title: DKO_PEG_12

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Assembly: Mus musculus - mouse (GRCm38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: MTOs

growth_protocol: MTOs were cultured in advanced DMEM/F12 medium supplemented with 10 mM HEPES, Glutamax, B-27, and 50 ng/ml recombinant human EGF. For injection,  100 μL cell suspension of equivalent to 0.5 × 106 cells of sgPrkci/Prkcz admixed with 30% Matrigel was directly injected subcutaneously into the right flank of 7 weeks old C57BL/6 mice

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: Veh or PEGPH20 (0.0375 mg/kg) were administrated 15 days after injection, twice a week for three weeks

value: MTO xenograft tumor

value: 13 weeks old

value: sgPrkci/Prkcz


title: DKO_PEG_19

status: Public on Dec 16 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

tag: genotype

tag: treatment


title: HCT116 DICER AA rescue AQ-seq replicate 2

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: AQ-seq

data_processing:
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the mouse genome (mm10) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Assembly: hg38
Supplementary files format and content: Tab-separated values (tsv) files containing sequence variants and corresponding read counts.

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNAs were subjected to AQ-seq (Kim et al., 2019) except that 100 µg of total RNAs were used for library construction, and that cDNAs were amplified with NEBNext Ultra II Q5 Master Mix (NEB). The libraries were sequenced on the NovaSeq 6000 platform.

tag: cell line


title: 2419N_KO_Fasted (RNA-seq)

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

description: RNA-Seq

data_processing:
Data quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Normalized counts were extracted from DESeq2.
Assembly: mm10
Supplementary files format and content: csv and xlsx (normalized counts and FDR)

source_name: Liver

growth_protocol: Gata4 fl/fl mice were injected with AAV8-Tbg-Cre or an empty AAV8 at 8 weeks of age. 7 days later mice were euthanized.

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Libraries were made with KAPA Stranded RNA-seq kit

treatment_protocol: Refed group were fasted for 12h starting at 9 - 10am and refed with High sucrose diet (69% sucrose, 10% fat D07042201 from Research Diets) for 12h starting at 9 - 10pm. Fasted group started fasting for 12h at 9 - 10pm. All mice were euthanized at 9 - 10am the following day.

value: Liver

tag: Sex

value: male

value: 9 weeks old

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)

value: Fasted


title: DKO_PEG_11


title: DKOtPEGPH203

library_source: transcriptomic single cell

data_processing:
Raw data was downloaded in Ubuntu using BaseSpaceCLI.
We used cellranger mkfastq to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files
We used cellranger count to take FASTQ files from cellranger mkfastq and perform alignment to mm10, filtering, barcode counting, and UMI counting
We used cellranger aggr to aggregate both sample outputs of cellranger count, normalizing  to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data
We used Seurat in R to analyzes the aggregated data
Assembly: mm10

source_name: Prkcif/fPrkczf/f;Villin-Cre tumor

growth_protocol: In vivo endogenous mouse model

extract_protocol:
Tumors were minced thoroughly and digested by 0.5mg/ml Liberase TH (Sigma) for 30 minutes at 37°C. Dead cells were removed by Annexin V (STEMCELL technologies).
scRNA-seq libraries were generated using the Chromium Single Cell 30 Reagent Kit v2 (10X Genomics). Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics),  (Single Cell 3′ library and Gel Bead Kit v.2) as described in the manufacturer’s protocol (10x User Guide, Revision B). On average, approximately 8,000 cells were loaded. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol. Individual sample quality was checked using a Bioanalyzer Tapestation (Agilent). Qubit was used for library quantification before pooling. The final library pool was sequenced on an Illumina NovaSeq6000 instrument using a S1 flowcell.Average cell recovery for Prkcif/fPrkczf/f;Villin-Cre tumors was 104,954 cells with a total of 209,907 cells captured at a mean depth of 14,568 read per cell and 895 mean genes per cell.

treatment_protocol: Veh or PEGPH20 (0.0375 mg/kg) were administrated  in 11-old-weeks mice twice a week for three weeks

value: Small intestine tumor

value: 14 weeks old

value: Prkcif/fPrkczf/f;Villin-Cre


title: DKO_veh_33

value: vehicle


title: DKOtPEGPH201

description: vehicle


title: AMI Patient (PE13) in day 9

city: Mulhouse

first: Anne

last: ARIES

address: 87 Av d'Alkirch

country: France

institute: IRHT

data_processing:
The normalization and differential expression analysis was performed with  the R/Bioconductor package edgeR v.3.28.1, for the genes annotated in the reference  genome. Lowly expressed genes were filtered, keeping genes that are expressed at a  reasonable level (10 counts in at least 7 samples). The filtered data were normalized  by the library size.
Assembly: GRCh38.p13
Supplementary files format and content:  normalized counts

source_name: ProtheraCytes (expanded CD34+ cells)

extract_protocol:
Total RNA was purified from ProtheraCytes® collected from 7 Frozen healthy donor and 8 Acute myocardiac infarcted  patients using RNAeasy plus minikit (QIAGEN,Courtabeuf, France). Briefly, sample  quality was assessed using a DNA High sensitivity chip (Agilent Technologies).
Single end 50 reads barcoded RNA-Seq sequencing library was performed on an Illumina HiSeq4000 with the TruSeq SBS v3 chemistry.

tag: individual

tag: condition

value: AMI

tag: cell type

value: ProtheraCytes (expanded CD34+ cells)


title: AMI Patient (PE14) in day 9


title: 1-to-3 randomization AQ-seq with miR-374b 20% cleavage

description: AQ-seq

data_processing:
The TruSeq 3′ adapter sequence was removed using cutadapt.
For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit.
Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Assembly: No alignment
Supplementary files format and content: Tab-separated values (tsv) files containing sequence variants and corresponding read counts.

extract_protocol:
Gel purification
The input and uncleaved pre-miRNAs were subjected to AQ-seq as previously described (Kim et al., 2019), with some modifications as follows. After 3′ adapter ligation, the ligated RNAs were purified on a 10% urea-polyacrylamide gel along with Century-Plus RNA Markers (Thermo Fisher) as a size marker. After reverse transcription, cDNAs were amplified with NEBNext Ultra II Q5 Master Mix (NEB). The libraries were sequenced on the NovaSeq 6000 platform.

tag: construct

value: 1-to-3 randomization AQ-seq with miR-374b 20percent cleavage


title: DKOtPEGPH202


title: 1-to-3 randomization AQ-seq with miR-374b 10% cleavage

description: AQ-seq

value: 1-to-3 randomization AQ-seq with miR-374b 10percent cleavage


title: 1-to-3 randomization AQ-seq with miR-374b 30% cleavage

description: AQ-seq

value: 1-to-3 randomization AQ-seq with miR-374b 30percent cleavage


title: HCT116 DICER ΔdsRBD rescue AQ-seq replicate 2

description: AQ-seq


title: AMI Patient (PE12) in day 9


title: DKO_PEG_37

value: MTO xenograft tumor


title: DKOtveh5

description: vehicle


title: DKO_veh_16

value: 13 weeks old


title: 1-to-3 randomization AQ-seq with miR-374b input

description: AQ-seq


title: AMI Patient (PE11) in day 9


title: DKOtveh4

description: vehicle


title: DKO_veh_14

value: sgPrkci/Prkcz


title: HCT116 DICER WT rescue AQ-seq replicate 2

description: AQ-seq


title: DPT6

source_name: Prkcif/fPrkczf/f;Villin-Cre


title: 1-to-3 randomization AQ-seq with let-7a-1 20% cleavage

description: AQ-seq

value: 1-to-3 randomization AQ-seq with let-7a-1 20percent cleavage


title: 1-to-3 randomization AQ-seq with let-7a-1 30% cleavage

description: AQ-seq

value: 1-to-3 randomization AQ-seq with let-7a-1 30percent cleavage


title: AMI Patient (PE09) in day 9


title: DPT5


title: DPT4


title: 1-to-3 randomization AQ-seq with let-7a-1 10% cleavage

description: AQ-seq

value: 1-to-3 randomization AQ-seq with let-7a-1 10percent cleavage


title: DKOtveh2

description: vehicle


title: DKOtveh1

description: treatment


title: DVT2


title: Minus1-to-1 randomization AQ-seq with miR-374b 30% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with miR-374b 30percent cleavage


