title: M-C57-DHT5, Male

city: Shijiazhuang

first: Dan

last: Qiao

state: Hbbei Province

address: 361 Zhongshan East Road, Chang 'an District, Shijiazhuang City, Hebei Province

institute: Hebei Medical University

data_processing:
The sequencing data generated by Illumina NovaSeq6000 is rawsequencing data, and the rawsequencing data is controlled by FastQC for sequencing quality.
After quality control, the reference genome was compared with Hisat2 software.
The StringTie software uses official database annotation information to estimate transcript abundance
The Ballgown package of R software was used to calculate Fragments Per Kilobase of gene model Per Million mapped fragments (FPKM) at the gene level, as well as to calculate differences in expression at the gene level to screen differentially expressed genes (DEGs) between samples or between groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: The animals were  housed under constant temperature (21–22°C) on a 12 h/12 h light-dark cycle (light, 7:00–19:00) with food and water available ad libitum.

extract_protocol:
Total RNA was extracted from hippocampal tissues using TRIzol reagent.   1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hippocampus

value: WT+DHT


title: M-C57-DHT3, Male

status: Public on Nov 04 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: RNA-TALL1-BRM014-6h_biol_rep_1

city: Kyoto

first: Kosuke

last: Yusa

state: Kyoto

address: 53 Shogoin Kawaharacho, Sakyo-ku

department: Institue for Life and Medical Sciences

country: Japan

institute: Kyoto University

description:
Aoki_RNA_Sample 37
CEM_KK1_TALL1_TPM.txt

data_processing:
Sequencing reads were mapped to reference human genome hg38 using HISAT2 (v2.2.1)
The reads assigned to genes were counted using featureCounts (v2.0.3)
Differentially expressed genes were analysed using DESeq2 (v1.38.2) with filtering out genes with low expression (average read counts in all conditions are less than 10)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
For Jurkat cells, RNA was extracted using Maxwell® simplyRNA Tissue Kit and Maxwell® RSC Instrument (Promega). For CCRF-CEM, KOPT-K1 and TALL-1 cells, RNA was extracted using RNeasy Mini Kit (QIAGEN)
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England BioLabs) for Jurkat cells, or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) for other T-ALL cells.

tag: cell line

tag: cell type

value: T-ALL

tag: treatment

value: 1 uM BRM014

tag: time

value: 6 hours


title: M-C57-Con5, Male

value: WT


title: M-C57-DHT4, Male


title: M-C57-DHT1, Male


title: RNA-TALL1-DMSO-6h_biol_rep_3

description:
Aoki_RNA_Sample 36
CEM_KK1_TALL1_TPM.txt


title: M-C57-Con3, Male


title: ATAC-Jurkat-DMSO_6h_biol_rep_3

description:
Aoki_ATAC_Sample 8
Jurkat_DMSO_6h.proper_pairs.rmdup_merged.BPM.bw

library_source: genomic

data_processing:
Sequencing reads were processed using fastp (v0.23.2) for adaptor trimming and quality filtering.
The reads were mapped to reference human genome hg38 using Bowtie2 (v2.5.0) (with the parameter --no-mixed --no-discordant --very-sensitive -X 2000).
Output files were converted to sorted bam files, and proper-paired reads were extracted using SAMtools (v1.16.1). Reads mapped to mitochondria genome or PCR duplicates were removed using SAMtools or Picard (v2.27.5) MarkDuplicates, respectively.
Bam files from replicates were merged, and coverage tracks were generated using deepTools (v3.5.1) bamCoverage for visualizing.
Peaks were called using MACS2 (v2.2.7.1) (with the parameter -f BAMPE  --keep-dup all)11, and all peaks from knockout experimental conditions were merged using BEDtools (v2.30.0)
Assembly: hg38

molecule: genomic DNA

source_name: Jurakt

extract_protocol:
Freshly isolated 50,000 cells were subjected to transposition reactions at 37°C for 30 min. Transposed DNA was purified using QIAGEN MinElute Reaction Cleanup Kit.
Transposed fragments were PCR-amplified.

value: Jurakt


title: ATAC-Jurkat-gAAVS1_biol_rep_3

description:
Aoki_ATAC_Sample 13
Jurkat_gAAVS1.proper_pairs.rmdup_merged.BPM.bw

value: gAAVS1 transduction

value: 10 days


title: ATAC-Jurkat-DMSO_6h_biol_rep_2

description:
Aoki_ATAC_Sample 7
Jurkat_DMSO_6h.proper_pairs.rmdup_merged.BPM.bw


title: RNA-TALL1-DMSO-6h_biol_rep_2

description:
Aoki_RNA_Sample 35
CEM_KK1_TALL1_TPM.txt


title: MIX300

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

library_source: transcriptomic single cell

data_processing:
For each sequencing library, the poly-A tail was trimmed from each raw sequencing read using Cutadapt. Subsequently, real cells were identified based on the number of reads per cell, utilizing a manually defined minimal read cutoff determined by the results of the UMI-tools whitelist function. Reads were then aligned to the GRCh38 reference genome using the STAR 2-pass mode, and only uniquely mapped reads were retained. Each read was assigned to its corresponding gene using the 'gene' tag within the GRCh38 GTF by employing featureCount. The digital gene expression matrix (DGE) was generated using the UMI-tools count function. Batches were defined as each sequencing library for each patient. For each batch, quality control (QC) was performed using Scanpy. Low-quality cells or potential doublets were removed by applying a manually defined cutoff for the number of UFIs and genes per cell, and genes expressed in less than 0.25% of the cells were also removed
Assembly: GRCm38/mm10 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: 2 cell lines

growth_protocol: 293T and 3T3 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell line was washed using PBS. Cell pellet (cell line or tissue powder) was lysed in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% Murine RNase inhibitor (Vazyme Biotech), 0.1% IGEPAL CA-630, 1 mM DTT) and incubated on ice for 2 minutes (tissue), 5 minutes (cell line). Then, 5 ml ice-cold RSBT buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added to quench the lysis reaction. The medium was then filtered using a 40μm strainer. The nuclei were centrifuged at 500 g for 5 min at 4 ℃ and washed with 1 ml cold RSBT buffer.
Library preparations were performed with the HH-seq protocol
snRNA-seq

tag: cell loading concentration in microfluidic


title: M-C57-Con2, Male


title: ATAC-Jurkat-DMSO_6h_biol_rep_1

description:
Aoki_ATAC_Sample 6
Jurkat_DMSO_6h.proper_pairs.rmdup_merged.BPM.bw


title: M-C57-Con1, Male


title: ATAC-Jurkat-BRM014_8d_biol_rep_3

description:
Aoki_ATAC_Sample 5
Jurkat_BRM014_8d.proper_pairs.rmdup_merged.BPM.bw

value: 8 days


title: RNA-KK1-BRM014-6h_biol_rep_3

description:
Aoki_RNA_Sample 33
CEM_KK1_TALL1_TPM.txt


title: Double-stressed LUHMES, biological rep 3

type: RNA

city: Sheffield

first: Irina

last: Vazquez Villasenor

address: 385a Glossop Road

department: Neuroscience

country: United Kingdom

institute: Sheffield Institute for Translational Neuroscience, The University of Sheffield

description:
DSL_3
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector

hyb_protocol: Hybridisation was performed using the 3’ IVT Pico Reagent kit from Affymetrix and following the supplier’s protocol. Briefly, GeneChip® Human Genome U133 Plus 2.0 Arrays were pre-hybridised with Pre-Hybridisation Mix. After removing the pre-hybridization mix, array cartridges were incubated with Hybridization cocktail (Hybridization Master Mix and fragmented and labeled ds-cDNA), Hybridization controls (bioB, bioC, bioD and cre) and control Oligo B2, for 16 hours, at 45°C and 60 rpm. Arrays were then washed with Wash Buffer A and placed in the Affymetrix GeneChip Command Console Fluidics Control (ThermoFisher Scientific) for staining. Arrays were stained using the Fluidics Protocol FS450_0001. After hybridisation, the hybridisation cocktail was removed and a series of washes was performed according to the Fluidics Protocol (FS450_0002).

scan_protocol: Scanning was performed on the Affymetrix® GeneChip® Command Console.

data_processing:
Data was analysed in the Affymetrix Expression Console 1.4.1.46 and normalised using the Robust Multi-Array Average (RMA). The Qlucore Omics Explorer software  was used for analysis of the normalised data. Two-group comparisons, setting p≤0.05 and a fold change (FC) ≥1.2, were performed (SSLs vs control; DSLs vs control; SSLs and DSLs).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: Post-mitotic LUHMES, exposed to two stresses of 50 μM H2O2. LUHMES were exposed to second stress 6 hours after the first.

label_protocol: ds-cDNA (6.6μg) was fragmented and labeled by mixing with Fragmentation and Labeling Master Mix (3’ IVT Pico Reagent kit) and following the incubation protocol suggested by the supplier (1hr at 37°C, 2 min at 93°C, and at least 2 min at 4°C). In this protocol, the fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Proliferating LUHMES were cultured in Advanced DMEM/F12 medium (Gibco), 1x N2-supplement (ThermoFisher Scientific), 40 ng/ml recombinant basic fibroblast growth factor (bFGF) (Peprotech EC Ltd) and 1% Penicillin/Streptomycin (Pen/Strep) (Lonza).  When cells reached 50-60% confluency, proliferating media was replaced by differentiation media, which consisted of Advanced DMEM/F12, 1x N2-supplement, 1 μg/ml tetracycline hydrochloride (tet) (Sigma-Aldrich) and 2 ng/ml recombinant human GDNF (Peprotech EC Ltd). After 2 days of culture, pre-differentiated LUHMES were trypsinised and replated on to 12-well coated plates at 4.5x105 cells/well for a further 3 days at which point they were considered fully differentiated.

extract_protocol: Control LUHMES, SSLs and DSLs  were harvested 96 hours after the second dose of H2O2 (day 10 after switching to differentiation medium) in TRIzol Reagent (ThermoFisher Scientific) and RNA was purified using the Direct-zol RNA MiniPrep extraction protocol (Zymo Research). RNA concentration and RNA integrity were assessed using the Agilent RNA 6000 Nano Chip (Agilent Technologies INC). RNA samples were amplified with the 3’ IVT Pico Reagent kit (Affymetrix) and the resulting double stranded-cDNA was used for microarray hybridisation.

treatment_protocol: Differentiated LUHMES (day 6 after switching to differentiation medium) were treated with either one stress of 50 μM H2O2 (single stressed LUHMES [SSL]) or two stresses of 50 μM H2O2 each (double stressed LUHMES [DSL]), with the cells being exposed to the second stress 6 hours after the first one; vehicle only (distilled H2O) was added to SSLs and control LUHMES and cells were then cultured for a further 96 hours with one media change at 48 hours.

value: Lund Human Mesencephalic cells (LUHMES)

tag: differentiation stage

value: Post-mitotic, day 10 in culture


title: RNA-KK1-BRM014-6h_biol_rep_1

description:
Aoki_RNA_Sample 31
CEM_KK1_TALL1_TPM.txt


title: ATAC-Jurkat-BRM014_6h_biol_rep_3

description:
Aoki_ATAC_Sample 3
Jurkat_BRM014_6h.proper_pairs.rmdup_merged.BPM.bw


title: Double-stressed LUHMES, biological rep 1

description:
DSL_1
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector

value: exposed to two stresses of 50 μM H2O2. LUHMES were exposed to second stress 6 hours after the first.


