCNd-a, S391


title: 11761918


title: SCNd-d, S387

value: depolarized


title: WT_NE_EdUseq_R90_rep2

value: Human Bone Osteosarcoma Epithelial Cells

value: Wild Type cells


title: 11761879


title: RPE/choroid complex, control 3

value: RPE/choroid complex


title: 11795586

value: blood


title: KM2_NE_EdUseq_R90

value: Substitution of K508M that inactivates helicase activity


title: 11795485

value: M


title: KM2_NE_EdUseq_R30


title: WT_NE_EdUseq


title: 11761925


title: KM2_NE_EdUseq


title: WT_NE_EdUseq_R90_rep1


title: SCNd+a, S388

value: interneurons of the suprachiasmatic nucleus


title: BMDM from KO 3

description: knockout 3

value: Abca1/Abcg1 flox/flox LysM-Cre


title: 11795478


title: KM2_OE_EdUseq


title: BMDM from control 4

description: control 4

value: Abca1/Abcg1 flox/flox


title: SCNd+a, S386

value: day

value: cFOS+


title: BMDM from KO 2

description: knockout 2


title: SCNd-a, S385

value: cFOS-


title: 11761862

value: COPD


title: BMDM from KO 1

description: knockout 1


title: 11761800

value: F


title: BMDM from control 2

description: control 2


title: KM1_OE_EdUseq_R30

value: Human cell line

value: U2OS (Tet-Off CCNE overexpression)


title: SCNd+a, S384

value: active


title: KM1_OE_EdUseq

value: Human Bone Osteosarcoma Epithelial Cells


title: BMDM from control 1

description: control 1

value: Bone marrow derived macrophage


title: KM1_OE_EdUseq_R90


title: SCNd+a, S383


title: 11757940


title: BMDM from control 3

description: control 3


title: SCNd-d, S381

value: depolarized


title: 11761709

value: blood


title: SCNd-s, S380

value: silent


title: KM1_NE_MiDASseq

value: Substitution of K508M that inactivates helicase activity


title: SCNd-a, S375

value: interneurons of the suprachiasmatic nucleus


title: 11757856


title: 11761817

value: M


title: SCNd+a, S378


title: 11757825


title: OE-H3p3_GFP, rep1

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: plasma cell differentiation

data_processing:
After sequencing, reads were cleaned by trim_galore (version0.6.10) and mapped to mm10 with Bowtie2(version 2.3.1).
Replicate samples were merged and peaks were identified by using MACS2(ChIL: -q 0.01 --nomodel –nolambda, ATAC: -q 0.01)
Bigwig files were prepared using deeptools with following options "--binSize 100 --centerReads --normalizeUsing CPM" for ATAC-seq and "--smoothLength 1000 --binSize 100 --normalizeUsing CPM" for ChIL-seq.
Assembly: mm10
Supplementary files format and content: peak summit files(.bed), bigwig files(.bigwig)
Library strategy: ChIL-seq

source_name: B cells

extract_protocol:
For B cell isolation, splenic B cells were purified by the negative selection of CD43+ cells with anti-CD43 magnetic beads (Militenyi Biotec). The purified B cell population was>95% positive for CD19 staining. Cell sorting was performed on FACSMelody (BD Biosciences) to isolate the following populations: activated B cells (CD138lowB220hi) ; plasma cells (CD138hiB220low) and retrovirus-infected cells (GFP+) .For B cell stimulation assays, purified B cells were cultured in RPMI 1640 medium. For plasma cell differentiation, B cells were stimulated with 5 μg/ml of lipopolysaccharide (LPS).
Assay for transposase-accessible chromatin sequencing (ATAC-seq):   ATAC-seq was performed following published protocol (Corces, M. et al., Nat Methods, 2017). 50,000 cells were used for each library.
Chromatin integration labelling (ChIL):   ChIL-seq for B cells was performed described previously (https://doi.org/10.1038/protex.2018.122), except following. Cells were biotinylated for 30 min at 4°C with 1mg/ml sulfoNHS-SS-biotin in PBS and plated on streptavidin-treated 96-well plates (Thermo Fisher Scientific). After fixed with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 5min at room temperature, fixation was stopped with 1 M Glycine/HCl.