title: MEF_OptRepliseq_R2_Early S Fraction

city: Minneapolis

first: Juan Carlos

last: Rivera-Mulia

state: MN

address: 420 Washington Ave SE

department: Department of Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota Medical School

library_source: genomic

data_processing:
Library strategy: Repli-seq
Reads were mapped to corresponding genome (hg38 or mm10) using BWA.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio was calculated in 20kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 10kb windows
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: processed data are 10kb windows in hg38 or mm10 genomes.

molecule: genomic DNA

source_name: MEFs

growth_protocol: H9 cells were cultured in mTeSR Plus (StemCell Technologies Cat. No. 05825) on Geltrex (Life Technologies Cat. No. A1413302) coated dishes according to WiCell instructions. U2OS cells were grown in DMEM media (Corning Cat.No. 15013CM) supplemented with 10% FBS (Corning Cat.No.35011CV), 1% Glutamine (Gibco Cat.No. 25030081), 1% Penicillin-Streptomycin (Gibco Cat.No. 15070-063). MEFs were cultured in 1:1 DMEM media (Corning Cat.No. 10-017-CV) and F10 media with Glutamax (Gibco Cat.No. 41550021), supplemented with 10% FBS (Sigma Cat.No. F2442), 1X NEAA (Gibco Cat.No. 11140050) and 1% Penicillin-Streptomycin (Corning Cat.No. 30002Cl).

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370) or by KAPA HyperPlus library preparation kit (Roche Cat. No.  07958978001).

tag: s-phase fraction

value: Early S fraction

tag: replicate


title: DVT3

value: Small intestine tumor


title: MEF_OptRepliseq_R1_Late S Fraction

value: Late S fraction


title: MEF_OptRepliseq_R1_Early S Fraction


title: Minus1-to-1 randomization AQ-seq with miR-374b 10% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with miR-374b 10percent cleavage


title: MEF_OptRepliseq_R2_Late S Fraction


title: Minus1-to-1 randomization AQ-seq with miR-374b 20% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with miR-374b 20percent cleavage


title: MD_18

source_name: MTO

treatment_protocol: No treatment

value: MTO


title: DVT1

value: 14 weeks old

value: Prkcif/fPrkczf/f;Villin-Cre

value: vehicle


title: rna-N-D28

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

description: Stem cells were plated in clumps in the presence of Y27632 (10mg/ml, 1000x, Axon MedChem). The hES colonies were allowed to grow in mTESR for another day before the media was switch to differentiation media (1X N2, 1X B27, DMEM/F12: Neurobasal=1:1 (Invitrogen), 0.1mM Ascorbic acid (Sigma)) with small molecules [SB431542, LDN193189 and CHIR99021 (Final concentration: 10µM, 100nM and 3µM from Stemgent and Tocris)]. To obtain anterior or posterior neural stem cells, SB431542/LDN194189 and SB431542/LDN193189/CHIR99021 were added respectively. The cells were allowed to differentiate in the media for 6 days before they were dissociated with Accutase and plated at the density of 1 million cells per well of 6 wells for infection. For Ngn2 day 2 post-dox induction cells, TetO-Ngn2-t2a-puro and FUW-rtTA were infected at day 0 in differentiation media followed by adding doxycycline and puromycin the next day. The cells were selected for two days in puromycin before collection for downstream HiChIP experiment.

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
TPM were obtained from the mapped by using RSEM with the following settings (--paired-end --seed-length 21 --no-bam-output --calc-pme --calc-ci –alignments).
Differential analysis was performed using limma with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include TPM values for each cell type with biological replicates summed

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) followed by cleanup using RNA Clean and Concentrator (Zymo) using the manufacturer’s protocol. Samples were then QCed using bioanalyzer and subjected to paired end sequencing (BGI platform). RNA-seq on Astrocyte biological replicates was performed using the Lexogen Quant-seq 3’ mRNA-seq Library Prep Kit FWD for Illumina protocol (cat# 015.96).
Double-stranded cDNA was synthesized and i7 adapters for Illumina sequencing were added during PCR amplification. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 instrument at a depth of 30 million reads per sample.

value: neuron

value: day 28


title: MD_17


title: atac-AST

description: Normal Human Astrocytes (Lonza, CC-2565) were cultured in Lonza Astrocyte Growth Media containing astrocyte basal medium, 7.5% FBS, ascorbic acid, rhEGF, GA-1000 (gentamicin sulfate-amphotericin), insulin, and L-glutamine. Astrocytes were seeded at a 5,000 cells/cm^2 density and maintained up to 70% confluence before splitting at 37C and 5% CO2. Growth medium was changed the day after seeding and every other day thereafter.

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
ATAC-seq read alignment, quality filtering, duplicate removal, transposase shifting, peak calling, and signal generation were all performed through the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapter sequences were trimmed, sequences were mapped to the hg19 reference genome using Bowtie2 (-X2000), poor quality reads were removed, PCR duplicates were removed (Picard Tools MarkDuplicates), chrM reads were removed, and read ends were shifted +4 on the positive strand or -5 on the negative strand to produce a set of filtered high-quality reads. These reads were put through MACS2 to get peak calls and signal files. Finally, IDR analysis was run on the two replicate peak files to produce an IDR peak file that is the reproducible set of peaks across both replicates. The full pipeline can be found on the ENCODE portal.
Differential analysis was performed using DESeq2 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: peak files of significantly called peak called between two biological replicates

source_name: primary

extract_protocol:
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

value: astrocyte

value: primary


title: Minus1-to-1 randomization AQ-seq with let-7a-1 30% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with let-7a-1 30percent cleavage


title: DKOtveh3

description: vehicle


title: AMI Patient (PE10) in day 9

value: AMI

value: ProtheraCytes (expanded CD34+ cells)


title: red-blood-Z-VAD

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

data_processing:
Hi-C raw FASTQ files and then mapped the trimmed files against mm10 reference genome using runHiC pipeline. Hi-C matrix was generated using run-cool2multirescool script from the 4DN consortium.
Genome_build: mm10
Supplementary_files_format_and_content: The .cool file were the matrix of Hi-C for each Sample.

source_name: erythroblast precursors cells

growth_protocol: Fetal liver HSPCs were isolated from the E13.5 fetal liver by depletion of Ter119-positive cells using a biotinylated anti-TER119 antibody, and bone marrow HSPCs were purified by depletion of lineage-negative cells using Lineage Cell Depletion Kit (BD Pharmingen, 559971) according to the manufacture’s protocol. Then incubated in EPO medium for differentiation and enucleation for 48 hours.