title: Double-stressed LUHMES, biological rep 2

description:
DSL_2
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector


title: RNA-KK1-DMSO-6h_biol_rep_3

description:
Aoki_RNA_Sample 30
CEM_KK1_TALL1_TPM.txt


title: ATAC-Jurkat-BRM014_6h_biol_rep_1

description:
Aoki_ATAC_Sample 1
Jurkat_BRM014_6h.proper_pairs.rmdup_merged.BPM.bw


title: Ifngr1Rag2dKO_12wks_rep_2

city: Suita-shi

first: Kazuyo

last: Moro

state: Osaka

address: 2-2 Yamadaoka

department: Department of Microbiology and Immunology

institute: Osaka University Graduate School of Medicine

data_processing:
NovaSeq Control Software v1.4.0 and Real Time Analysis (RTA) v3.3.3 were used for basecalling.
Basecalls were converted to fastq files by using bcl2fastq2 v2.20 software.
Cell Ranger v3.1.0 was used to map sequenced reads to mm10 whole genome.
Genome_build: mm10
Supplementary_files_format_and_content: The matrix table of the number of UMIs associated with a feature (row) and a barcode (column).
Supplementary_files_format_and_content: TSV files with feature and barcode sequences corresponding to row and column indices respectively.

source_name: Lungs

extract_protocol:
Lungs were isolated and dissociated, and single-cell RNA was harvested using the Chromium Single Cell 3’ v2 Reagents kit (10x Genomics).
single-cell RNA libraries were prepared for sequencing using the Chromium Single Cell 3’ v2 Reagents kit (10x Genomics).
single-cell RNA-Seq

tag: strain

value: Lungs

tag: age

value: 12 weeks old


title: Ifngr1Rag2dKO_16wks_rep_2

value: 16 weeks old


title: Single-stressed LUHMES, biological rep 3

description:
SSL_3
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector

source_name: Post-mitotic LUHMES, exposed to one stress of 50 μM H2O2

value: exposed to one stress of 50 μM H2O2


title: RNA-KK1-DMSO-6h_biol_rep_2

description:
Aoki_RNA_Sample 29
CEM_KK1_TALL1_TPM.txt


title: RNA-TALL1-DMSO-6h_biol_rep_1

description:
Aoki_RNA_Sample 34
CEM_KK1_TALL1_TPM.txt


title: Ifngr1Rag2dKO_7wks_rep_2

value: 7 weeks old


title: Single-stressed LUHMES, biological rep 1

description:
SSL_1
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector


title: Control LUHMES, biological rep 3

description:
Control_3
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector

source_name: Post-mitotic LUHMES, control (vehicle)

value: control (vehicle)


title: RNA-KK1-DMSO-6h_biol_rep_1

description:
Aoki_RNA_Sample 28
CEM_KK1_TALL1_TPM.txt

value: T-ALL


title: B35T4C [ATAC-seq]

city: Beijing

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
ATAC-seq peak calling was performed with MACS2 v2.2.6 using the parameter “-- nomodel" and default parameters otherwise.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: bronchial epithelium

growth_protocol: The cells were cultured in serum-free LHC-8 medium (Gibco,   USA) at 37°C in an atmosphere containing 95% air and 5% CO2. The culture medium was   changed every 3 days. When cells reached 90% confluency, they were detached by using   trypsin (Sigma-Aldrich, USA) for 5 min, and the suspension  was  separated by   centrifugation to collect the cells. The cells were then subjected to subculturing.

extract_protocol:
DNA was extracted, purified and amplified with TruePrepTM Index Kit V2 for Illumina® (Vazyme)
Libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified by real-time PCR. Finally, DNA libraries were sequenced on the Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The malignant transformed cell lines BERP35T1 and BERP35T4 were derived from BEP2D cells irradiated with 1.5 Gy of α-particles emitted from a 238Pu source and were described in detail in a previous paper (Sun, J.F.  et al.  International Journal of Radiation Biology, 2002.).

value: bronchial epithelium


title: Ifngr1Rag2dKO_24wks_rep_2

value: 24 weeks old


title: Rag2KO_18wks_rep_2

value: 18 weeks old


title: RNA-KK1-BRM014-6h_biol_rep_2

description:
Aoki_RNA_Sample 32
CEM_KK1_TALL1_TPM.txt

value: 1 uM BRM014

value: 6 hours


title: RNA-CEM-BRM014-6h_biol_rep_3

description:
Aoki_RNA_Sample 27
CEM_KK1_TALL1_TPM.txt

source_name: CCRF-CEM

value: CCRF-CEM


title: ATAC-Jurkat-BRM014_8d_biol_rep_1

description:
Aoki_ATAC_Sample 4
Jurkat_BRM014_8d.proper_pairs.rmdup_merged.BPM.bw

value: Jurakt

value: 8 days


title: Ifngr1Rag2dKO_19wks_rep_2

value: 19 weeks old


title: Single-stressed LUHMES, biological rep 2

description:
SSL_2
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector

value: Lund Human Mesencephalic cells (LUHMES)

value: Post-mitotic, day 10 in culture


title: Sample4: Atm lost in tumor cells, status post focal brain irradiation

city: Durham

first: Zachary

middle: J

last: Reitman

state: NC

address: B227 LSRC, 308 Research Dr

country: USA

institute: Duke University

hyb_protocol: 5um FFPE tissue sections are placed on a 10x Genomics Xenium slide and dried at room temperature. Once dried, tissue slides are incubated at 60C for 2 hours and then deparaffinized and decrosslinked. Briefly, sections are deparaffinized via xylene immersion to solubilize the paraffin, ethanol to remove the solubilized paraffin and slowly hydrate the tissue, and then immersed in water to remove residual ethanol. Once hydrated, tissues slides are decrosslinked. Briefly, tissue slides are inserted into 10x Genomics Xenium slide cassettes. Decrosslinking buffer is then added to the well created by the cassette and incubated. After incubation, buffer is removed and the sample is washed. Tissue is then processed through Hybridization, Ligation & Amplification protocols. Briefly, pre-designed probe panels, with optional custom probe content, are added to the tissue. Each circularizable DNA probe contains two regions that hybridize to target RNA and a third region that encodes a gene-specific barcode. The two ends of the probes bind the target RNA and are ligated to generate a circular DNA probe. Following ligation, the circularized probe is amplified, producing multiple copies of the gene-specific barcode for each target. Prepared tissue slides are then loaded for imaging on the Xenium Analyzer for in situ analysis. Fluorescently-labeled oligos bind to the amplified DNA probes. Cyclical rounds of fluorescent probe hybridization, imaging, and removal generate optical patterns specific for each barcode, which are converted into a gene identity. Identified transcripts are then visualized using Xenium Explorer software.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Image pre-processing, puncta detection, transcript decoding and quality score assignment was perofrmed via on-board analysis software Xenium Analyzer.
Xenium analyzer performed read quantification and generated cell by gene count matrix.
*matrix.mtx.gz: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
*features.tsv.gz: Gene feature info
*barcodes.tsv.gz: Barcode sequences that correspond to column indices in matrix.mtx.
*transcript.csv.gz: Transcript quality and localization info
*cells.csv.gz: Cell summary and transcript count info for each identified cell
*morpholoy.ome.tif.gz: Image file in tif format
*gene_panel.json: JSON file

label: Xenium Mouse Probe Set

source_name: Primary p53/H3.3K27M diffuse midline glioma-bearing mouse brain

label_protocol: Xenium Mouse Probe Set

extract_protocol: Tumor-bearing brains subjected to Xenium ISS were detected by in vivo imaging 37-48 days after birth and collected seven days after tumor detection, either after three daily treatments of 10 Gy initiated within two days of tumor detection, or mock treatment.

value: 10 Gy x 3 focal brain irradiation


title: Sample3: Atm lost in tumor cells

value: Primary p53/H3.3K27M diffuse midline glioma-bearing mouse brain


title: Control LUHMES, biological rep 2

description:
Control_2
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector


title: B35T4B2 [ATAC-seq]


title: ATAC-Jurkat-BRM014_6h_biol_rep_2

description:
Aoki_ATAC_Sample 2
Jurkat_BRM014_6h.proper_pairs.rmdup_merged.BPM.bw


title: Control LUHMES, biological rep 1

description:
Control_1
Lund Human Mesencephalic Neuronal cell line originated from a human 8-week fetus mesencephalon and genetically modified with a v-myc retroviral vector


title: Ifngr1Rag2dKO_24wks_rep_1

value: Lungs


title: Sample2: Atm intact, status post focal brain irradiation


title: RNA-CEM-BRM014-6h_biol_rep_2

description:
Aoki_RNA_Sample 26
CEM_KK1_TALL1_TPM.txt


title: B35T4A2 [ATAC-seq]


title: RNA-CEM-BRM014-6h_biol_rep_1

description:
Aoki_RNA_Sample 25
CEM_KK1_TALL1_TPM.txt


title: RMT-XN

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

data_processing: Illumina RNA-seq raw reads were trimmed using trim galore (https://github.com/FelixKrueger/TrimGalore, command line, trim galore --phred33 --gzip --trim-n -o trim_galore_out_dir --paired RMT_1.fastq.gz RMT_2.fastq.gz). Trimmed paired reads were pooled and aligned with the reference genomes of the PEDV (RMT or dORF3-EGFP) using Python2 script ViReMa (50) (command line, python2 ViReMa.py RMT.fa trim_galore_out_dir/ RMT_ trim_.fq.gz RMT.sam --Output_Dir RMT_out/ --Output_Tag RMT -BED --p 60 --MicroInDel_Length 5 --Defuzz 0 -FuzzEntry).

organism: Porcine epidemic diarrhea virus

source_name: Gn Pigs inoculated with RMT-XN and Iowa106 co-infection

extract_protocol: RNA-seq was performed by CD Genomics (Shirley, NY, USA). The cDNA library was prepared from total RNA extracted from the small intestinal contents of the virus-infected pigs following ribosome RNA depletion. 150 bp paired-end (PE) and 100 million raw data per sample were requested.

treatment_protocol:
The PEDV mutants were generated from the five-plasmid (A, B, C, D, and E) reverse genetic system for a highly virulent PEDV strain PC22A (28). For dORF3-EGFP, the accessory gene, ORF3, was removed and a reporter gene, EGFP, was inserted into plasmid E under the control of the original TRS for ORF3, designated as pE-dORF3. As for the RMT mutant, the wildtype leader TRS-CS (5’-CUAAAC-3’) in plasmid A was recoded (5’-GUGAAC-3’) using a NEB Q5® Site-Directed Mutagenesis Kit (NEB, Ipswich, MA). And the pE-dORF3 were modified accordingly to rewire all body TRS-CS to 5’-GUGAAC-3’, except the one for EGFP gene. Then the sequencing confirmed plasmids were digested with restriction enzymes for purification of DNA fragments that were assembled to form the full-length cDNA of PEDV mutants by in vitro ligation with T4 ligase (NEB, Ipswich, MA) at 4 °C overnight in an equal molar ratio. After purification with chloroform extraction, the cDNA was used as templates for in vitro transcription to generate the PEDV mutant mRNA genome using a mMessage mMachine T7 transcription kit (Ambion, Austin, CA). Meanwhile, a polyadenylated PEDV N gene transcript was generated to be co-electroporated with the mRNA genome into Vero cells at 450 V and 50 μF using a Gene Pulser II electroporator (Bio-Rad, Hercules, CA). At 6 hours post electroporation, cells were washed with PBS and cultured in the maintenance medium in the presence of 5 μg/mL of trypsin. Cells were monitored for CPE daily and harvested when CPE was observed for about 50% cells. This rescued virus was designed as P0 virus. The P0 virus was subjected to plaque purification and one clone was propagated. After the whole genome was confirmed by sanger sequencing, it was designated as the P1 stock of the mutants.
To evaluate the pathogenesis of the recombinant viruses, experimental inoculation was performed in 5-day-old Gn pigs as described previously (12). All experiments carried out in this study were approved by the Institutional Animal Care and Use Committee (IACUC) of The Ohio State University.