value: B cells

value: OE H3.3-GFP

tag: chil antibody

value: GFP (1A5)


title: OE-H3p3_GFP, rep2

description: plasma cell differentiation


title: fsH2_OE_EdUseq

tag: cell line

value: KO - CRISPR frameshift mutation in the helicase domain of the RECQL4 gene


title: 11761723

value: COPD


title: OE-H3p3_H3p3, rep2

description: plasma cell differentiation

tag: cell type


title: fsN2_OE_EdUseq

value: KO – CRISPR frameshift mutation in the N-terminal domain of the RECQL4 gene


title: fsH2_NE_EdUseq

value: Human cell line


title: 11757786


title: SCNd-s, S373

value: day

value: cFOS-


title: 11757849


title: OE-H3p3_H3p3, rep1

description: plasma cell differentiation

tag: genotype


title: fsN2_NE_EdUseq

value: U2OS (Tet-Off CCNE overexpression)

value: Human Bone Osteosarcoma Epithelial Cells

tag: treatment


title: SCNd-s, S361


title: SCNd+s, S372

value: cFOS+


title: OE-Ctrl_H3p3, rep2

description: plasma cell differentiation

value: OE GFP


title: 11757452

tag: tissue

value: blood


title: 11757731

tag: Sex


title: fsH1_NE_MiDASseq


title: SCNd-s, S360

value: silent


title: γH2AX ChIP-Seq ICRF 3h rls rep2

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to the mm10 mouse genome assembly using Bowtie2 with the parameters: -q -N 1 -X 1000.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bamCoverage from deepTools software with RPKM normalization.

growth_protocol: NIH3T3 MEFs were cultured in DMEM supplemented with 10% Newborn Calf Serum (NCS), 100 U/ml Pen/Strep and 2 mM L-Glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Cells were treated with negative control (DMSO) or 5μM ICRF-193 for 4h, which was subsequently removed from from culturing media for 0 or 3 hours

value: MEFs

value: ICRF 3h rls

tag: chip antibody

value: γH2AX antibody (Abcam/ab2893/5μg)


title: 11757351

value: M

tag: disease


title: γH2AX ChIP-Seq ICRF 0h rls rep2

value: ICRF 0h rls


title: OE-Ctrl_H3p3, rep1

description: plasma cell differentiation

value: B cells


title: SCNd+a, S356

value: interneurons of the suprachiasmatic nucleus

value: active


title: OE-Ctrl_GFP, rep2

description: plasma cell differentiation

value: GFP (1A5)


title: OE-Ctrl_GFP, rep1

description: plasma cell differentiation


title: γH2AX ChIP-Seq DMSO rep2

value: DMSO


title: SCNd+a, S355

value: day


title: Input ICRF 3h rls rep2


title: PC_H3p3, rep2

description: plasma cell differentiation

source_name: plasma cells

value: plasma cells

value: WT


title: 215T

value: Tumor

value: Primary

value: Whole tumor

value: ccRCC


title: PC_H3p3, rep1

description: plasma cell differentiation


title: SCNd+a, S354

value: cFOS+


title: 220T


title: SCNd+d, S352

value: depolarized


title: nonPC_H3p3, rep2

description: plasma cell differentiation


title: SCNd+a, S351


title: 248N

value: matched normal


title: Input DMSO rep2

value: MEFs


title: SCNd-a, S357

value: cFOS-


title: 248T


title: SCNd+s, S350

value: silent


title: γH2AX ChIP-Seq ICRF 0h rls rep1

value: ICRF 0h rls

value: γH2AX antibody (Abcam/ab2893/5μg)


title: Naive_H3p3, rep2

description: B cells

value: B cells


title: lacrimal gland, control, replicate 4

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

description:
CTRL_04
Instrument used to create the reads: Illumina NovaSeq X

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic (parameter LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:5)
Trimmed sequence reads were mapped to Homo sapiens genome (GRCh38-p10) using STAR
Read count extraction was done by featureCount, and differential expression analysis was further conducted with the R package DESeq2
Assembly: GRCh38-p10
Supplementary files format and content: TAB-delimited file with the read counts from featureCount.

source_name: lacrimal gland

extract_protocol:
RNA was isolated using the RNeasy Mini Kit, following the manufacturer's specifications for animal cells.
RNA libraries for control samples were prepared using NEBNext RNA Ultra II directional protocol 2x150bp Directional RNA Library Prep Kit for Illumina and polyA selection.
RNA libraries for the clone samples were prepared using Lexogen Quantseq FWD 1x75bp kit for Illumina with polyA selection. Libraries were sequenced at Core Facility Genomics (CEITEC Brno, Czech Republic)

treatment_protocol:
Control samples come from lacrimal gland biopsies of patients undergoing lacrimal gland debulking surgery for refractory epiphora.
Clone samples originated from lacrimal gland tissue after removal of orbit due to malignant disease, and they have been controled to be not pathological using histological analysis.