extract_protocol:
Hi-C in cell and tissue was performed following the manufacturer's protocol (A510008, Arima Genomics). Cells were cultured and crosslinked using 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for five minutes at RT. A total of 3 million cells were used for each Hi-C experiment. Tissue samples were frozen with liquid nitrogen and pulverized using mortar and pestle until the sample resembles a fine powder, then crosslinked using the same condition as cell lines.
Hi-C libraries were generated and quality checked per manufacturer's protocol. 300-600M reads per each sample was generated based on total usable reads above 20Kb.

value: erythroblast precursors cells

value: Z-VAD


title: red-blood-DMSO

value: DMSO


title: atac-P-D2

value: day 2


title: MD_16

value: sgPrkci/Prkcz


title: red-blood-0h


title: atac-P-NPC

value: posterior neural progenitor cell


title: 1-to-3 randomization AQ-seq with let-7a-1 input

description: AQ-seq


title: MW9

value: MTO

value: sgC


title: MW8


title: atac-A-D2


title: Con_390

city: Guangzhou

first: Xue

last: Bai

address: No. 1023-1063, Shatai South Road, Baiyun District

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
HISAT2 software was used to conduct genome mapping analysis of preprocessed sequencing sequences. Usually we compare clean No RNA reads to the genome, which is the basis of subsequent analysis. HISAT2 uses global and local search methods, which can perform efficient mapping and effectively compare splICED reads in RNA Seq sequencing data. The default parameters are set, and the reference genome version is GRCm38.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: LKB1-deficient lung adenocarcinoma

extract_protocol:
Tumors were harvested, and total RNA was isolated and reverse transcribed into cDNA to construct an indexed Illumina library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: subcutaneous tumor

value: Vehicle


title: MW7


title: Minus1-to-1 randomization AQ-seq with let-7a-1 input

description: AQ-seq


title: rna-N-D10

value: neuron

value: day 10


title: Con_389


title: Minus1-to-1 randomization AQ-seq with miR-374b input

description: AQ-seq


title: Con_388


title: atac-A-NPC

value: anterior neural progenitor cell


title: Minus1-to-3 randomization AQ-seq with let-7a-1 5% cleavage

description: AQ-seq

value: Minus1-to-3 randomization AQ-seq with let-7a-1 5percent cleavage


title: Lung, Hypoxia, ABT-263, Day2 [X527]

city: Créteil

first: Emmanuelle

last: Born

address: 8 rue du Général SARRAIL

department: Faculté de Santé

institute: IMRB, Inserm U955

data_processing:
Primary data analysis, including base calling and quality scoring is, performed by real-time analysis or RTA on the instrument. RTA performs image analysis and base calling during the sequencing run. The NextSeq 500 uses a new implementation of RTA called RTA 2.0.
Fastq were filtered using trimmomatic with parameters SlidingWindow:5:20 and minLen=50bp
High quality reads were mapped on the GRCm38 genome using STAR
Abundance estimation were done using RSEM
Assembly: mouse genome GRCm38.92
Supplementary files format and content: tab-delimited text files include ensembID and counts values for each Sample

source_name: Lung

extract_protocol:
Total RNA from tissues were extracted with RNeasy Plus Mini Kit (Qiagen, Courtaboeuf, France).
Sequencing libraries were generated with TruSeq®. Stranded mRNA Library Prep kit and sequenced on a NextSeq 500 analyzer (Illumina)

value: Lung

value: Male

value: Hypoxia


title: atac-N-D28

value: day 28


title: Minus1-to-3 randomization AQ-seq with let-7a-1 input

description: AQ-seq


title: Lung, Hypoxia, ABT-263, Day2 [X526]


title: PAL_368

value: Palbociclib


title: Minus1-to-1 randomization AQ-seq with let-7a-1 20% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with let-7a-1 20percent cleavage


title: atac-N-D10


title: PAL_367


title: KDM5C_CUT&Tag

city: Shanghai

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

data_processing:
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC
Quality filtered reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks and an initial threshold q-value of 0.05 as cutoff
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: HTR-8/SVneo were cultured in DMEM/F12 with 10% fetal bovine serum (FBS) plus Penicillin/ Streptomycin antibiotics (Invitrogen), at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
CUT_Tag experiments was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901-01).  Cells were incubated with pG-Tn5 and DNA were digested 1 h at 37 ℃. Sample DNA was extracted by phenol-chloroform-isoamyl alcohol and amplified by PCR followed by sequencing.
Library was construct by PCR, CUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE50 mode.


title: Lung, Hypoxia, ABT-263, Day2 [X525]


title: Lung, Hypoxia, ABT-263, Day2 [X524]


title: atac-N-D4

value: day 4


title: PAL_366


title: U2OS_OptRepliseq_R3_Late S Fraction

source_name: Osteosarcoma cells

value: Late S fraction


title: U2OS_OptRepliseq_R3_Early S Fraction

value: Early S fraction


title: atac-N-D2

value: day 2


title: Lung, Hypoxia, ABT-263, Day2 [X523]


title: PD_364


title: Minus1-to-1 randomization AQ-seq with let-7a-1 10% cleavage

description: AQ-seq

value: Minus1-to-1 randomization AQ-seq with let-7a-1 10percent cleavage


title: U2OS_OptRepliseq_R2_Late S Fraction


title: Lung, Hypoxia, ABT-263, Day2 [X522]


title: atac-ES

value: stem cell


title: plasmid_DNA_library

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

institute: Broad Institute

description:
Column name in the processed data file: pDNA
300k_conditions.txt
300k_reference.txt
300k_counts.txt

data_processing:
Data were processed with PoolQ to split sample reads by Illumina barcode (conditions) and count barcode sequences (references).
Reference sequences can be found with prefixes: "TTTTTT" for U6 (S pyogenes) barcode and "CGTGCAC" for H1 (S aureus) barcodes.

organism: synthetic construct

growth_protocol: Cells were continuously cultured in RPMI 1640 supplemented with 10% FBS and penicilin/streptomycin.

extract_protocol:
gDNA was isolated with Qiagen Blood and Tissue kit according to the manufacturer's protocol.
PCR amplification was carried out with primers flanking sgRNA barcode pairs (Najm et al NBT 2017, Supplementary Note 1 for layout).

treatment_protocol: Cells carrying SpCas9 were transduced with lentivirus delivering SaCas9 and guide pair (300k or validation library). After 21 days, cells were harvested for gDNA extraction.