tag: host animal

value: Gn Pigs

tag: viral genotype

value: RMT-XN

value: RMT-XN and Iowa106 co-infection


title: Ifngr1Rag2dKO_16wks_rep_1

value: 16 weeks old


title: Sample1: Atm intact


title: Ifngr1Rag2dKO_19wks_rep_1


title: RNA-CEM-DMSO-6h_biol_rep_3

description:
Aoki_RNA_Sample 24
CEM_KK1_TALL1_TPM.txt

value: T-ALL


title: B35T4A1 [ATAC-seq]

value: bronchial epithelium


title: dORF3

source_name: Gn Pigs inoculated with dORF3-EGFP and Iowa106 co-infection

value: dORF3-EGFP and Iowa106 co-infection


title: Ifngr1Rag2dKO_12wks_rep_1

value: 12 weeks old


title: Index_fresh_1

data_processing:
For each sequencing library, the poly-A tail was trimmed from each raw sequencing read using Cutadapt. Subsequently, real cells were identified based on the number of reads per cell, utilizing a manually defined minimal read cutoff determined by the results of the UMI-tools whitelist function. Reads were then aligned to the GRCh38 reference genome using the STAR 2-pass mode, and only uniquely mapped reads were retained. Each read was assigned to its corresponding gene using the 'gene' tag within the GRCh38 GTF by employing featureCount. The digital gene expression matrix (DGE) was generated using the UMI-tools count function. Batches were defined as each sequencing library for each patient. For each batch, quality control (QC) was performed using Scanpy. Low-quality cells or potential doublets were removed by applying a manually defined cutoff for the number of UFIs and genes per cell, and genes expressed in less than 0.25% of the cells were also removed
the 7 samples are paired-end. They have different cell barcode numbers.
Read 1 only has cell barcode1 and UFI.
Read 2 has cell barcode 2 in Index_frozen_59, Index_frozen_60, and Index_fresh_65;
Read 2 has no cell barcode 2 in No_index_frozen_57, No_index_frozen_58, No_index_fresh_61, No_index_fresh_63.
To reduce confusion, cell barcode and UFI were extracted from read1 (30bp cell barcode1, 8bp UFI)/read2(10bp or 0 bp barcode 2) and then added onto the read name of read2 using UMItools extract. For each sample, only read2 from different experimental batch were reserved.
Read Name Example:
@E100051605L1C001R00100002278_ATATGTGTGATACTTAAGGCGGCGGAAACGGAGTGGCATG_ATCTCGGT
@E100051605L1C001R00100002278: Read Name from Sequencing Platform
ATATGTGTGATACTTAAGGCGGCGGAAACGGAGTGGCATG: 40bp Cell Barcode (First 30bp: Cell Barcode from read1 & Last 10bp: cell barcode 2 from read2)
ATCTCGGT: UFI
Assembly: GRCm38/mm10 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fresh brain

growth_protocol: 293T and 3T3  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Mouse tissues were ground in liquid nitrogen using a tamping tank. Cold tissue powder was rapidly transferred into a 1.5-ml centrifuge tube. Cell line was washed using PBS. Cell pellet (cell line or tissue powder) was lysed in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% Murine RNase inhibitor (Vazyme Biotech), 0.1% IGEPAL CA-630, 1 mM DTT) and incubated on ice for 2 minutes (tissue), 5 minutes (cell line). Then, 5 ml ice-cold RSBT buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added to quench the lysis reaction. The medium was then filtered using a 40μm strainer. The nuclei were centrifuged at 500 g for 5 min at 4 ℃ and washed with 1 ml cold RSBT buffer.
Library preparations were performed with the HH-seq protocol

treatment_protocol: The 7 mouse brain samples were analyzed in four conditions of HH-seq: different reverse transcription primer (No_index, RT primer without cell barcode 2; Index, RT primer with cell barcode 2), different sample storage (frozen, nuclei isolated from frozen sample; fresh, nuclei isolated from fresh sample).

value: fresh brain

value: reverse transcription using RT primer with cell barcode 2


title: RNA-CEM-DMSO-6h_biol_rep_2

description:
Aoki_RNA_Sample 23
CEM_KK1_TALL1_TPM.txt

value: CCRF-CEM

value: 6 hours


title: B35T1B [ATAC-seq]


title: Rag2KO_18wks_rep_1

value: 18 weeks old


title: Ifngr1Rag2dKO_7wks_rep_1

value: 7 weeks old


title: B35T1C [ATAC-seq]


title: RNA-CEM-DMSO-6h_biol_rep_1

description:
Aoki_RNA_Sample 22
CEM_KK1_TALL1_TPM.txt


title: No_index_fresh_1


title: B35T1A [ATAC-seq]


title: No_index_fresh_2


title: 1hr post-wounding, biol. rep 3

city: Philadelphia

first: Janice

middle: Lynn

last: Walker

state: PA

address: 1020 Locust Street; 571 JAH

department: Pathology and Genomic Medicine

institute: Thomas Jefferson University

data_processing:
Quality control for data analysis was performed by taking Raw reads (fastq format) and processing them through through Novogene in-house perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Q20, Q30, and GC content of clean data were calculated and downstream analyses were performed on clean data with high quality.
Reads were mapped using Hisat2. Mapped reads of each sample were assembled by StringTie (v1.3.3b). featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gnee and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-valuse <=0.05 by DESeq2 software were assigned as differentially expressed.
Assembly: Assembly: Index of reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Supplementary files format and content: tab-delimited xls files include raw counts for each Sample
Supplementary files format and content: Supplementary files format and content: tab-delimited xls files include DEG set for each Sample

organism: Gallus gallus

source_name: Lens

growth_protocol: Post-cataract surgery chicken lens explants 1hr post-injury were maintained in Media 199 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% penicillin/stretomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using  using Rneasy mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared following Novogene's protocols and sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Libarary preparation was performed by Novogene. mRNA purified from total RNA using poly-T oligo-attached  magnetic beads. PCR products purfied on AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. Index-coded samples were clustered on a cBot Cluster Generation System via TruSeq PE Cluster Kit v3-cBot-Hs (Illumia). Library preparations were sequenced on an Illumina Novaseq platform to generate 150bp paired reads.

value: Lens

value: cataract sugery wounding

value: 1 hour


title: BEP2D3 [ATAC-seq]


title: 1hr post-wounding, biol. rep 2


title: B35T4B1 [ATAC-seq]


title: Fluvastatin_1, A375 Cells

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to human genome release hg38 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: hg38
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

growth_protocol: Human melanoma cell line A375 (a generous gift of Dr. John Letterio, CWRU) were maintained in standard growth media consisting of RPMI1640 + 10% FBS + 2 mM glutamine and grown in a 5%CO2 humidified atmosphere at 37˚C. For gene expression studies A375 cells were seeded at 2.5E6 per 10cm2 dish and allowed to adhere overnight.

extract_protocol:
Cells were harvested and RNA extraction using the RNeasy Plus Mini Kit (Cat. #74134, Qiagen, Germantown, MD) as per manufacturer’s instructions. Untreated control cells grown side by side were used as the reference control for differential expression analysis.  RNA was quantified using the Qubit Broad Range RNA kit (Catalog #Q10210; Thermo Fisher Scientific, Waltham, MA) and diluted to 50ng/ul for RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Test samples (in triplicate) were treated with fluvastatin (purchased from MilliporeSigma, St Louis, Mo) at 3 μM concentration for 24 hours

value: A375 Cells

value: melanoma

value: Fluvastatin


title: Index_frozen_2

source_name: frozen brain

value: frozen brain

value: reverse transcription using RT primer without cell barcode 2


title: 1hr post-wounding, biol. rep 1


title: BEP2D2 [ATAC-seq]

value: bronchial epithelium


title: BEP2D1 [ATAC-seq]


title: Index_frozen_1


title: Control_2, A375 Cells

source_name: Human melanoma cell line A375 (a generous gift of Dr. John Letterio, CWRU)

value: control


title: No_index_frozen_2


title: ZOZ hybrid juvenile, 6 birds, RA

city: Sapporo

first: Noriyuki

last: Toji

state: Hokkaido

address: North10-West8, Kita-ku,

department: Department of Biological Sciences

institute: Hokkaido university

data_processing:
what-is-cell-ranger)
bTaeGut1.4.pri, GCF_003957565.2 based custom reference genome
Supplementary files format and content: Tab-separated values files

organism: Taeniopygia guttata x Taeniopygia bichenovii

source_name: brain

extract_protocol:
Frozen brain sections were cut at 300 µm-thickness in the sagittal plane with a cryostat microtome (Leica Biosystems). Area X and RA tissues were punched out with Miltex Biopsy Punch (0.5–1.0 mm diameter; Ted-pella Inc.) and stored at –80 ℃ until nuclei isolation. Punched tissues from animals were mixed by brain regions and homogenized in 750 µl of ice-cold Nuclei PURE Lysis Buffer using a glass Dounce tissue grinder (Wheaton) (AreaX; 40–70 times with tight pestle) or pipetting with micropipettes (RA; 10 times with 1000 uL-tip, 20 times with 200 uL-tip and 40 times with 10 uL-tip), centrifuged at 500 x g for 10 minutes at 4 ℃, washed with 1 mL of Nuclei Wash and Resuspension Buffers. After centrifugation, the supernatant was removed, while the nuclei were suspended in 120 µL of Nuclei Wash and Resuspension Buffers with DAPI and filtered with 40 µm cell strainers. Isolated cell nuclei were purified with a cell sorter (SH800, Sony) using DAPI fluorescence.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, nuclei 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.
snRNA-seq

value: brain


title: Control_1, A375 Cells


title: Fluvastatin_2, A375 Cells


title: ZOZ hybrid juvenile, 6 birds, Area X

extract_protocol:
Frozen brain sections were cut at 300 µm-thickness in the sagittal plane with a cryostat microtome (Leica Biosystems). Area X tissues were punched out with Miltex Biopsy Punch (0.5–1.0 mm diameter; Ted-pella Inc.) and stored at –80 ℃ until nuclei isolation. Punched tissues from animals were mixed by brain regions and homogenized in 750 µl of ice-cold Nuclei PURE Lysis Buffer using a glass Dounce tissue grinder (Wheaton) (AreaX; 40–70 times with tight pestle) or pipetting with micropipettes (RA; 10 times with 1000 uL-tip, 20 times with 200 uL-tip and 40 times with 10 uL-tip), centrifuged at 500 x g for 10 minutes at 4 ℃, washed with 1 mL of Nuclei Wash and Resuspension Buffers. After centrifugation, the supernatant was removed, while the nuclei were suspended in 120 µL of Nuclei Wash and Resuspension Buffers with DAPI and filtered with 40 µm cell strainers. Isolated cell nuclei were purified with a cell sorter (SH800, Sony) using DAPI fluorescence.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, nuclei 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.
snRNA-seq


title: No_index_frozen_1


title: Control_0, A375 Cells


title: Time 0 post-wounding, biol. rep 2

value: time 0


title: Time 0 post-wounding, biol. rep 1


title: Fluvastatin_0, A375 Cells


title: Time 0 post-wounding, biol. rep 3


title: Tumor sample 4, bulkRNA-seq

status: Public on Nov 03 2023

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado

description:
910
910

data_processing:
data were mapped to the human genome (hg19) by gSNAP
expression (FPKM) was derived by Cufflinks
differential expression was analyzed with ANOVA in R
Assembly: hg19

source_name: high grade glioma - pediatric

extract_protocol: Libraries were prepared by using the TruSeq Library Preparation Kit v2 (Agilent).