value: lacrimal gland

tag: donor

value: control


title: SCNd+a, S347

value: interneurons of the suprachiasmatic nucleus

tag: time of_day

value: day

value: active


title: lacrimal gland, control, replicate 3

description:
CTRL_03
Instrument used to create the reads: Illumina NovaSeq X


title: OE-H3p3-noSort, rep3

description: plasma cell differentiation

data_processing:
After sequencing, reads were cleaned by trim_galore (version0.6.10) and mapped to mm10 with Bowtie2(version 2.3.1).
Replicate samples were merged and peaks were identified by using MACS2(ChIL: -q 0.01 --nomodel –nolambda, ATAC: -q 0.01)
Bigwig files were prepared using deeptools with following options "--binSize 100 --centerReads --normalizeUsing CPM" for ATAC-seq and "--smoothLength 1000 --binSize 100 --normalizeUsing CPM" for ChIL-seq.
Assembly: mm10
Supplementary files format and content: peak summit files(.bed), bigwig files(.bigwig)

value: OE H3.3-GFP


title: Naive_H3p3, rep1

description: B cells

value: WT


title: γH2AX ChIP-Seq DMSO rep1

value: DMSO


title: lacrimal gland, control, replicate 2

description:
CTRL_02
Instrument used to create the reads: Illumina NovaSeq X


title: 11757313

data_processing:
Low qaulity of reads in the raw reads were trimmed using the Trimmomatic (v0.39)
Trimmed reads were align using HISAT2 (v2.2.1)
FeatureCounts (v2.0.3) was used for the quantification of aligned reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

value: blood

value: M

value: COPD


title: Input ICRF 0h rls rep2

value: MEFs


title: SCNd+s, S346

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to GRCm38.p4  to get gene counts (Data-sce-count.txt)
Cells that passed quality control were normalized (Data-sce-normed.txt, Lab-Sara-sce-log.txt)
Differential gene expression was analyzed using DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: Data-sce-count.txt; raw counts
Supplementary files format and content: Data-sce-normed.txt; normalized counts
Supplementary files format and content: Data-sce-log.txt; log of normalized counts

tag: electrophysiology

value: cFOS+


title: lacrimal gland, control, replicate 1

description:
CTRL_01
Instrument used to create the reads: Illumina NovaSeq X


title: OE-H3p3-noSort, rep2

description: plasma cell differentiation


title: Input ICRF 0h rls rep1


title: SCNd+a, S345

tag: cfos expression


title: Input DMSO rep1


title: OE-H3p3-noSort, rep1

description: plasma cell differentiation


title: γH2AX ChIP-Seq ICRF 3h rls rep1

value: ICRF 3h rls


title: nonPC_H3p3, rep1

description: plasma cell differentiation


title: OE-Ctrl-PC, rep3

description: plasma cell differentiation

value: plasma cells

value: OE GFP


title: lacrimal gland, clone 6, replicate 3


title: msPSOrganoids_Cdk12_BC KO-3

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
Cdk12_KO organoid
SI_28852
SI_28847-51.cts.csv

data_processing:
Transcripts were quantified by kallisto with mouse reference genome (mm10) and then summarized to obtain gene level counts and TPM.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts of each sample

source_name: prostate organoid

extract_protocol:
RNA was extracted from cell pellets  using Qiagen RNA extraction kit. RNA quality was determined using a Bioanalyzer RNA Nano Chip
Poly-A selection was performed with Sera-Mag Oligo(dT)-Coated Magnetic Particles (38152103010150; GE Healthcare Life Sciences), and libraries were generated using a KAPA RNA HyperPrep kit (KK8541; Roche Sequencing Solutions).