title: PD_362

value: subcutaneous tumor


title: Lung, Hypoxia, Vehicle, Day2 [X521]

value: Vehicle


title: U2OS_OptRepliseq_R2_Early S Fraction


title: PD_361


title: HEK293 shTHOC5-40min TT-Seq

city: Hanover

first: Mareike

last: Polenkowski

address: Carl-Neuberg-Straße 1

department: Cell Biochemistry

country: Germany

institute: Medical School Hannover

description:
elongation rate single gene analysis-shTHOC5.csv
wave peaks analysis.xlsx

data_processing:
Nanopore: Basecalls performed using Guppy version 3.3.3+fa743a6
Nanopore: Mapping using minimap2
Nanopore: Trimming of long read sequencing data using NanoFilt version 2.5.0
ChIp-Seq: FASTQ files were generated by CASAVA (v1.8.2). Galaxy workflow for RNA-Seq (www.usegalaxy.org) was used for subsequent data analysis. Reads were mapped to the human reference genome (GRCh38) using Bowtie2 (Galaxy Version 2.3.4.1). Metagene analysis was performed using deepTools 2.0
TT-Seq: Raw reads were mapped to the human reference genome (GRCh38) using Bowtie2 (Galaxy Version 2.3.4.1). Read coverage of individual gene was normalized and visualized using Seqmonk. To measure the progression of Pol II molecules into the gene body we applied a pipeline described by Gregersen et al. (33) for calling RNA Pol II transcription wave peak positions and elongation rates from DRB/TT-seq time-series data using R. Metagene analysis was performed using deepTools 2.0.
Assembly: GRCh38
Supplementary files format and content: For the identification of 3’cleavage sites the tool NanoFilt (Filtering and trimming of long read sequencing data) was used to trim the mRNA sequences from 5’end to a uniform length so that we keep always the last 200 nucleotides (python get_read_ends.py --bases_from_end 200 reads.fastq.gz | gzip > last_200_bp.fastq.gz). Trimmed reads were aligned to the GRCh38 human genome reference using minimap2. The quantification of 3’ cleavage was perform with Seqmonk using the human polyA database as reference. Genes that contain more than two annotated polyadenylation sites (PAS) and more than 5 reads at distal PAS sites were selected. The ratios between proximal- and distal cleavage site were calculated.
Library strategy: TT-Seq

source_name: kidney

growth_protocol: HEK293 cells were grown in Dulbecco´s modified Eagle's medium supplemented with 10% (v/v) FCS.

extract_protocol:
RNAs were isolated using TRIzol reagent and fragmented in 166 mM NaOH on ice for 20 min.. To biotinylate 4SU-RNAs 3 μL of biotin buffer (833 mM Tris-HCl, pH 7.4, and 83.3 mM EDTA) and 50 μL of 0.1 mg/ml MTSEA biotin-XX linker (Biotium) were added to the 200 μL of fragmented RNA and incubated at RT for 30 min in the dark. Biotinylated RNAs were isolated by adding equal volume of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)) and subsequently precipitated in NaCl/isopropanol. Biotinylated RNA fragments were then separated from non-biotinylated fragments using μMACS streptavidin MicroBeads (μMACS Streptavidin Kit, Miltenyi Biotec).
library preparation using TruSeq ChIP Library Preparation Kit (Illumia). Libraries were prepared and indexed according to manufacturer’s protocol. Indexed libraries were pooled and sequenced on an Illumina HiSeq 2500.

treatment_protocol: Cells were treated with 100 μM 5,6-dichlorobenzimidazole (DRB) for 3.5 h for each time point after release. The DRB inhibition was released with three washes in 10 mL of PBS pre-warmed to 37 °C. Fresh medium containing 1 mM 4SU was directly added to the cells after PBS washes

value: kidney

value: Human embryonic kidney 293 cells

value: lentiviral infection carrying shTHOC5, 4 days, 100 μM DRB for 3.5 h, 1 mM 4SU


title: H9_100cells_R3_Late S Fraction

source_name: Human ESC


title: H9_100cells_R3_Early S Fraction


title: HEK293 shTHOC5-20min TT-Seq


title: Comb_360


title: HEK293 shTHOC5-30min TT-Seq


title: H9_100cells_R2_Late S Fraction


title: Comb_357


title: Lung, Hypoxia, Vehicle, Day2 [X518]

value: Lung


title: Lung, Hypoxia, Vehicle, Day2 [X517]

value: Male


title: HEK293 shCtrl-20min TT-Seq

description:
elongation rate single gene analysis-shCtrl.csv
wave peaks analysis.xlsx

value: lentiviral infection carrying shCtrl, 4 days, 100 μM DRB for 3.5 h, 1 mM 4SU


title: Lung, Hypoxia, Vehicle, Day2 [X519]

value: Hypoxia


title: HEK293 shTHOC5-10min TT-Seq


title: HEK293 shCtrl-30min TT-Seq


title: Lung, Hypoxia, Vehicle, Day2 [X516]


title: U2OS_OptRepliseq_R1_Early S Fraction


title: H9_100cells_R2_Early S Fraction


title: Comb_359


title: HEK293 shCtrl-40min TT-Seq


title: H9_100cells_R1_Late S Fraction


title: HEK293 shCtrl-10min TT-Seq


title: Lung, Normoxia, ABT-263, Day2 [X513]

value: Normoxia


title: Lung, Normoxia, ABT-263, Day2 [X515]


title: H9_100cells_R1_Early S Fraction


title: Lung, Normoxia, ABT-263, Day2 [X514]


title: U2OS_OptRepliseq_R1_Late S Fraction


title: Lung, Hypoxia, Vehicle, Day2 [X520]


title: Liver_KO_2

type: RNA

city: Berkeley

first: Danica

last: Chen

address: 335 Morgan Hall

institute: University of California, Berkeley

description: Gene expression data from the liver of a SIRT7 KO mouse

hyb_protocol: Hybridized to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/affymetrix.html) for the GenChip

scan_protocol: Affymetrix standard protocols with GneChip Scanner 3000 7G (https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-instruments/genechip-scanner.html) (ThermoFisher)

data_processing: Microarray data were normalized using the GCRMA algorithm (Bolstad et al., 2003, Irizarry et al., 2003a, Irizarry et al., 2003b); ratios of normalized probe set intensity values were calculated for each sample pair. To facilitate the ranking of genes for further analysis, we used the average value of each sample.

label: Biotin

source_name: Liver, KO2

label_protocol: Biotin using Affymetrix protocol & kit

extract_protocol: Total RNA was isolated from the livers of wild type and SIRT7 KO mice using an RNA isolation kit (Qiagen)

treatment_protocol: Livers from WT and SIRT7 KO mice were collected for total RNA isolation

value: Liver

value: SIRT7 KO


title: Liver_KO_3

source_name: Liver, KO3


title: Liver_KO_4

source_name: Liver, KO4


title: Liver_KO_1

source_name: Liver, KO1


title: HEK293 PolII shTHOC5-repeat ChIP-Seq

data_processing:
Nanopore: Basecalls performed using Guppy version 3.3.3+fa743a6
Nanopore: Mapping using minimap2
Nanopore: Trimming of long read sequencing data using NanoFilt version 2.5.0
ChIp-Seq: FASTQ files were generated by CASAVA (v1.8.2). Galaxy workflow for RNA-Seq (www.usegalaxy.org) was used for subsequent data analysis. Reads were mapped to the human reference genome (GRCh38) using Bowtie2 (Galaxy Version 2.3.4.1). Metagene analysis was performed using deepTools 2.0
TT-Seq: Raw reads were mapped to the human reference genome (GRCh38) using Bowtie2 (Galaxy Version 2.3.4.1). Read coverage of individual gene was normalized and visualized using Seqmonk. To measure the progression of Pol II molecules into the gene body we applied a pipeline described by Gregersen et al. (33) for calling RNA Pol II transcription wave peak positions and elongation rates from DRB/TT-seq time-series data using R. Metagene analysis was performed using deepTools 2.0.
Assembly: GRCh38
Supplementary files format and content: For the identification of 3’cleavage sites the tool NanoFilt (Filtering and trimming of long read sequencing data) was used to trim the mRNA sequences from 5’end to a uniform length so that we keep always the last 200 nucleotides (python get_read_ends.py --bases_from_end 200 reads.fastq.gz | gzip > last_200_bp.fastq.gz). Trimmed reads were aligned to the GRCh38 human genome reference using minimap2. The quantification of 3’ cleavage was perform with Seqmonk using the human polyA database as reference. Genes that contain more than two annotated polyadenylation sites (PAS) and more than 5 reads at distal PAS sites were selected. The ratios between proximal- and distal cleavage site were calculated.