value: high grade glioma - pediatric


title: HUVECs, siATGL (3), Day2

first: Yifan

last: Yang

address: 3400 Spruce Str

institute: University of Pennsylvania

data_processing:
fastqc to check the quality of the paired-end reads
STAR aligner to align the reads to Homo sapiens GRCh37 reference genome
pcard package to mark the duplicate
Rsubread package to count the number of raw reads
Assembly: GRCh37
Supplementary files format and content: Limma-Voom package to normalize the data and test the differential expression

source_name: HUVEC

growth_protocol: HUVECs were maintained in EGM2 media (lonza) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). Ribosomal RNAs were depleted by polyA selection prior to library prep.
RNA libraries for RNA-seq were prepared by Genewiz.

treatment_protocol: siRNA transfection at 10nM was made by using RNAiMAX reagent 2-day post full confluency

value: HUVEC

value: endothelial cell

value: siATGL

value: siRNA transfection

value: Day 2


title: Tumor sample 3, bulkRNA-seq

description:
905_3
905_3


title: HUVECs, siCTL (3), Day2

value: siCTL


title: HUVECs, siCTL (2), Day2


title: HUVECs, siATGL (1), Day2


title: HUVECs, siATGL (2), Day2


title: HUVECs, siCTL (1), Day2


title: Tumor sample 2, bulkRNA-seq

description:
868
868


title: Retinal organoid, D200 rep3

city: Bethesda

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
llumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.39.
Transcript-level counts were performed by kallisto v0.45.0 package and summarized to gene level using tximport.
Gene level counts were converted to count per million (CPM) and then TMM normalized using edgeR
Assembly: GRCh38.p7 and Ensembl v102
Supplementary files format and content: TSV file with CPM for each gene and sample.

source_name: Retinal organoid

growth_protocol: On day 0 (termed as D0) of differentiation, 90% confluent human ESCs in one well of 6-well plate were detached by 5 mM EDTA. Cells were dissociated into small clumps by pipetting gently and were then resuspended in 9 ml mTeSR™1 medium containing 10 mM ROCK inhibitor (Y027632, TOCRIS) in a 90-mm ultra-low-attachment dish (S-bio, PrimeSurface® Dish90, Cat#MS-90900Z). From D1 to D3, culture medium was gradually transitioned to neural induction medium (NIM) containing DMEM/F12 (1:1) and supplemented with 1% N2 supplement (ThermoFisher Scientific), 0.1 mM nonessential amino acids (NEAA, ThermoFisher Scientific) and 2 μg/ml heparin. On D7, Cell aggregates were then seeded onto three wells of growth-factor-reduced (GFR) Matrigel-coated 6-well plate for adherent culture. On D16, the culture medium was switched to DMEM/F12 (3:1 NIM) and supplemented with 2% B27 (without vitamin A, ThermoFisher Scientific), 0.1 mM NEAA and 1% antibiotic–antimycotic (ThermoFisher Scientific) and changed daily.   From D28 to D42, horseshoe-shaped neural retinal domains were manually detached with glass needle with curved tip under inverted microscope, transferred to each well of ultra-low attachment round bottom 96-well microplate (S-bio, PrimeSurface® Dish90, Cat#MS-9096UZ) and cultured in suspension with 3:1 NIM plus 20 ng/ml IGF-1 (Invitrogen). At D42, 10% (v/v concentration) fetal bovine serum (FBS, R&D Systems, Atlanta) and 100 μM Taurine (Sigma) were added to the culture medium. 9-cis Retinal were added to the differentiation medium from D63 with a final concentration of 1 μM and was subsequently reduced to 0.5 μM from D92. Medium were changed every 2-3 days.

extract_protocol:
Total RNA was extract from 3-4 pulled frozen organoids per sample using the RNeasy Mini kit (Qiagen) according to manufacturer’s protocol. Concentration and quality were evaluated with the Agilent 2100 Bioanalyzer system (Agilent Tech).
RNA samples with RIN more than 7 were introduced for library generation using TruSeq Library Preparation Kit (Illumina Inc.). Paired-end sequencing was performed to 125 bases on Illumina HiSeq 2500.

value: Retinal organoid


title: Retinal organoid, D200 rep2


title: Cont. fibro._DMSO_rep3

city: Tokyo

first: Yoshihiro

last: Mezawa

institute: Juntendo University

hyb_protocol: According to manufacturer's protocol of GeneChip 3’ IVT PLUS Reagent Kit.

data_processing: Normalization was performed with MAS5 method in R.

label: biotin

source_name: Control fibroblasts

growth_protocol: Fibroblasts were cultured in DMEM high glucose (Nacalai Tesque, Kyoto, Japan #08459) supplemented with 10% fetal bovine serum (FBS) and 1% Pen Strep (100 U/mL penicillin and 100 μg/mL streptomycin) (Nacalai Tesque #26253-84).

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Takara) according to the manufacturer’s protocol.

treatment_protocol: 5×105 cells were seeded onto 6 cm dishes 24 h prior to treatment with DMSO (1:1000), TSA (1 µM) or SB431542 (10 µM) for 24 h in triplicate.

tag: disease state

value: Control

value: Control fibroblasts

value: DMSO


title: Retinal organoid, D200 rep1


title: Retinal organoid, D120 rep2


title: exp-CAF2_SB431542_rep3

scan_protocol: According to manufacturer's protocol of GeneChip 3’ IVT PLUS Reagent Kit.

source_name: experimental CAF2

value: Cancer

value: experimental CAF2


title: Retinal organoid, D120 rep3


title: exp-CAF2_TSA_rep2

label_protocol: According to manufacturer's protocol of GeneChip 3’ IVT PLUS Reagent Kit.

value: TSA


title: exp-CAF2_DMSO_rep2


title: Cont. fibro._DMSO_rep2


title: exp-CAF2_DMSO_rep3


title: Retinal organoid, D120 rep1


title: Retinal organoid, D90 rep3


title: Cont. fibro._DMSO_rep1


title: exp-CAF2_DMSO_rep1


title: exp-CAF2_TSA_rep1


title: exp-CAF2_SB431542_rep2


title: Retinal organoid, D90 rep2


title: exp-CAF2_TSA_rep3


title: Retinal organoid, D90 rep1


title: Retinal organoid, D70 rep3


title: Retinal organoid, D70 rep2


title: exp-CAF2_SB431542_rep1


title: Retinal organoid, D60 rep1


title: Retinal organoid, D60 rep2


title: D200 HiC

data_processing:
Hi-C analysis was performed with HiCUP (Wingett et al., 2015) using Arima-specific in silico digested hg38 genome for the retina samples and the HCT116.
Filtered bam files produced by HiCUP have been converted to .hic files using Juicer (Durand et al., 2016) and to HOMER (Heinz et al., 2013; Heinz et al., 2018) tag directories.
mcool files were made using the hicConvertFormat tool from HiCExplorer.
Compartments have been called using HOMER using 100kb sliding windows with a step of 50kb (using options superRes and res, respectively)
Loops were called with Mustache
TADs calling has been performed on the merged samples using domaincaller (Dixon et al., 2012), using raw contact maps of 10kb bins.
TAD cliques were defined as described previously (Ali et al., 2021). Briefly, significant TAD-TAD interactions were found using the NCHG (Paulsen, et al., 2014) tool with the default settings then TAD cliques were identified via the igraph R package. 100 sets of random TAD cliques were generated by shuffling the size of cliques among the TADs.
We computed the total number of loop feet coverage using 30kb genomic windows with a step of 3kb using bedtools. For each sample, we selected the windows with a minimum coverage of 5 loop feet and stitched them together allowing a gap of up to 30kb between two windows using bedtools. We then merged these regions across samples and, for each sample, computed the total number of loop feet covering each region. For each sample, we selected the regions overlapping with at least 5 loop feet as a hub for further analysis.
We computed the organoids gene networks by integrating 5kb resolution loops and genes, associated to their expression level, at each time point. Genes overlapping and genes interacting through chromatin loops were associated into communities using home-made scripts
We computed the organoids loops networks using the method described previously (Phanstiel et al., 2017) using consensus, gained and lost loops at 5kb resolution.
We calculated domain score for each consensus TAD i.e., the ratio of intra-TAD contacts to inter-TAD contacts as defined previously (Krijger, et al., 2016)
Assembly: GRCh38.p7 and Ensembl v102
Supplementary files format and content: DXXX.hic - .hic formatted contact map
Supplementary files format and content: DXXX.compartments.PC1.bedGraph - bedGraph file showing the PC1 scores calculated by DomainCaller and used to identify compartment types
Supplementary files format and content: DXXX_TADs_10kb.bed - BED file identifying TADs as called by domaincaller
Supplementary files format and content: TAD_TAD_clique_size_DXXX.bed - BED file listing TAD locations and the number of significantly interacting TADs identified
Supplementary files format and content: DXXX.mcool - mcool formatted contact map
Supplementary files format and content: Domain_scores.tsv - Domain scores for each consensus TAD
Supplementary files format and content: loops_community_coord.bedpe - Bedpe file listing loop community participants by community and type of community
Supplementary files format and content: loops_hubs_with_loop_feet_counts.txt - TSV file showing the position of hubs and detailing the number of loops present in that hub at each time point
Supplementary files format and content: DXXX_loops_mustache.bedpe - Bedpe file showing loops called by mustache at this point
Supplementary files format and content: Loop_comparison_5kb_gaps.csv -CSV summarizing presence or absence of loops across samples
Supplementary files format and content: Loop_comparison_5kb_gaps_with_counts.csv -CSV summarizing presence or absence of loops across samples with contact counts for each loop
Supplementary files format and content: DXXX_genes_communities.txt - TSV file showing the members of each gene community

extract_protocol:
Hi-C was performed on 8-10 organoids from each time point according to the manufacturer’s instruction of Arima Genomics. In brief, organoids were dissociated to single cell following an optimized protocol of papain system (Fadl, et al., 2020) and then crosslinked with 2% paraformaldehyde (PFA, FDNeuroTechnologies) for 10 min. Subsequently, the crosslinked samples were quenched by 125 mM glycine for 5 min and frozen until use at -80 ℃ until use for Hi-C experiments. Freshly dissected human retina tissue was crosslinked with 1% formaldehyde in PBS for 10 min, quenched with 125 mM glycine for 5 min and frozen until use for Hi-C experiments. Before processing for Hi-C, samples were crosslinked again in 2% formaldehyde for 10 minutes, then quenched with 125 mM glycine 5 min. For HCT116 cell line (ATCC, VA, USA), 7x106 cells were crosslinked with 2% formaldehyde for 10 min, quenched for 5 min with stop solution I, lysed, and processed for Hi-C using ARIMA-Hi-C kit.
Hi-C was performed on isolated nuclei using Arima-Hi-C kit (Arima Genomics, CA, USA) and Hyper Prep DNA-seq library prep kit (KK8502; Kapa Biosciences, MA, USA), following the manufacturers’ instructions. The libraries were sequenced on HiSeq 2500 platform (Illumina, CA, USA) at a read length of 101 to 126 base pairs and approximately 600 million read pairs per sample.