value: prostate organoid

value: Epithelial

value: Cdk12 mutant


title: SCNd-s, S341

value: interneurons of the suprachiasmatic nucleus

value: silent

value: cFOS-


title: SCNd-d, S349

value: day

value: depolarized


title: msPSOrganoids_Cdk12_BC KO-2

description:
Cdk12_KO organoid
SI_28851
SI_28847-51.cts.csv


title: OE-Ctrl-PC, rep2

description: plasma cell differentiation


title: lacrimal gland, clone 6, replicate 2

value: lacrimal gland


title: msPSOrganoids_Cdk12_BC KO-1

description:
Cdk12_KO organoid
SI_28850
SI_28847-51.cts.csv


title: OE-Ctrl-PC, rep1

description: plasma cell differentiation


title: lacrimal gland, clone 6, replicate 1


title: SCNd+s, S339


title: OE-Ctrl-noSort, rep3

description: plasma cell differentiation

value: B cells


title: msPSOrganoids_Cdk12_BC WT-3

description:
Cdk12_WT organoid
SI_28849
SI_28847-51.cts.csv


title: lacrimal gland, clone 3, replicate 4


title: SCNd+a, S338

value: active


title: Input ICRF 3h rls rep1


title: SCNd-s, S336


title: OE-Ctrl-noSort, rep2

description: plasma cell differentiation


title: msPSOrganoids_Cdk12_BC WT-2

description:
Cdk12_WT organoid
SI_28848
SI_28847-51.cts.csv

value: Cdk12 wildtype


title: lacrimal gland, clone 3, replicate 3


title: lacrimal gland, clone 6, replicate 4


title: SCNd-a, S335


title: SCNd-s, S344


title: msPSOrganoids_Cdk12_BC WT-1

description:
Cdk12_WT organoid
SI_28847
SI_28847-51.cts.csv


title: OE-Ctrl-noSort, rep1

description: plasma cell differentiation


title: SCNd+s, S334


title: lacrimal gland, clone 3, replicate 2


title: lacrimal gland, clone 3, replicate 1


title: SCNd+a, S333


title: OE-Ctrl-nonPC, rep2

description: plasma cell differentiation


title: OE-Ctrl-nonPC, rep3

description: plasma cell differentiation


title: ChIP against H3K27ac in E18.5 mouse female urogenital sinus replicate 1

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ChIP-seq single-reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for single-reads and  -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Truseq or Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 with bowtie2 version 2.4.5 with the default parameters. Only alignments with a mapping quality above 30 were kept (Samtools v1.16.1).
Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with with  --call-summits -B (and --nomodel --extsize 200 for single-read). Coverages were normalized to million mapped reads/pairs.
Assembly: mm39
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

source_name: urogenital sinus

extract_protocol:
Male and female UGS were isolated separately and placed into 1x PBS containing 10% FCS on ice.
ChIP-seq experiments were performed as previously described in (10.1101/gad.281055.116). Briefly, they were fixed for 10 mn in 1% formaldehyde at room temperature and the crosslinking reaction was quenched with glycine. Subsequently, nuclei were extracted and chromatin was sheared using a water-bath sonicator (Covaris E220 evolution ultra-sonicator). Immunoprecipitation was done using the following anti- H3K27ac (Abcam, ab4729) or anti-H3K27me3 (Merck Millipore, 07–449). Libraries were prepared using the TruSeq protocol, and sequenced on the Illumina HiSeq system (100 bp single-end reads) according to manufactures instructions.

value: urogenital sinus

value: female

tag: Stage

tag: antibody

value: H3K27ac (Abcam, ab4729)

value: wild type


title: OE-Ctrl-nonPC, rep1

description: plasma cell differentiation

tag: strain

value: OE GFP


title: SCNd-s, S331


title: ChIP against H3K27ac in E18.5 mouse male urogenital sinus replicate 1

value: male


title: lacrimal gland, clone 1, replicate 4


title: ChIP against H3K27me3 in E18.5 mouse male urogenital sinus replicate 1

value: H3K27me3 (Merck Millipore, 07–449)


title: SCNd+s, S329

value: cFOS+


title: lacrimal gland, clone 1, replicate 3


title: m4 Old Rep4 ATAC

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: m4 Old technical rep2, biological rep2

data_processing:
Raw reads quality were checked using FastQC v0.10.0
Raw reads were trimmed with threshold quality score > 20 using Trimgalore v0.3.0
Trimmed reads were aligned to mm9 using bowtie2
Duplicated reads were marked using Picard Tools v1.98.
Peaks were called using macs2 with parameter --nomodel
Assembly: mm9
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: liver

extract_protocol:
Nuclei were extracted from whole liver and lysed using diluted 10x (LB): 100mM Tris.Hcl pH 7.5, 100mM NaCl, 30mM MgCl2, 1% Igepal CA-630 with 2% BSA and protease inhibitor diluted in PBS.
Tagmentation reaction was for 30 minutes at 37C then DNA was isolated and 6-PCR cycles (72C 3m, 95C 30s, (95C for 10s, 63C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C) with i5xx and i7xx primers followed by a gel size selection of 220-1000bp.