extract_protocol:
5x10^6 cells were fixed in 1% PFA for 5 minutes and subsequently quenched in 125 mM glycine. Nuclear fraction was isolated and resuspended in sonication buffer (0.1% SDS, 50 mM TrisHCl, pH 8.0, 0.2 mM EDTA, 1x Protease inhibitor cocktail (Sigma)). Chromatin was sheared into 500 bp DNA fragments using Covaris AFA™ (Adaptive Focused Acoustics, Woburn, MA, USA) technology according to the manufacturer’s instructions. After shearing, NaCl and NP40 were added to final concentration of 150 mM and 1%, respectively. Aliquots of extracts were precipitated by pre-coated Protein G Agarose-PLUS (Santa Cruz Biotechnology Inc.) with anti- RNA polymerase II (Abcam), THOC5 (Bethyl Laboratories. Inc.), CDK12 (Cell signaling), FLAG M2 antibodies or control IgG. Following 4 h rotation at 4°C, the beads were washed three times in RIPA buffer (150 mM NaCl, 1% NP40, 0.1 % SDS, 50 mM TrisHCl at pH 8), and two times in wash buffer (500 mM NaCl, 1% NP40, 0.1 % SDS, 100 mM TrisHCl at pH 8). Cross-links were reversed for 8 h at 65°C (250 mM NaCl) in the presence of RNAse A. Following proteinase K digestion at 55°C for 1 hour, the bound DNA fraction was isolated using NucleoSpin Extract II (Macherey-Nagel, Dueren, Germany).
5 ng of ChIP derived DNA were subjected to library preparation using TruSeq ChIP Library Preparation Kit (Illumia). Libraries were prepared and indexed according to manufacturer’s protocol. Indexed libraries were pooled and sequenced on an Illumina HiSeq 2500.

treatment_protocol: Infection of HEK293 cells with lentiviruses carrying either shCr or shTHOC5. The treatment was applied for 4 days.

tag: chip antibody

value: Pol II (Abcam)


title: H9_500cells_R2_Late S Fraction

value: Late S fraction


title: H9_500cells_R2_Early S Fraction

value: Early S fraction


title: Lung, Normoxia, ABT-263, Day2 [X511]


title: HEK293 PolII shTHOC5 ChIP-Seq


title: H9_500cells_R1_Late S Fraction


title: Lung, Normoxia, ABT-263, Day2 [X510]


title: HEK293 PolII shCtrl ChIP-Seq


title: HEK293 TAP-THOC5 ChIP-Seq

value: THOC5 (Benthyl)


title: Lung, Normoxia, Vehicle, Day2 [X509]


title: CD8_S_3

city: Suzhou

first: Qiao

last: Cheng

state: Jiangsu Province

address: Shizi Street

department: Institute of Blood and Marrow Transplantation (IBMT)

institute: The First Affiliated Hospital of Soochow University

data_processing:
Data were filtered using the following specifications fastq software, The filtering standards from raw data to clean reads are:  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation:  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
The spleens were dissected and prepared into single-cell suspensions and CD8+ T cells were isolated by CD8+ T cell isolation kit (STEMCELL, VAN, Canada ). Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: Balb/c

value: spleen

value: allo-HSCT (donor :C57BL/6, host:Balb/c)


title: H9_500cells_R1_Early S Fraction


title: CD8_S_2


title: H9_1Kcells_R2_Early S Fraction


title: Lung, Normoxia, Vehicle, Day2 [X508]

value: Vehicle


title: Lung, Normoxia, Vehicle, Day2 [X507]


title: Sequencing of HEK293 Input.

value: kidney

value: Human embryonic kidney 293 cells


title: CD8_S_1


title: Liver_WT_2

description: Gene expression data from the liver of a WT mouse

source_name: Liver, WT2

value: WT


title: Liver_WT_1

source_name: Liver, WT1


title: CD8_A_3

value: syn-HSCT (donor :Balb/c, host:Balb/c)


title: Lung, Normoxia, Vehicle, Day2 [X506]

value: Lung

value: Male


title: Liver_WT_3

source_name: Liver, WT3


title: Lung, Normoxia, ABT-263, Day2 [X512]

value: Normoxia


title: HEK293 PolII shCtrl-repeat ChIP-Seq


title: Lung, Normoxia, Vehicle, Day2 [X505]


title: H9_1Kcells_R1_Early S Fraction


title: HEK293 Ctrl-repeat ChIP-Seq

value: IgG (Santa Cruz)


title: CD8_A_2


title: HEK293 Ctrl ChIP-Seq


title: Lung, Normoxia, Vehicle, Day2 [X504]


title: H9_1Kcells_R2_Late S Fraction


title: CD8_A_1


title: H9_5Kcells_R1_Late S Fraction


title: HEK293 TAP ChIP-Seq


title: Sequencing of HEK293 Input

data_processing:
Nanopore: Basecalls performed using Guppy version 3.3.3+fa743a6.
Nanopore: Mapping using minimap2.
Nanopore: Trimming of long read sequencing data using NanoFilt version 2.5.0.
ChIP-Seq: FASTQ files were generated by CASAVA (v1.8.2). Galaxy workflow for RNA-Seq (www.usegalaxy.org) was used for subsequent data analysis. Reads were mapped to the human reference genome (GRCh38) using Bowtie2 (Galaxy Version 2.3.4.1). Metagene analysis was performed using deepTools 2.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: For the identification of 3’cleavage sites the tool NanoFilt (Filtering and trimming of long read sequencing data) was used to trim the mRNA sequences from 5’end to a uniform length so that we keep always the last 200 nucleotides (python get_read_ends.py --bases_from_end 200 reads.fastq.gz | gzip > last_200_bp.fastq.gz). Trimmed reads were aligned to the GRCh38 human genome reference using minimap2. The quantification of 3’ cleavage was perform with Seqmonk using the human polyA database as reference. Genes that contain more than two annotated polyadenylation sites (PAS) and more than 5 reads at distal PAS sites were selected. The ratios between proximal- and distal cleavage site were calculated.
Supplementary_files_format_and_content: bigWig files

source_name: Human embryonic kidney 293 cells

extract_protocol:
5x10^6 cells were fixed in 1% PFA for 5 minutes and subsequently quenched in 125 mM glycine. Nuclear fraction was isolated and resuspended in sonication buffer (0.1% SDS, 50 mM TrisHCl, pH 8.0, 0.2 mM EDTA, 1x Protease inhibitor cocktail (Sigma)). Chromatin was sheared into 500 bp DNA fragments using Covaris AFA™ (Adaptive Focused Acoustics, Woburn, MA, USA) technology according to the manufacturer’s instructions. After shearing, NaCl and NP40 were added to final concentration of 150 mM and 1%, respectively. Aliquots of extracts were precipitated by pre-coated Protein G Agarose-PLUS (Santa Cruz Biotechnology Inc.) with anti-RNA polymerase II (Abcam), THOC5 (Bethyl Laboratories. Inc.), CDK12 (Cell signaling), FLAG M2 antibodies or control IgG. Following 4 h rotation at 4°C, the beads were washed three times in RIPA buffer (150 mM NaCl, 1% NP40, 0.1 % SDS, 50 mM TrisHCl at pH 8), and two times in wash buffer (500 mM NaCl, 1% NP40, 0.1 % SDS, 100 mM TrisHCl at pH 8). Cross-links were reversed for 8 h at 65°C (250 mM NaCl) in the presence of RNase A. Following proteinase K digestion at 55°C for 1 hour, the bound DNA fraction was isolated using NucleoSpin Extract II (Macherey-Nagel, Dueren, Germany).
5 ng of ChIP derived DNA were subjected to library preparation using TruSeq ChIP Library Preparation Kit (Illumina). Libraries were prepared and indexed according to manufacturer’s protocol. Indexed libraries were pooled and sequenced on an Illumina HiSeq 2500.