title: D90 HiC


title: D70 HiC


title: D60 HiC


title: THP1 cells, shPRMT9-2 [20451_OCI-shP9-2_S41]

city: Monrovia

first: Ling

last: Li

state: CA

address: 1218 S 5TH AVE, MONROVIA

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

description:
PolyA-RNAseq
counts_Thp1.txt

data_processing:
RNA-Seq reads were aligned to the human hg38 reference genome assembly using Tophat2 (v2.0.8) with default settings.
Gene expression levels were counted to obtain raw counts with HTSeq (v0.11.2).
The counts data were normalized using the trimmed mean of M values (TMM) method, implemented in the Bioconductor package edgeR (v.3.30.3) to obtain the normalized RPKM (Reads Per Kilobase of transcript, per Million mapped reads) value.
Genes were considered differentially-expressed if the fold-change was <1.5 or <0.67, FDR <0.05, and at least one sample showed RPKM>1.
Enrichment analysis on pathways of Hallmark, kegg and cgp (chemical genetic perturbation) was performed using Gene Set Enrichment Analysis (GSEA), implemented in GSEA v.4.0.3.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was isolated from AML cell linesusing Trizol Reagent (Life technologies) following the manufacturer’s instructions. RNA quality (the RNA integrity number [RIN]) was assessed using an Agilent Bioanalyzer, and all samples were evaluated as RIN >8.
RNA sequencing libraries were prepared using a Kapa mRNA HyperPrep kit (Roche) and sequenced on a HiSeq 2500 system (Illumina).

value: AML cells

value: PRMT9 knockdown

value: Dox induction


title: Molm13 cells, shCtrl-1 [44527_C1]

description:
PolyA-RNAseq
counts_Molm13.txt

value: WT


title: THP1 cells, shCtrl-1 [20446_OCI-shC-1_S37]

description:
PolyA-RNAseq
counts_Thp1.txt


title: Molm13 cells, shPRMT9-1 [44529_91]

description:
PolyA-RNAseq
counts_Molm13.txt


title: Molm13 cells, shCtrl-2 [44528_C2]

description:
PolyA-RNAseq
counts_Molm13.txt


title: THP1 cells, shCtrl-2 [20447_OCI-shC-2_S38]

description:
PolyA-RNAseq
counts_Thp1.txt


title: THP1 cells, shPRMT9-1 [20450_OCI-shP9-1_S40]

description:
PolyA-RNAseq
counts_Thp1.txt


title: Molm13 cells, shPRMT9-2 [44530_92]

description:
PolyA-RNAseq
counts_Molm13.txt


title: Col-0, input

city: BeiJing

first: Qin

state: BeiJing

address: Tsinghua University,Hai Dian, Beijing

institute: Tsinghua University

data_processing:
Illumina RTA software was used for basecalling.
Reads were aligned to the TAIR10 genome using bowtie2.
The ssDRIP-seq reads coverage was normalized to RPKM (Reads Per Kilobase Million)
Assembly: TAIR10
Supplementary files format and content: bs
Library strategy: ssDRIP

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Surface-sterilized seeds were sown on 1/2 MS medium and incubated at 4˚C for 2 days for stratification. The plants were grown vertically in the chamber under long-day conditions (day/night cycle of 16/8 h) at 22°C in white light and 18°C in the dark for 5days.

extract_protocol:
The roots were cut with scalpel and then ground in 1 ml ice-cold Honda buffer. The homogenate was filtrated through 40 µm nylon cell strainers and centrifuged at 2000 g/4°C for 10 min. Then the pellet was suspended in 1ml NRBT buffer and centrifuged at 1200 g/4°C for 10 min. The nuclei were then suspended in 800 μl TE buffer with 0.5% SDS and 0.1mg/ml proteinase K. Then the mixture was incubated at 37°C for 6-8 hwith shaking. Add 200 μl 5M KAc was added and placed the tube on ice for 20 min. The genomic DNA was purified by phenol/chloroform/isoamyl alcohol (25:24:1, v/v/v) and precipitated with an equal volume of isopropyl alcohol at -20°C for 2 h. The DNA was fragmented with 5 U of DdeI, MseI, MboI, and NlaIII at 37°C overnight and then purified as mentioned above. 1 µg of purified fragment DNA was incubated with 10 µg of S9.6 antibody for 8 h at 4°C . Samples were further incubated with 50 µl Protein G beads for 4 h at 4°C. The immunoprecipitated DNA was purified as mentioned above.
The library were consturcted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

treatment_protocol: 5-day-old seedlings were treated on 1/2 MS liquid medium contaning CPT drugs or DMSO (contol) for 2 hours.

value: root

value: nucleus

value: Col-0 WT


title: atm, input

value: atm mutant


title: pol2a_CPT_rep1

data_processing:
Illumina RTA software was used for basecalling.
Reads were aligned to the TAIR10 genome using bowtie2.
The ssDRIP-seq reads coverage was normalized to RPKM (Reads Per Kilobase Million)
Assembly: TAIR10
Library strategy: ssDRIP

source_name: pol2a, CPT

extract_protocol:
The  roots were cut with scalpel and then ground in 1 ml ice-cold Honda buffer. The homogenate was filtrated through 40 µm nylon cell strainers and centrifuged at 2000 g/4°C for 10 min. Then the pellet was suspended in 1ml NRBT buffer and centrifuged  at 1200 g/4°C for 10 min. The nuclei were then suspended in 800 μl TE buffer with 0.5% SDS and 0.1mg/ml proteinase K. Then the mixture was incubated at 37°C  for 6-8 hwith shaking. Add 200 μl 5M KAc was added and placed the tube on ice for 20 min. The genomic DNA was purified by phenol/chloroform/isoamyl alcohol (25:24:1, v/v/v) and precipitated with an equal volume of isopropyl alcohol at -20°C for 2 h. The DNA was fragmented with 5 U of DdeI, MseI, MboI, and NlaIII at 37°C overnight and then purified as mentioned above. 1 µg of purified fragment DNA was incubated with 10 µg of S9.6 antibody  for 8 h at 4°C . Samples were further incubated with 50 µl Protein G beads  for 4 h at 4°C. The immunoprecipitated DNA was purified as mentioned above.
The library were consturcted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: pol2a mutant

value: CPT


title: pol2a_DMSO_rep2

source_name: pol2a, DMSO


title: pol2a_CPT_rep2


title: RNaseH, Control

value: RNaseH


title: Retinal organoid, D70 rep1

value: Retinal organoid


title: Retinal organoid, D60 rep3


title: pol2a_DMSO_rep1


title: asr20_CPT_rep2

source_name: asr20, CPT

value: asr20 mutant


title: asr20_CPT_rep1


title: D120 HiC


title: asr20_DMSO_rep2

source_name: asr20, DMSO

value: DMSO


title: asr20_DMSO_rep1


title: atm_CPT_rep2

source_name: atm, CPT


title: atm_CPT_rep1


title: Col-0_CPT_rep2

source_name: Col-0, CPT


title: Col-0_CPT_rep1


title: Col-0_DMSO_rep2

source_name: Col-0, DMSO


title: Col-0_DMSO_rep1


title: RN_brain_Saline

city: Vienna

first: Daniel

last: Bormann

state: Vienna

address: Waehringer Guertel 18-20

department: Department of Thoracic Surgery

country: Austria

institute: Medical University of Vienna

description: 10x Genomics Next GEM 5'v2 generated single nucleus cDNA library

data_processing:
Raw sequencing data were demultiplexed, aligned to the rattus norvegicus reference genome mRatBN7.2  and counted using Cell Ranger (version 7.0.0; 10x Genomics).
Assembly: mRatBN7.2
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files contain filtered count gene UMI counts for each sample (=Filtered feature-barcode matrix). Files represent standard barcodes.tsv, features.tsv and matrix.mtx outputs from Cell Ranger  (version 7.0.0; 10x Genomics).

organism: Rattus norvegicus

extract_protocol:
Nuclei extraction buffer (Miltenyi) and discontinuous iodixanol gradient separation were used to generate single nuclei suspensions, in accordance with manufacturers' protocols.
Libraries were prepared using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Next GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA), as per standard manufacturers' protocols.

value: brain

value: Crl:CD(SD) (Charles River)

tag: Sex

value: Female

value: 12 weeks old

value: Saline


title: RN_brain_PIC


title: RN_brain_LPS

value: LPS


title: MG1655_Hi-C_LB_rep1

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

data_processing: HiC-Pro was used to analyze datasets. Normalization is done by ICED, and the heatmap visualization is done in R.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: E. coli MG1655 K-12 was grown in LB or M9+glycerol at 37 °C with shaking at 200 rpm to OD600.

extract_protocol:
3% formaldehyde cross-linked cells were lysed and digested at 37°C with 100 U of HpaII (NEB) for 2 hr.
The DNA ends were marked with biotin-14-dCTP (ThermoFisher) and ligated for 4 hours at 16°C. DNA was treated with proteinase K overnight at 65°C to digest proteins and remove crosslinks. DNA was then purified with phenol:chloroform:isoamyl alcohol and precipitated with isopropanol. Biotin was removed from unligated ends and DNAs were sheared by sonication and size-selected to 200-500 bp. DNA was then end-repaired, A-tailed, ligated to Y-shaped Illumina adapters, and then biotinylated junctions were pulled down with MyOne Streptavidin C1 Dnyabeads (ThermoFisher). Libraries were amplified with KAPA HiFi Master Mix (Roche), purified with Ampure XP, and sequenced with 40 bp paired-end reads on an Illumina NextSeq500.

treatment_protocol: Cells were fixed with 3% formaldehyde for 10 min at room temperature before quenching with 0.375 M final concentration glycine for 15 min. Fixed cells were pelleted, washed twice with 1X M2 salts, twice with 1X TE buffer, before resuspension in 1X TE, and storage at -80 °C.

tag: enzyme

value: HpaII

value: LB medium


title: T.2

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

data_processing:
Read alignment with STAR (v.2.7.9a)
all downstream analyses were performed in R(v4.0.3)
Sum of exonic and intronic TPM values  were calculated using the scater package (v1.18.6).
Assembly: GRCm39 and Gencode vM27
Supplementary files format and content: comma delimited text, matrix of combined exonic/introinc TPMs

source_name: sSC

growth_protocol: All animal procedures were approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and European Union animal law (license number: BMWF-66.018/0007-II/3b/2012 and BMWFW-66.018/0006-WF/V/3b/2017). Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at IST Austria. Mice were housed at 21±1°C ambient temperature and 40–55% humidity in 12 hrs dark/light cycles. All mouse lines were kept in mixed C57/Bl6, FVB and CD1 genetic background. In some experiments, wild-type CD1 mice were also used. Both male and female littermates of the desired genotypes were used randomly. Mice were used at an age range from 2 – 8 months for breeding and from E9.5 to P30 for experiments. All efforts were made to minimize the number of animals used following the 3R principles.

extract_protocol:
The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (doi: 10.7554/eLife.52951; doi: 10.1038/nprot.2017.120) and optimized for speed and coverage of sparsely labelled cells of MADM clones. For details see publication.
cDNA libraries from E12 clones were prepared using SMART-Seq Single Cell PLUS Kit (Takara).

treatment_protocol: MADM clone induction in the SC was adapted from previously described protocols (doi: 10.3791/61147; doi: 10.1016/j.neuron.2010.09.027).