treatment_protocol: Mice were aged for 6 and 23 months under IACUC supervision and provided normal CHOW (Teklad global 18% protein)

value: liver

tag: age (months)

value: Aging


title: PC, rep3

description: plasma cell differentiation

value: plasma cells

value: WT


title: PC, rep2

description: plasma cell differentiation


title: m4 Old Rep3 ATAC

description: m4 Old technical rep1, biological rep2


title: lacrimal gland, clone 1, replicate 1


title: lacrimal gland, clone 1, replicate 2


title: SCNd-s, S328

value: interneurons of the suprachiasmatic nucleus

value: day

value: silent

value: cFOS-


title: SCNd+a, S327

value: active


title: m3 Old Rep2 ATAC

description: m3 Old technical rep2, biological rep1


title: PC, rep1

description: plasma cell differentiation


title: m3 Old Rep1 ATAC

description: m3 Old technical rep1, biological rep1


title: SCNd-d, S324

value: depolarized


title: RFX4-G1 D15 RNA Replicate 4

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b).
Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file containing raw counts for each sample

source_name: ventral telencephic MGE-like neuronal precursors

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Vitronectin coated cultureware.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (Takara Bio)
RNA-seq library preparation was performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) per the manufacturer’s instructions.

tag: stem cell_source

value: H9 hESC

tag: passage

tag: timepoint

tag: grna


title: Naive, rep2

description: B cells

tag: cell type

value: B cells

tag: genotype


title: SCNn+a, S319

source_name: interneurons of the suprachiasmatic nucleus

value: night


title: RFX4-G1 D15 RNA Replicate 3

value: ventral telencephic MGE-like neuronal precursors


title: RFX4-G1 D15 RNA Replicate 2


title: RFX4-G1 D15 RNA Replicate 1


title: Naive, rep1

description: B cells


title: m2 Young Rep3 ATAC

description: m2 Young technical rep1, biological rep2

tag: tissue

tag: Sex

value: male

tag: treatment


title: SCNn-a, S318


title: m1 Young Rep2 ATAC

description: m1 Young technical rep2, biological rep1


title: SCNn+s, S315


title: Glullflox/flox,  liver injury 2

city: Shanghai

first: Menglin

last: Shi

address: Dongan Road 130

country: China

institute: Fudan university

data_processing:
Base calling was performed with RTAv2.7.6, and the fastq files were generated by bcl2fastqv 2.15.0 (Illumina,Inc.).
Alignment of the trimmed RNA-seq reads to the ensemble mouse genome assembly (GRCm39 (GCA_000001635.9)
The counts of the reads mapped to individual genes were calculated by feature Countsv 2.0.3.
DEGs were identified by the DESeq2 (version3.15; https://bioconductor.org/packages/DESeq2/), a cut-off of padj<0.05 and |log2(foldchange)|>1 was applied.
Assembly: GRCm39
Supplementary files format and content: Excel file includes FPKM values for all samples

extract_protocol:
RNA was extracted from liver tissues by TRIzol (TaKaRa, 9109).
The libraries were prepared by the NEBNext Ultra RNA Library Prep Kit and performed on Illumina NovaSeq 6000 platform in Mingma Technologies Co., Ltd (Shanghai, China).

treatment_protocol: Acute liver injury was induced by intraperitoneal injection of 1 mg/kg LPS  and 200 mg/kg D-GalN

value: Glulflox/flox

value: Acute liver injury induction by  LPS/D-GalN  injection


title: Glullflox/flox,  liver injury 1

value: liver


title: RFX3-G1 D15 RNA Replicate4


title: RFX3-G1 D15 RNA Replicate3


title: m1 Young Rep1 ATAC

description: m1 Young technical rep1, biological rep1

value: Aging


title: SCNn+a, S314

first: Csaba

last: Földy

extract_protocol:
single cell extraction via patch pipette
Nextera XT DNA Library Preparation kit

value: cFOS+


title: Glulflox/flox , control 2

value: Peritoneal injection of H2O


title: Glulflox/flox , control 1


title: RFX3-G1 D15 RNA Replicate2


title: SCNn+a, S313

value: interneurons of the suprachiasmatic nucleus


title: wildtype brain arteries (12 months) rep7

city: Paris

first: Anne

last: JOUTEL

address: 102 rue de la Sante

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20) and reads shorter than 40 bases were discarded for further analysis. Reads mapping to rRNA were also discarded (this mapping was performed using bowtie version 2.2.8).
Reads were then mapped onto the mm39 assembly of mouse genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 106.
Assembly: mm39
Supplementary files format and content: tab-delimitated text file includes raw count for each sample