value: embryonic kidney cell line


title: Liver_WT_4

source_name: Liver, WT4

value: Liver


title: H9_5Kcells_R1_Early S Fraction


title: H9_10Kcells_R2_Late S Fraction

value: Late S fraction


title: CD4_S_3

data_processing:
Data were filtered using the following specifications fastq software, The filtering standards from raw data to clean reads are:Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation:Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

extract_protocol:
The spleens were dissected and prepared into single-cell suspensions and CD4+ T cells were isolated by CD4+ T cell isolation kit (STEMCELL, VAN, Canada ). Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.


title: KDM5C_K3K4me3_ChIP

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using BWA(0.7.10)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 version 2.1.1 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: human invasive extravillous trophoblasts (EVTs)

tag: genotype/variation

value: KDM5C-expression vector

value: H3K4me3 (Abcam, ab8580)


title: CD4_S_2

value: Balb/c

value: spleen


title: Lung, Hypoxia, ABT-263, Day8 [X550]

data_processing:
Primary data analysis, including base calling and quality scoring is, performed by real-time analysis or RTA on the instrument. RTA performs image analysis and base calling during the sequencing run. The NextSeq 500 uses a new implementation of RTA called RTA 2.0.
Fastq were filtered using trimmomatic with parameters SlidingWindow:5:20 and minLen=50bp
High quality reads were mapped on the GRCm38 genome using STAR
Abundance estimation were done using RSEM
Assembly: Mouse genome GRCm38.92
Supplementary files format and content: tab-delimited text files include ensembID and counts values for each Sample

extract_protocol:
Total RNA from tissues were extracted with RNeasy Plus Mini Kit (Qiagen, Courtaboeuf, France).
Sequencing libraries were generated with TruSeq®. Stranded mRNA Library Prep kit and sequenced on a NextSeq 500


title: H9_1Kcells_R1_Late S Fraction


title: Vector_H3K4me3_ChIP


title: Lung, Hypoxia, ABT-263, Day8 [X551]


title: H9_10Kcells_R2_Early S Fraction

value: Early S fraction


title: Lung, Hypoxia, ABT-263, Day8 [X549]


title: KDM5C_input

value: control vector


title: CD4_S_1

value: allo-HSCT (donor :C57BL/6, host:Balb/c)


title: H9_10Kcells_R1_Late S Fraction


title: Lung, Hypoxia, ABT-263, Day8 [X548]


title: CD4_A_3


title: Vector_input


title: H9_10Kcells_R1_Early S Fraction


title: CD4_A_2


title: Lung, Hypoxia, ABT-263, Day8 [X546]

value: Vehicule


title: H9_20Kcells_R2_Late S Fraction


title: Lung, Hypoxia, Vehicle, Day8 [X545]


title: CD4_A_1

value: syn-HSCT (donor :Balb/c, host:Balb/c)


title: KDM5C_shRNA-2_rep3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: expression analysis result of  EdgeR and annotation

source_name: HTR-8/Svneo_KDM5C shRNA-2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: KDM5C shRNA-2


title: KDM5C_shRNA-2_rep2


title: Lung, Hypoxia, Vehicle, Day8 [X544]

value: Lung

value: Male


title: KDM5C_shRNA-2_rep1


title: H9_20Kcells_R1_Late S Fraction

data_processing:
Library strategy: Repli-seq
Reads were mapped to corresponding genome (hg38 or mm10) using BWA.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio was calculated in 20kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 10kb windows
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: processed data are 10kb windows in hg38 or mm10 genomes.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370) or by KAPA HyperPlus library preparation kit (Roche Cat. No.  07958978001).


title: H9_20Kcells_R2_Early S Fraction


title: H9_20Kcells_R1_Early S Fraction


title: NC_shRNA_rep3

source_name: HTR-8/Svneo_NC shRNA

value: NC shRNA


title: S3

extract_protocol:
The spleens were dissected and prepared into single-cell suspensions and CD3+ T cells were isolated by T cell isolation kit (STEMCELL, VAN, Canada ). Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.


title: Lung, Hypoxia, Vehicle, Day8 [X542]


title: H9_40Kcells_R2_Late S Fraction


title: Lung, Hypoxia, Vehicle, Day8 [X541]


title: NC_shRNA_rep2


title: NC_shRNA_rep1


title: S2


title: S1


title: H9_40Kcells_R2_Early S Fraction


title: A2


title: H9_40Kcells_R1_Late S Fraction


title: A3


title: Lung, Normoxia, ABT-263, Day8 [X539]


title: ChIPseq_Input_3D7_PfSETvs-KO_10-16h

first: Xuan

last: Cao

address: 320 Yueyang Road

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

data_processing:
ChIP-Seq reads were mapped to the P. falciparum 3D7 reference genome (PlasmoDB release 43) by using bowtie v.1.1.1 with default parameters. Duplicate reads were excluded and kept only one read for each genomic site.
ChIP-seq signals were quantile normalized to remove the bias across the samples by using haystack_bio v.0.5.5.BedGraph files were normalized for total mapped read counts and signal was calculated as per million per kilo-base(RPM).
Genome_build: P. falciparum 3D7 (PlasmoDB release 43)

organism: Plasmodium falciparum 3D7

source_name: PfSETvs-KO P. falciparum

growth_protocol: Crosslinked chromatin was sheared by sonication in a Q-Sonica for 10min at 30-s intervals, power setting high, to a size of 200–300 bp.Chromatin samples werefrozen and stored at -80℃.

extract_protocol:
After washing with buffers containing 100, 150 and 250mM NaCl, immuno-precipitated DNA was eluted and purified using PCR purification columns (Qiagen).
The ChIP-seq library construction was processing with QIAseq ultralow input library kit.

treatment_protocol: Antibodies to HP1 were added to crosslinked samples of wild-type 3D7 and 3D7SETvsΔ, and incubated at 4C,followed by the addition of 10ml A/G beads and further incubation for 2 h.

tag: Stage

value: ring

value: PfSETvs-KO

tag: antibody


title: A1

tag: strain


title: H9_40Kcells_R1_Early S Fraction


title: Lung, Normoxia, ABT-263, Day8 [X538]

source_name: Lung

tag: tissue


title: Lung, Hypoxia, Vehicle, Day8 [X543]


title: ChIPseq_Input_3D7_wild-type_10-16h

source_name: wild-type P. falciparum

value: wild-type


title: Lung, Normoxia, ABT-263, Day8 [X537]


title: ChIPseq_HP1_3D7_wild-type_10-16h


title: H9_R2_Early S Fraction


title: Lung, Normoxia, ABT-263, Day8 [X536]


title: H526, 24_dpt

city: Los Angeles

first: David

last: Shia

address: 630 Charles E Young Dr S

institute: UCLA

data_processing:
Sequencing was performed on Illumina HiSeq 3000 for SE 1x50 run.
Data quality check was done on Illumina SAV 2.1.8
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing raw counts for each Sample