value: sSC

value: Neuron


title: R.1


title: S.2


title: atm_DMSO_rep1

source_name: atm, DMSO

value: root

value: nucleus

value: atm mutant


title: O.1

source_name: dSC

value: dSC


title: N.2


title: U.1


title: S.1


title: Q.2


title: R.2


title: O.2


title: U.2


title: N.1


title: Q.1


title: atm_DMSO_rep2


title: L.2


title: M.1


title: K.2


title: L.1


title: M.2


title: J.2


title: K.1


title: I.2


title: J.1


title: MG1655_Hi-C_LB_rep2


title: T.1


title: I.1


title: H.2

source_name: PAG

value: PAG


title: H.1


title: F.2


title: D.2


title: C.2


title: B.2


title: B.1


title: C.1


title: A.1


title: A.2


title: PS48.6

extract_protocol:
The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (doi: 10.7554/eLife.52951; doi: 10.1038/nprot.2017.120) and optimized for speed and coverage of sparsely labelled cells of MADM clones. For details see publication.
cDNA libraries from E10 clones were prepared followed by Smart-seq2 protocol (doi: 10.1038/nprot.2014.006) using custom reagents (VBCF GmbH, Vienna)


title: PS48.5


title: PS46.7


title: PS46.9


title: PS48.3


title: PS46.10


title: PS48.1


title: PS45.10


title: PS48.7


title: PS48.4


title: PS46.4


title: PS46.5


title: PS46.6


title: PS48.2


title: PS46.2


title: PS45.9


title: PS45.8


title: PS46.1


title: PS46.3


title: PS45.7


title: F.1


title: PS45.6


title: PS46.8


title: PS45.4


title: PS45.5


title: D.1


title: PS45.2


title: PS47.9


title: PS45.1


title: PS47.8


title: PS47.6


title: Negative control.30


title: PS47.2


title: PS47.5


title: PS47.1


title: PS44.4


title: PS47.3


title: PS47.4


title: PS47.7


title: PS44.1


title: PS43.10


title: PS44.2


title: PS44.3


title: PS43.8


title: PS42.8


title: PS42.7


title: PS43.7


title: PS42.6


title: PS45.3


title: PS42.4


title: PS42.5


title: PS42.3


title: PS43.5


title: PS43.6


title: PS43.4


title: PS42.2


title: PS42.1


title: PS43.3


title: PS43.2


title: PS43.1


title: Negative control.29


title: PS43.9


title: PS41.10


title: PS41.8


title: PS41.6


title: PS41.3


title: PS41.2


title: PS41.1


title: PS41.7


title: PS41.5


title: PS40.1


title: PS39.2


title: PS39.4


title: PS39.1


title: Negative control.28


title: PS39.5


title: PS39.3


title: PS38.10


title: LB, attached, rep2

city: Iowa City

first: Timothy

middle: E

last: Mattes

address: 4105 Seamans Center

institute: University of Iowa

data_processing:
galaxy server
Fastq files were trimmed and filtered with fastp.
Trimmed paired-end reads were joined with Fastq interlacer and mapped to the Paraburkholderia xenovorans strain LB400 genome using HISAT2.
HISAT2-generated BAM files were used to generate transcript count tables with FeatureCount.
Differential gene expression analysis among BC-attached cells and between BC-attached cells and suspended cells was performed with DESeq2.
Assembly: Genbank accession nos. NC_007951–NC_007953
Supplementary files format and content: DESeq2 results of comparing gene expression of attached vs suspended cells
Supplementary files format and content: DESeq2 results of comparing gene expression of attached cells on various black carbon feedstocks, including SB vs GAC, LB vs GAC, and SB vs LB

organism: Paraburkholderia xenovorans

source_name: Strain LB400

growth_protocol: Paraburkholderia xenovorans LB400 was growing in 30mL K1 medium containing 0.76g/L biphenyl and 0.9g of specific black carbon (e.g., small corn kernel biochar, large corn kernel biochar, and granular activated carbon). Samples were stored at -80℃ before RNA extraction.

extract_protocol:
RNA was extracted with the RNeasy PowerSoil Total RNA kit (Qiagen), purified and concentrated with the RNA Clean & Concentrator kit (Zymo Research, Irvine, California). LB400 ribosomal RNA was depleted by custom probes. 228ng of total RNA for each sample was used for library construction.
RNA-seq libraries were prepared with the Illumina TruSeq stranded Total RNA prep kit following manufacture's protocol.

value: Strain LB400

tag: condition

value: attached

value: LB


title: LB, attached, rep1


title: SB, attached, rep2

value: SB


title: PS38.11


title: PS41.9


title: SB, attached, rep1


title: PS41.11


title: PS38.8


title: GAC, attached, rep2

value: GAC


title: PS38.7


title: PS41.4


title: GAC, attached, rep1


title: SB, suspended, rep1

value: suspended


title: PS40.2


title: SB, suspended, rep2


title: LB, suspended, rep1


title: PS38.4


title: LB, suspended, rep2


title: PS38.5


title: PS38.3


title: PS38.2


title: PS38.1


title: GAC, suspended, rep2


title: PS37.17


title: GAC, suspended, rep1


title: PS37.16


title: PS37.15


title: HCT116 cells,  Mock2, Size match input (SMI)

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
reads were trimmed and adapters were removed using Cutadapt: Quality cutoff 14, Minimum length 18, NextSeq trimming 20
reads were mapped to repetitive elements using RNA-STAR. Mapped reads were removed
reads were mapped to hg38 genome using RNA-STAR. --alignEndsType EndToEnd
PCR duplicates were removed using UMI
Peaks were called for each treatment differently, on merged bam files for each replicate using PureCLIP
reads were counted to the peaks
Read counts were normalized, and differential enrichment between the eCLIP and their inputs was calculated by the NOISeq R package
Assembly: hg38
Supplementary files format and content: bed files containing peaks called for each treatment
Supplementary files format and content: tabular files containing raw count for each file on peaks

extract_protocol:
Cells were crosslinked with 400mJ/cm^2 UV at 254nm. Cell were lysed and sonicated with Covaris E220. RNA was cleaved by 40 units of RNase I for 3 minutes at 37°C.
3' RNA adapter were ligated to the RNA. RT performed by SuperScript III using a primer for the RNA adapter. Second adapter were ligated to the 3' end of the cDNA. Library amplify by PCR using Q5 polymerase. Library were size selected by 3% low melt agarose gel

treatment_protocol: DNA damage: 20µM VP16 for 18 hours

value: Mock

tag: rip antibody


title: PS37.14

tag: tissue


title: HCT116 cells,  Mock1, Size match input (SMI)


title: HCT116 cells,  DNA_damaged2, Size match input (SMI)


title: PS38.6

tag: genotype


title: HCT116 cells,  DNA_damaged1, Size match input (SMI)

tag: cell line


title: HCT116 cells,  Mock2, RBM42 eCLIP


title: HCT116 cells,  Mock1, RBM42 eCLIP


title: PS37.11

tag: cell type


title: HCT116 cells,  DNA_damaged1, RBM42 eCLIP

tag: treatment


title: PS37.13


title: PS37.12


title: PS37.9


title: HCT116 cells,  DNA_damaged2, RBM42 eCLIP


title: SRS4 biopsy

city: Toulouse

first: Anthony

last: Lemarie

address: 2 Av. Hubert Curien

country: France

institute: INSERM

data_processing:
bcl2 files conversion to FASTQ format using bcl2fastq algorithm
align to the GRCh38 reference transcriptome using bowtie2
Expression calculation using rsem-calculate-expression
Preprocessing, normalization of counts, and QC, and downstream analysis were performed using the R
The processed (sample x gene) matrix of counts are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw counts for every gene and every sample

source_name: Glioblastoma_SRS4 biopsy

extract_protocol:
RNA was extracted using RNeasy lipid Tissue Mini Kit (Qiagen) combined with Qiazol Reagent (Qiagen)
RNA libraries were prepared with the Illumina TruSeq Stranded Total RNA (Illumina)