source_name: brain arteries

extract_protocol:
Brain arteries were homogenized on ice in lysis buffer using a polytron homogenizer, and total RNA was extracted following the manufacturer’s protocol (RNeasy MicroKit, Quiagen).
libraries were generated from 150 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94°C for 8 minutes. DNA libraries were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France). The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

value: brain arteries

tag: age

value: 12 months

value: non-Tg


title: Naive, rep3

description: B cells

value: WT


title: wildtype brain arteries (12 months) rep8


title: GlulΔlyz2, liver injury 2


title: SCNn-s, S312

city: Zurich

address: Winterthurerstrasse 190

tag: time of_day

value: silent

value: cFOS-


title: KRAB D15 RNA Replicate4

value: H9 hESC


title: wildtype brain arteries (12 months) rep5


title: GlulΔlyz2, liver injury 1


title: wildtype brain arteries (12 months) rep6


title: m2 Young Rep4 ATAC

description: m2 Young technical rep2, biological rep2


title: SCNn-a, S311

value: night

tag: electrophysiology

value: active


title: SCNn+a, S317

tag: cfos expression


title: SCNn+s, S310


title: wildtype brain arteries (12 months) rep4


title: GlulΔlyz2, control 2


title: KRAB D15 RNA Replicate2

value: ventral telencephic MGE-like neuronal precursors


title: SCNn-a, S309


title: KRAB D15 RNA Replicate1


title: wildtype brain arteries (12 months) rep3


title: GlulΔlyz2, control 1


title: wildtype brain arteries (12 months) rep2


title: SCNn-a, S307


title: SCNn-s, S306


title: RFX3-G1 D15 RNA Replicate1


title: wildtype brain arteries (12 months) rep1


title: SCNn-a, S302


title: WT D60 IgG Replicate 3

data_processing:
Raw reads were processed using AIAP (v1.1) for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file
Supplementary files format and content: narrowPeak or broadPeak file containing output from MACS2 peakcalling
Library strategy: CUT&Tag

source_name: matured cortical interneurons

extract_protocol:
Genomic DNA was processed using CUT&Tag (Epicypher) and isolated using phenol-chloroform follow by the NucleoSpin® Gel and PCR Clean-Up kit (Macherey-Nagel).
After PCR amplification samples with unique dual-end indexes were pooled in equimolar concentrations.

value: matured cortical interneurons

value: IgG


title: WT D60 IgG Replicate 2


title: CADASIL brain arteries (12 months) rep8


title: WT D60 IgG Replicate 1


title: SCNn-s, S298


title: KRAB D15 RNA Replicate3


title: CADASIL brain arteries (12 months) rep7


title: CADASIL brain arteries (12 months) rep6


title: SCNn+a, S295


title: SCNn-s, S293


title: WT D60 H3K9me3 Replicate 3


title: CADASIL brain arteries (12 months) rep5


title: WT D60 H3K9me3 Replicate 1


title: Exercise_ATMs_Biological_rep_3

type: RNA

city: Guangzhou

first: Wenbai

last: Huang

state: Guangdong

address: 601 Huangpu Ave. Tianhe Dist.

department: School of Physical Education

institute: Jinan University

description: adipose tissue macrophages of mice with 8-week moderate aerobic exercise

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix  GeneChip miRNA 4.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After staining, the microarray chip was scanned using a GeneChip Scanner 3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: 15-week male mouse post 8-week exercise

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

growth_protocol: 6-week- old male C57BL/6 mice were housed individually in ventilated caging system under a 12:12-hour light-dark cycle at 23±2℃ and 45%–55% humidity.

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

treatment_protocol: Forty male C57BL/6 mice were randomly assigned to either a sedentary (S) or an exercise (E) group. The S group remained inactive, while the E group underwent a one-week treadmill adaptation, followed by an 8-week aerobic treadmill exercise protocol (60 min/ day, 5 days/ week, at 65%-75% VO2max). ATMs harvested from visceral adipose tissues.

tag: gender

value: male

value: adipose tissue


title: Exercise_ATMs_Biological_rep_1


title: CADASIL brain arteries (12 months) rep4