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
Standard RNA extraction protocol via Qiagen RNeasy RNA Extraction Kit (cat. no 74004)
Libraries were constructed with Illumina Nextera XT DNA library preparation kit (cat. no TG-131-1096). Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: Cells were treated for 72 hours with 500 nM of cisplatin and etoposide. Drug media was washed out and cells were sampled for RNA over time.

value: Small cell lung cancer cell

value: 500 nM cisplatin, 500 nM etoposide

tag: time

value: Day 24


title: H526, 21_dpt

value: Day 21


title: H526, 18_dpt

value: Day 18


title: hichip-P-D2

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
HiChIP paired-end reads were aligned to the hg19 genome using the HiC-Pro pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. HiC-Pro filtered reads were then processed using hichipper using the {EACH, ALL}  settings to call HiChIP peaks to MboI restriction fragments. HiC-Pro valid interaction pairs and hichipper HiChIP peaks were then processed using FitHiChIP to call significant chromatin contacts using the default settings except for the following: MappSize=500, IntType=3, BINSIZE=5000, QVALUE=0.01, UseP2PBackgrnd=0, Draw=1, TimeProf=1. We note that N-D28 samples were removed from subsequent analysis because of poor QC metrics.
Differential analysis was performed using diffloop and limma with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: looped regions outputed plus the count frequencies of the loop called between the two loops

extract_protocol:
The HiChIP protocol was performed for Astrocytes, ESC cells, N-D2, N-D4, N-D10, and N-D28 as previously described (Mumbach 2016) using antibody H3K27ac (Abcam, ab4729) with the following modifications. Samples were sheared using a Covaris E220 using the following parameters: Fill Level = 10, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 4 minutes and then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C.  We used 4 ug of antibody to H3K27ac and captured the chromatin-antibody complex with 34 uL Protein A beads (Thermo Fisher). Qubit quantification following ChIP ranged from 125-150 ng. The amount of Tn5 used and number of PCR cycles performed were based on the post-ChIP Qubit amounts.
HiChIP samples were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina NovaSeq 6000 instrument to an average read depth of 300 million total reads.
H3K27ac HiChIP

value: neuron

tag: age

value: day 2


title: Lung, Normoxia, ABT-263, Day8 [X535]

tag: genotype

tag: treatment


title: Lung, Hypoxia, Vehicle, Day8 [X540]

tag: Sex


title: H526, 11_dpt

tag: cell line

value: Day 11


title: siSFV-2 in 293T

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

description: total RNA

data_processing:
Fo small RNAs, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were mapped to the human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0) by using Bowite 2.2.5, and the cellular miRNA expression level was determined on the basis of the number of reads, which were 100% identical to the annotated miRNA sequences in miRBase version 22 (https://www.mirbase.org/ftp/CURRENT/genomes/dme.gff3). The vsRNA reads that cannot be mapped to the host genome were then mapped to the viral genome allowing 2 nt mismatch. The vsRNA reads were counted and normalized by the number of total vsRNA reads (counts per million of total vsRNA reads) to show the size distribution and abundance of vsRNAs in different size, and 21-23 nt size vsRNA reads mapping to the viral genome were counted to show the distribution across the viral genome. The vsRNA Reads mapped to (+)-strand and (-)-strand of the viral genome were intersected using BedTools (v2.29.2).
For total RNAs, libraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. Then all reads were mapped to the human genome (release hg19) using Hisat2. DEseq2 (v1.34.0) was used to detect differentially expressed genes.
Assembly: Human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0)

source_name: Human  HEK293T cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina) (for small RNAs); MGIEasy RNA Library Preparation Kits (BGI) (for total RNAs)

value: HEK293T cells

value: transfection of siRNA targeting SFV for 24 hours


title: Lung, Normoxia, ABT-263, Day8 [X534]

value: Vehicule


title: H526, 7_dpt

value: Lung

value: Day 7


title: hichip-P-NPC

value: posterior neural progenitor cell


title: siSFV-1 in 293T

description: total RNA


title: hichip-A-D2


title: Lung, Normoxia, Vehicle, Day8 [X533]

value: Male


title: siNC-3 in 293T

description: total RNA

value: transfection of non-specific siRNA for 24 hours


title: H526, 5_dpt

value: Day 5


title: ChIPseq_HP1_3D7_PfSETvs-KO_10-16h

value: ring

value: PfSETvs-KO


title: hichip-A-NPC

value: anterior neural progenitor cell


title: Lung, Normoxia, Vehicle, Day8 [X532]


title: H9_R2_Late S Fraction

source_name: Human ESC

value: Late S fraction


title: H526, 0_dpt

value: Small cell lung cancer cell

value: 500 nM cisplatin, 500 nM etoposide

value: Day 0


title: siNC-2 in 293T

description: total RNA


title: Lung, Normoxia, Vehicle, Day8 [X531]


title: hichip-N-D28

value: neuron

value: day 28


title: H526, initial

value: Control

value: Day -3


title: siNC-1 in 293T

description: total RNA

value: HEK293T cells


title: hichip-N-D10

value: day 10


title: siSFV-3 in 293T

description: total RNA

value: transfection of siRNA targeting SFV for 24 hours


title: Lung, Normoxia, Vehicle, Day8 [X530]

value: Lung

value: Male

value: Vehicule


title: H82, 24_dpt

value: Day 24


title: hichip-N-D2

value: day 2


title: WT Diaphragm

city: Cleveland

first: Brian

middle: P

last: Rubin

state: OH

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Alignment to the mm10 genome and demultiplexing was performed with CellRanger
Assembly: mm10

molecule: polyA RNA

source_name: Diaphragm

extract_protocol:
Tumors were cryopreserved in 10%DMSO in fetal bovine serum and slow frozen to -80˚C. Following histologic confirmation, samples were rewarmed and dissociated with the MACS tumor kit.
Single Cell library preparations with the 10X genomics platform

value: Diaphragm

value: WT


title: H82, 21_dpt

value: Small cell lung cancer cell

value: Day 21


title: hichip-ES

value: stem cell


title: WT Liver

source_name: Liver

value: Liver


title: H82, 18_dpt

value: 500 nM cisplatin, 500 nM etoposide

value: Day 18


title: MEF_R1_Early S Fraction

source_name: MEFs

value: Early S fraction


title: WT Lung


title: H82, 11_dpt

value: Day 11


title: KDM5C_rep2

source_name: HTR-8/Svneo_KDM5C-expression vector

value: human invasive extravillous trophoblasts (EVTs)

value: KDM5C-expression vector


title: H82, 7_dpt

value: Lung

value: Day 7


title: 30h_r2

city: Chicago

first: Peng

last: Ji

state: Illinois

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
Peaks were determined using HOMER v4.11.1
Differential peak analysis was performed using HOMER v4.11.1
bigWig files were created using deepTools
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: mouse fetal liver cell

growth_protocol: E13.5 fetal liver cells were harvested and purified for Ter-119 negative cells. Purified cells were then cultured in EPO containing medium for analysis.