value: glioblastoma

tag: individual

value: Patient Sub-021

value: brain tumor tissue

tag: tumor region

value: (4) CE/CNI+


title: SRS2 biopsy

source_name: Glioblastoma_SRS2 biopsy

value: (2) FLAIR/CNI+


title: SRS1 biopsy

source_name: Glioblastoma_SRS1 biopsy

value: (3) CE/CNI-


title: PS38.9

value: Neuron


title: PS37.8

value: sSC


title: PS37.7


title: SRS3 biopsy

source_name: Glioblastoma_SRS3 biopsy

value: (1) FLAIR/CNI-


title: PS37.6


title: SRR4 biopsy

source_name: Glioblastoma_SRR4 biopsy

value: Patient Sub-020


title: PS37.5


title: PS37.4


title: SRR2 biopsy

source_name: Glioblastoma_SRR2 biopsy


title: Negative control.27


title: SRQ3 biopsy

source_name: Glioblastoma_SRQ3 biopsy

value: Patient Sub-019


title: SRQ2 biopsy

source_name: Glioblastoma_SRQ2 biopsy


title: SRN4 biopsy

source_name: Glioblastoma_SRN4 biopsy

value: Patient Sub-015


title: PS37.10


title: PS36.8


title: PS36.7

value: dSC


title: SRN2 biopsy

source_name: Glioblastoma_SRN2 biopsy


title: PS36.6


title: SRN1 biopsy

source_name: Glioblastoma_SRN1 biopsy


title: PS37.2


title: PS37.1


title: SRM3 biopsy

source_name: Glioblastoma_SRM3 biopsy

value: Patient Sub-014


title: PS34.16

source_name: sSC


title: PS37.3


title: SRN3 biopsy

source_name: Glioblastoma_SRN3 biopsy


title: SRL3 biopsy

source_name: Glioblastoma_SRL3 biopsy

value: Patient Sub-013


title: SRM2 biopsy

source_name: Glioblastoma_SRM2 biopsy


title: SRR3 biopsy

source_name: Glioblastoma_SRR3 biopsy


title: PS35.5

source_name: PAG

value: PAG


title: SRL4 biopsy

source_name: Glioblastoma_SRL4 biopsy


title: PS36.4

source_name: dSC


title: PS36.3


title: SRL1 biopsy

source_name: Glioblastoma_SRL1 biopsy


title: PS34.15


title: SRR1 biopsy

source_name: Glioblastoma_SRR1 biopsy


title: PS35.4


title: PS36.1


title: SRK2 biopsy

source_name: Glioblastoma_SRK2 biopsy

value: Patient Sub-012


title: PS36.5


title: PS36.2


title: PS34.14


title: SRK1 biopsy

source_name: Glioblastoma_SRK1 biopsy

value: glioblastoma


title: PS34.13


title: SRJ3 biopsy

source_name: Glioblastoma_SRJ3 biopsy

value: Patient Sub-010


title: PS34.12


title: SRJ2 biopsy

source_name: Glioblastoma_SRJ2 biopsy

value: brain tumor tissue


title: SRJ4 biopsy

source_name: Glioblastoma_SRJ4 biopsy

value: (4) CE/CNI+


title: PS34.10


title: PS34.11


title: SRI4 biopsy

source_name: Glioblastoma_SRI4 biopsy

value: Patient Sub-009


title: SRL2 biopsy

source_name: Glioblastoma_SRL2 biopsy


title: SRH3 biopsy

source_name: Glioblastoma_SRH3 biopsy

value: Patient Sub-008

value: (2) FLAIR/CNI+


title: SRK3 biopsy

source_name: Glioblastoma_SRK3 biopsy


title: PS35.1

value: Neuron


title: SRH2 biopsy

source_name: Glioblastoma_SRH2 biopsy

value: (3) CE/CNI-


title: SRH1 biopsy

source_name: Glioblastoma_SRH1 biopsy

value: (1) FLAIR/CNI-


title: PS34.9

source_name: sSC

value: sSC


title: PS34.8


title: SRG5 biopsy

source_name: Glioblastoma_SRG5 biopsy

value: Patient Sub-007


title: PS34.7


title: SRG2 biopsy

source_name: Glioblastoma_SRG2 biopsy


title: PS34.6


title: SRJ1 biopsy

source_name: Glioblastoma_SRJ1 biopsy


title: SRG1 biopsy

source_name: Glioblastoma_SRG1 biopsy


title: PS34.4


title: SRF4 biopsy

source_name: Glioblastoma_SRF4 biopsy

value: Patient Sub-006


title: PS34.3


title: SRF1 biopsy

source_name: Glioblastoma_SRF1 biopsy


title: SRF5 biopsy

source_name: Glioblastoma_SRF5 biopsy


title: PS35.3

source_name: PAG


title: PS34.1


title: PS34.2


title: SRC4 biopsy

source_name: Glioblastoma_SRC4 biopsy

value: Patient Sub-003


title: SRF3 biopsy

source_name: Glioblastoma_SRF3 biopsy


title: SRC2 biopsy

source_name: Glioblastoma_SRC2 biopsy


title: Negative control.26


title: SRG4 biopsy

source_name: Glioblastoma_SRG4 biopsy


title: SRC3 biopsy

source_name: Glioblastoma_SRC3 biopsy


title: PS35.2


title: PS33.27

source_name: dSC

value: dSC


title: PS33.26


title: SRC1 biopsy

source_name: Glioblastoma_SRC1 biopsy


title: SRB3 biopsy

source_name: Glioblastoma_SRB3 biopsy

value: Patient Sub-002


title: PS33.25

source_name: sSC


title: PS34.5


title: PS33.23

value: PAG


title: PS33.22


title: PS33.24


title: SRB1 biopsy

source_name: Glioblastoma_SRB1 biopsy

value: glioblastoma


title: SRA5 biopsy

source_name: Glioblastoma_SRA5 biopsy

value: Patient Sub-001


title: SRA4 biopsy

source_name: Glioblastoma_SRA4 biopsy

value: brain tumor tissue


title: PS33.20


title: PS33.19


title: SR02 biopsy

source_name: Glioblastoma_SRO2 biopsy

value: Patient Sub-017


title: SR03 biopsy

source_name: Glioblastoma_SRO3 biopsy


title: PS33.18


title: PS33.17


title: PS33.16


title: SR01 biopsy

source_name: Glioblastoma SRO1 biopsy


title: PS33.13


title: PS33.15


title: PS33.11


title: PS33.12


title: PG15_ctrl_P1

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSAT2 (v2.0.4) with default settings and --rna-strandness FR.
Aligned reads were counted using featureCounts (v1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (v3.30.3) using the GLM approach. Genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to define differentially expressed genes. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting. Gene ontology analysis was performed using Metascape.
Alternative splicing events were analyzed using rMATS (v4.0.2), and events with |IncLevelDifference| > 0.1 and FDR < 0.05 were considered as significant.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw count values from featurecount
Supplementary files format and content: excel spreadsheet files for differential expression analysis results from edgeR
Supplementary files format and content: excel spreadsheet files for normalized RPKM expression values from RNA-seq expression profiling
Supplementary files format and content: excel spreadsheet files for alternative splicing analysis from rMATS

source_name: heart ventricle

growth_protocol: Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.

extract_protocol:
Mice were euthanized and heart ventricles from control and Rbpms cKO mice were dissected. RNA was extracted using the RNeasy mini kit (QIAGEN, 74104) according to the manufacturer's protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8580) following manufacturer’s protocol.

value: heart ventricle

value: Rbpms fl/fl

value: male


title: SRB2 biopsy

source_name: Glioblastoma_SRB2 biopsy

value: (4) CE/CNI+


title: PG12_ctrl_P1


title: PG16_cKO_P1

value: Myh6-Cre, Rbpms fl/fl

value: female


title: PG14_cKO_P1


title: PG11_ctrl_P1


title: PS33.14

value: sSC

value: Neuron


title: PG13_ctrl_P1


title: PS33.10


title: PG08_cKO_8wk

description:
Rbpms.cKO.count_table.txt
Rbpms.cKO.edgeR.xlsx
Rbpms.cKO.RPKM.xlsx
P8wk_cKO_rMATs_summary.xlsx

value: 8 weeks


title: PS33.21

source_name: PAG


title: PG07_cKO_8wk


title: PS33.9


title: PG10_cKO_P1


title: PG09_cKO_P1


title: PS33.8


title: PG05_cKO_8wk


title: PG03_ctrl_8wk


title: PG06_cKO_8wk


title: PG04_ctrl_8wk


title: PS33.3


title: PS33.6


title: PS33.7


title: PS33.4


title: PS33.5


title: PG01_ctrl_8wk


title: Negative control.25


title: PS33.2


title: PS32.8


title: PS33.1


title: PS32.9


title: Cerebellum, Fmr1 KO, rep2

city: Worcester

first: Suna

last: Jung

state: MA

address: 373 Plantation street. Suit 204

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
RNAseq.DE.log2FC_Brain.tsv
CB.A3SS.MATS.JC.txt
CB.A5SS.MATS.JC.txt
CB.MXE.MATS.JC.txt
CB.RI.MATS.JC.txt
CB.SE.MATS.JC.txt

data_processing:
CASAVA (version/parameters are internal Novogene information) was used for brain tissue.
Fastqc (v0.11.8) and Trimmomatic (v0.39) was to generate sequence quality reports and trim/filter the sequences respectively.
The reads mapped to rRNA by Bowtie2 (v2.3.5) were further filtered out
The cleaned reads were aligned to the mouse reference genome (Ensembl GRCm38) using STAR (v2.6.1) , and gene expression was quantified by RSEM (v1.3.1)
Both expression normalization and differentially expressed gene (DEG) analysis was performed using DESeq2 (v1.16.1).Allternative splicing analysis was performed using rMATS software (v3.0.9)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene expression level for each Sample
Supplementary files format and content: tab-delimited text files include level of exon inclusion for each Sample

source_name: Cerebellum

growth_protocol: Mouse N2a cells were cultured in Dulbecco’s Modified Eagels Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For RNA extraction, TRIzol was added to the tissue powder and homogenized with Dounce tissue homogenizer. The RNA was treated with TurboDNase (Invitrogen, AM2238) to remove genomic DNA contamination. For peripheral tissues and N2a cells, total RNA was extracted and the integrity analyzed by a fragment analyzer.
For peripheral tissues and N2a cells, total RNA was extracted and the integrity analyzed by a fragment analyzer. Library preparation and RNA sequencing were performed by Novogene (CA, USA). For brain samples, polyadenylated mRNA was enriched using Nextflex Poly(A) Beads (NEXTflex, Bioo Scientific Corp, 512980) and cDNA libraries were prepared using a NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific Corp, NOVA-5130-03D).

treatment_protocol: siRNA targeting Fmr1 was transfected using Lipofectamine 3000.

value: Cerebellum

value: Fmr1 KO


title: Cerebellum, Fmr1 KO, rep1


title: Cerebellum, WT, rep1

value: WT


title: Cerebellum, WT, rep2


title: PS32.5


title: PS32.6


title: Hippocampus, Fmr1 KO, rep2

description:
RNAseq.DE.log2FC_Brain.tsv
HC.A3SS.MATS.JC.txt
HC.A5SS.MATS.JC.txt
HC.MXE.MATS.JC.txt
HC.RI.MATS.JC.txt
HC.SE.MATS.JC.txt

source_name: Hippocampus

value: Hippocampus


title: PS32.4

value: dSC


title: Hippocampus, Fmr1 KO, rep1


title: Hippocampus, WT, rep3


title: PS31.10

value: PAG


title: PG02_ctrl_8wk


title: Hippocampus, WT, rep2


title: PS32.2


title: PS32.3


title: Hippocampus, WT, rep1


title: PS32.1


title: PS31.9


title: PS32.7


title: PS31.8


title: Cerebellum, WT, rep3


title: Cortex, Fmr1 KO, rep3

description:
RNAseq.DE.log2FC_Brain.tsv
CTX.A3SS.MATS.JC.txt
CTX.A5SS.MATS.JC.txt
CTX.MXE.MATS.JC.txt
CTX.RI.MATS.JC.txt
CTX.SE.MATS.JC.txt

source_name: Cortex

value: Cortex


title: Cortex, Fmr1 KO, rep1


title: PS31.7


title: 3

city: Vancouver

first: Victor

last: Viau

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: The University of British Columbia

data_processing:
Data were aligned to a rat reference sequence using STAR and cufflinks
In R, individual spreadsheets with gene count data were loaded, compiled, organized, and genes with low reads (< 5 in all groups) were removed.
A Linear model (limma and voom) and variancePartition were used to assess main effects of sex, genotype and age, and their interactions.
Assembly: Rnor_5.0
Supplementary files format and content: CSV includes raw counts for each sample.
Supplementary files format and content: CSV includes log CPM normalized values for each sample.
Supplementary files format and content: .fastq.gz inclued raw sequences.

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent (Thermo Fisher Scientific) and Ultra Turrax T-25 Basic (IKA) homogenizer following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using NEBnext Ultra ii Stranded mRNA (New England Biolabls) following the manufacturer's protocol.

value: Charles River Sprague Dawley

value: Liver

value: M

value: KO


title: Hippocampus, Fmr1 KO, rep3


title: 14


title: 12


title: 25


title: 27


title: Cortex, WT, rep3


title: 4


title: PS31.5


title: PS31.6

source_name: dSC


title: 23


title: 60

value: F


title: Cortex, WT, rep2


title: 58


title: Cortex, Fmr1 KO, rep2


title: Root sample 3

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
RNAseq fastq files were first processed using Trimmomatic v0.38, in order to filter and trim low-quality sequences out from raw Illumina reads. A pseudo-mapping approach relying on Salmon v0.14.1 (Patro et al., 2017) was then used to associate each read to a predicted gene in reference genomes. To do so, an index containing all CDS sequences from the microbial and host genomes was built. Resulting read counts associated with each microbial gene were then used to perform differential expression analyses, in roots vs soil matrix samples. To perform one differential expression analysis per strain, inter-strain identical genes identified by Salmon were excluded. We could then identify differentially expressed genes in each strain independently, if the number of reads was sufficient. To compare microbial transcriptomes, for each orthogroup defined by OrthoFinder (see subsection Reference genomes), read counts mapped on paralog genes were summed. This allowed us to perform a differential expression analysis at the orthogroup scale, for each microbe independently. Orthogroup differential expression was then compared between strains. Finally, read counts associated to a given orthogroup across all species were also summed, allowing differential expression analyses at the kingdom level. All differential expression analyses were performed with DESeq2 (Love et al. 2014), using shrinkage algorithm apeglm (Zhu et al., 2018) to correct LogFoldChange values.
Assembly: reference.fasta.gz (we used as a reference for our mapping, a simulated metagenome prepared by combining predicted transcript sequences from 107 genomes published in diverse databases (i.e. at-sphere.com, mycocosm.jgi.doe.gov, arabidopsis.org))
Supplementary files format and content: tar archives containing the Salmon mapping outputs

source_name: Roots

growth_protocol: Before inoculation, A. thaliana Col-0 seeds were sterilized using ethanol and bleach and stratified for four days in the dark at 4°C. Between 4 and 5 hours after microbial inoculation, ten seeds were sown per pot and the closed boxes incubated at 21°C, for 10 hours with light (intensity 4) at 19°C and 14 hours in the dark for four weeks. After two weeks, boxes were opened under a sterile hood and excess seedlings were removed to keep 3 seedlings per FlowPot.

extract_protocol:
After 4 weeks of FlowPot incubation, roots were harvested from planted pots and peat matrix was sampled from unplanted pots. The roots of all plants from three FlowPots were combined for a total of 9 plants per sample. Roots were thoroughly washed in water, dried on sterilized Whatman glass microfiber filters (GE Healthcare Life Sciences), transferred into eppendorf tubes and frozen in liquid nitrogen and stored at −80°C. Roots and peat matrix samples were homogenized in 2mL eppendorf screw cap tubes using the Precellys 24 tissue lyzer (Bertin Technologies, Montigny-le-Bretonneux, France) after deep freezing twice at 6,200 rpm for 30 s.  DNA and RNA were co-extracted from both peat matrix and roots using the RNeasy PowerSoil Total RNA Kit (Qiagen, Hilden, Germany) and its extension for co-extraction of DNA. The RNA precipitation step temperature was adjusted to -20°C for roots samples.
The quality and concentration of RNA samples were quantified using a Bioanalyzer (Agilent, Waldbronn, Germany). Plant, bacterial and fungal ribosomal RNA were depleted from the roots samples using a combination of Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ribo-Zero rRNA Removal Kit (Yeast) and Ribo-Zero rRNA Removal Kit (Plant Seed/Root)(Illumina, San Diego, USA) following manufacturer’s protocol while only bacterial and fungal ribosomal RNA were depleted the for matrix samples. The quality and quantity were then quantified again using a Bioanalyzer (Agilent, Waldbronn, Germany). Library prep was done using the SMARTer Stranded RNA-Seq Kit (Takara Bio IncSaint-Germain-en-Laye, France) following manufacturer’s protocol. The quality and quantity were then quantified again using a Bioanalyzer (Agilent, Waldbronn, Germany). Illumina sequencing was then performed in-house using the HiSeq sequencer and custom sequencing primers.

treatment_protocol: The FlowPot experiment was set up following the previously described protocol in Duran et al., 2018 and Kremer et al., 2018 with slight modifications. Briefly, the 84 bacterial strains were cultivated from glycerol stocks first on TSB + agar (Tryptic Soy Broth, Sigma) for a week and then transferred to deep well 96-well- plates containing 800 μl of 50% TSB. 96-well-plates were left for six days at 25°C and subsequently pooled (in equal quantities, i.e. 600μl). This bacterial pool was centrifuged at 4,000 x g for 10 min and re-suspended in 10 mM MgCl2. OD600nm was adjusted to 0.05 (107 cells/mL) before inoculation. Fungal strains were cultivated from glycerol stocks on PGA (Potato Glucose Agar, Sigma-Aldrich) for two weeks. Pieces of mycelium were harvested using sterile tips into 1 mL of MgCl2 containing one stainless steel bead (3.2 mm) and subsequently crushed with a paint shaker (SK450, Fast & Fluid Management, Sassenheim, Netherlands) for 20 min and pooled in equal ratios (i.g. 800μl). Microbial mixtures were adjusted to a biomass ratio of 4:1 (eukaryotes:prokaryotes, as assessed by Joergensen and Emmerling, 2006), using 200μL  bacterial inoculum and 200μL of fungal inocula in 50 mL 1/2 MS (Murashige + Skoog Medium including Vitamins, Duchefa) supplemented with MES buffer (2-(N-morpholino)ethanesulfonic acid), which were then inoculated into the FlowPot using a 50 mL syringe.

tag: soil type

value: Roots

tag: ecotype

value: Microbial community inoculated

tag: time

value: Day 28


title: PS31.3

value: Neuron


title: 57

tag: strain

tag: age


title: PS31.2

value: sSC


title: Root sample 2


title: 51


title: Root sample 1


title: 63


title: 62


title: PS31.1


title: 61


title: day15 E2A-KO-rep2

city: Shanghai

first: xiuya

last: li

address: Dongan Road 130

institute: Fudan University

data_processing:
Duplicated biological samples were analyzed using Illumina HiSeqX10, Clean reads were mapped to human genome (hg38,GRCh38) using BWA software.
Genome_build: hg38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: cardiomyocytes

extract_protocol:
RNA was harvested from cells using Trizol reagent. NGS Multiplex Oligos for Illumina (ExCell Biotech, NGS00-103A, 96rxn) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human ESC-derived cardiomyocytes

tag: day


title: 18-1 L

tag: Sex


title: 19-2 L


title: day15 E2A-KO-rep1


title: PS31.4


title: 17-1 L


title: Negative control.22


title: 53


title: 10


title: Negative control.24


title: Cortex, WT, rep1


title: 8-2 L


title: 16-1 L


title: 15-1 L


title: Negative control.23


title: day15 WT-rep1

value: wild type


title: PS30.11

source_name: sSC


title: 13-1 L

value: WT


title: PS30.10


title: 3-1 L


title: day15 WT-rep2


title: PS30.9


title: Negative control.21


title: 12-2 L


title: 11-2 L


title: day7 E2A-KO-rep2


title: PS30.13


title: PS30.12


title: 9-2 L


title: day7 E2A-KO-rep1


title: PS30.8


title: 7-2 L


title: 544 DMSO_replicate 2

data_processing:
The sequence reads were mapped onto hg19 with Bowtie (version 1.2.3). SAM files were conveted into BAM files.
Those BAM files obtained in duplicate were merged by experimental condition.
Peak colling was performed with MACS (version 1.4.2). The output files included WIG files.

source_name: Mammary

extract_protocol:
9.7×105 cells were fixed with 0.5% formaldehyde in serum-free DMEM for 5 min at room temperature. Fixation was quenched with 1.25 M glycine. Fixed cells were washed three times with 0.5% BSA-PBS and lysed with lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0) containing protease inhibitor cocktail for 10 min on ice. The chromatin was sheared by Covaris Focused-ultrasonicator S220 for 10 min.
The complex of anti-acetylated histone H3 lysine 27 (H3K27ac) rabbit IgG with protein G dynabeads (Invitrogen #10004D) was mixed with sheared chromatin. After incubation 4℃ overnight, the complex was washed with low salt buffer, high salt buffer, LiCl salt buffer and Tris-EDTA. The complex was incubated in 1% SDS and 0.1 M NaHCO3 buffer, followed by incubation at 65℃ for 4 h to reverse cross linking. Released DNA was purified using AMPure (Beckman #A63881). 70 pg of DNA was used for library preparation using ThruPLEX DNA-seq Kit (Takara #R400674).

treatment_protocol: 5.7×105 cells were seeded onto 25 cm2 dishes two days prior to treatment in duplicates. Then, cells were treated with dimethyl sulfoxide (DMSO) (1:1000), TSA (1 µM) or SB431542 (10 µM) in 2% FCS culture medium for 24 h.

value: Mammary

value: fibroblasts

value: experimental CAF2

value: DMSO 1:1000 for 24 h

tag: antibody

value: anti-H3K27ac (D5E4, CST)

tag: desciption


title: 4-1 L

value: Charles River Sprague Dawley

value: Liver


title: PS30.7

value: dSC


title: 544 TSA_replicate 1

value: TSA 1 µM 24 h


title: day3 E2A-KO-rep2

source_name: cardiac mesoderm cells

value: human ESC-derived cardiac mesoderm cells


title: day7 WT-rep2


title: 2-1 L

value: F


title: 522 DMSO_replicate 2

value: control fibroblasts


title: PS30.6

value: Neuron


title: 5-2 L


title: 10-2 L

value: KO


title: day3 WT-rep1


title: 544 TSA_replicate 2


title: 522 DMSO_replicate 1


title: 544 SB_replicate 2


title: day3 E2A-KO-rep1


title: PS30.5

value: sSC


title: day7 WT-rep1

value: human ESC-derived cardiomyocytes

value: wild type


title: 251LRhsv_3

city: Xiamen

first: Yipeng

last: Rao

address: Xiangan Campus, Xiamen University, Xiangan Road, Xiangan District, Xiamen City, Fujian Province, China

institute: national insititute of diagnostics and vaccine development in infectious diseases（xiamen university）

data_processing:
RNA-seq analysis was performed by GeneWiz.
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances .We used scripts in house to enrich significantdifferential expression gene in KEGG pathways.
Assembly: hg38
Supplementary files format and content: rawreads, FPKMs

extract_protocol:
Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: U-251 MG cells were seeded at a density of 1 × 106 in 6-well plates and allowed to attach for 24 h. The next day, cells were pretreated for 4 h with LRRK2i (10 μM) or the vehicle. After pretreatment, the cells were infected with oHSV-GFP at an MOI of 0.5 or mock-infected. Four hours after infection, biological triplicates for each group were collected using Tripure Isolation Reagent (Roche).

value: Glioma cell

value: WT

tag: infection

value: oHSV-GFP at an MOI of 0.5 infected


title: Soil sample 3

organism: unidentified soil bacteria

value: Cologne CAS soil

value: Microbial community inoculated

value: Day 28


title: Soil sample 2


title: 251hsv_1

value: control


title: 544 SB_replicate 1

tag: tissue

value: Mammary

value: fibroblasts

value: experimental CAF2

value: anti-H3K27ac (D5E4, CST)


title: PS30.4

tag: genotype


title: 544 DMSO_replicate 1

tag: cell line

value: DMSO 1:1000 for 24 h


title: day3 WT-rep2

tag: cell type

value: human ESC-derived cardiac mesoderm cells


title: SUVKO 1928z-VDJ Day 16 Rep-1

first: Michel

last: Sadelain

address: 1275 York Avenue, Box 182

institute: Memorial Sloan Kettering Cancer Cener

data_processing:
library strategy: CITE-seq
The scRNA-seq reads were aligned to the human transcriptome (GRCh38) and unique molecular identifier (UMI) counts quantified to generate a gene-barcode matrix using Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1). CITE-seq antibody expression matrices were generated using the Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1).  TCR reads were aligned to the GRCh38 reference genome and consensus TCR annotation was performed using Cell Ranger vdj pipeline (10X Genomics, version cellranger-5.0.1).
Assembly: hg38
Supplementary files format and content: R object file in .rds format

source_name: T cells

growth_protocol: CAR T cells were generated from healthy donors (Day 0) or flow sorted from tumor bearing mice at Day 9 or Day 16.

extract_protocol:
Pre-infusion T cells (day 0), and flow-sorted CAR T cells from mouse bone marrow (day 9 and 16) were stained for 30 minutes at room temperature with a custom panel of 101 Total-Seq-C antibodies (Biolegend), and washed 3x using the HT1000 laminar wash system (Curiox). Cells were then counted using the Cellaca MX High-throughput Automated Cell Counter as described in the manufacturer’s protocol (Nexcelom) and loaded on the 10x Chromium Next GEM Chip K Kit.
TCR CDR3 sequences were enriched using the human V(D)J T cell enrichment. Libraries were prepared according to manufacturer’s protocol (5’ V2 kit, 10x Genomics) and sequenced on a NovaSeq 6000 System using the S4 2x 150 kit (Illumina).

value: T cells

value: Primary T cells

value: SUVKO


title: Soil sample 1

tag: treatment


title: PS30.3

value: PAG

value: Neuron


title: SUVKO 1928z-antibody capture Day 16 Rep-2

library_source: other

molecule: protein


title: PS30.1

value: dSC


title: WT 1928z-VDJ Day 16 Rep-1

value: WT


title: 251LRhsv_1

value: Glioma cell

value: oHSV-GFP at an MOI of 0.5 infected


title: 251LRhsv_2