extract_protocol:
Cells were lysed and DNA were transposed and purified.
ATAC-seq libraries were prepared for sequencing using standard Nextera XT protocols

treatment_protocol: DMSO or Z-VAD-FMK were added at 24h and cells were havested at 30h

tag: progenitor cell

value: progenitor cells

value: DMSO


title: KDM5C_rep1

tag: cell type


title: 30h_r1


title: H82, 5_dpt

value: Day 5


title: CDKN2A WT Lung Tumor

source_name: EHE Tumor

value: CDKN2A KO


title: CDKN2A WT Liver Tumor

value: CDKN2A WT


title: H82, 0_dpt

value: Small cell lung cancer cell

value: Day 0


title: CDKN2A KO Diaphragm Tumor

value: Diaphragm


title: Lung, Normoxia, Vehicle, Day8 [X528]

value: Male

value: Vehicule


title: H82, initial

value: Control

value: Day -3


title: CDKN2A KO Lung Tumor


title: Vector_rep2

source_name: HTR-8/Svneo_control vector

value: control vector


title: 0hr_r2

value: no treatment


title: Vector_rep3

value: human invasive extravillous trophoblasts (EVTs)


title: MEF_R1_Late S Fraction

value: Late S fraction


title: KDM5C_rep3

value: KDM5C-expression vector


title: Vector_rep1


title: Primary prostate tumor cells

status: Public on Dec 15 2022

city: Daegu

first: Ji-Hak

last: Jeong

address: 80 Daehakro, Bukgu

institute: Kyungpook National University

description:
Exp165-JHJ-RawGeneCounts
Exp165-JHJ-NormalizedGeneCounts

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality bases using cutadapt version (-m 32 --max-n 0.1 --nextseq-trim=20)
Trimmed reads were mapped to the mouse genome (mouse-UCSC : M.musculus-UCSC-mm10 : downloaded March 22, 2016) using the star version 2.5.2a aligner
Gene abundance was estimated with python version 2.7.11, and htseq version 0.6.0
Assembly: mouse-UCSC : M.musculus-UCSC-mm10 : downloaded March 22, 2016
Supplementary files format and content: Both Exp165-JHJ-RawGeneCounts and Exp165-JHJ-NormalizedGeneCounts are formatted the same. Rows represent genes and columns represent samples.

source_name: PPC

growth_protocol: Myc-CaP cells were cultured in RPMI 1640 medium supplemented with 1% antibiotic-antimycotic and 10% fetal bovine serum (FBS), and incubated at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNase Mini kit (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.
Illumina TruSeq Stranded Total RNA Sample Prep

treatment_protocol: Myc-CaP cells (1 x 106) in 50 μL sterile PBS were mixed with 50 μL Growth Factor Reduced (GFR) Matrigel (BD Biosciences), and the mixture was subcutaneously inoculated in the flanks of FVB mice. FVB male mice (6 week-old) were used for castration model. To obtain primary prostate cancer cells (PPC cells), mice were euthanized when tumors reached a volume of 500 mm3. To obtain shrunk prostate cancer cells (S-PC), male mice with primary prostate tumor size of about 500 mm3 were anesthetized and castrated. After 10 days of castration, the mice were euthanized. Tumors were collected and tumor cells were isolated and purified. To obtain castration-resistant prostate cancer cells (CRPC cells), male mice with primary prostate tumor size of about 500 mm3 were anesthetized and castrated. When tumors recurred and reached a volume of 500 mm3 after castration, the mice were euthanized. Tumors were collected and tumor cells were isolated and purified by using ACCUMAX™ (Innovative Cell Technologies) according to manufacturer’s instructions.

value: PPC

value: primary prostate tumor cells

value: WT


title: Castration-resistant prostate tumor cells

source_name: CRPC

value: CRPC

value: Castration

value: Day 30


title: CDKN2A WT Diaphragm Tumor

value: CDKN2A WT


title: Shrunk prostate tumor cells

source_name: S-PC

value: S-PC

value: Day 10


title: 0hr_r1

value: progenitor cells


title: Tgαq*44, 14 months, mouse 5

city: Cracow

first: Piotr

last: Berkowicz

address: Bobrzyńskiego 14

country: Poland

institute: Jagiellonian Centre for Experimental Therapeutics

description:
51_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)

data_processing:
Adaptor sequences, primers and poly-A tails were trimmed from sequencing raw reads by Cutadapt, and the quality of the raw reads was checked by FastQC.
The raw reads were mapped towards the mouse reference genome using Star.
HTSeq software was used to count reads that mapped to the exons of the coding genes. Normalisation of the count data was performed using the TMM method.
Analysis of differentially expressed genes (DEGs) was performed using Limma Voom software.
Analyses were generated in R environment.
Assembly: GRCm38.p6
Supplementary files format and content: counts_matrix (Excel file) – file involves raw number of reads per gene for each sample
Supplementary files format and content: DEGs_FVB_vs_FVB_analysis (Excel file) – file involves number of DEGs for each measured comparison in FVB vs. FVB analysis
Supplementary files format and content: DEGs_Tg_vs_FVB_analysis (Excel file) – file involves number of DEGs for each measured comparison (month) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: overrepresented_processes_Tg_vs_FVB_analysis (Excel file) - file involves number of overrepresented biological processes (from Gene Ontology database) for each measured comparison (month) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: overrepresented_processes_FVB_vs_FVB_analysis (Excel file) - file involves number of overrepresented biological processes (from Gene Ontology database) for each measured comparison in FVB vs. FVB analysis
Supplementary files format and content: ageing_processes_in_HF (Tg_vs_FVB_analysis) (Excel file) - file involves the number of ‘cardiac ageing processes’ at 4-, 8-, 10-, 12-, 14 months in Tgαq*44 vs. FVB analysis; ratio of the number of 'cardiac ageing processes' to the respective number of overrepresented biological processes at each measured month in Tgαq*44 vs. FVB analysis; number of 'processes of ageing heart' (n=8) that occured as overrepresented biological processes at each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis; number of 'processes of aged heart' (n=0) that occured as DEGs in each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file) – file involves the number of ‘cardiac ageing genes’ at 4-, 8-, 10-, 12-, 14 months in Tgαq*44 vs. FVB analysis; ratio of the number of 'cardiac ageing genes' to the respective number of DEGs at each measured month in Tgαq*44 vs. FVB analysis; number of 'genes of ageing heart' (n=26) that occured as DEGs at each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis; number of 'genes of aged heart' (n=8) that occured as DEGs in each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file) – file involves number of DEGs that were or were not annotated to overrepresented biological processes (from Gene Ontology database) in the respective comparisons in FVB vs. FVB analysis
Supplementary files format and content: annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file) – file involves number of DEGs that were or were not annotated to overrepresented biological processes (from Gene Ontology database) in the respective comparisons (months) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file) – file involves 26 biological processes (from Gene Ontology database) which were overrepresented in each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis. This file also involves values of gene frequency in 26 overrepresented biological processes at 4-, 8-, 10-, 12-, 14 months
Supplementary files format and content: 156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file) – file involves 156 genes which were differentially expressed in each measured months (4-, 8-, 10-, 12-, 14 months) in Tgαq*44 vs. FVB analysis
Supplementary files format and content: genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file) – file involves the number of ‘genes of aged heart’(n=454) and ‘processes of aged heart’ (n=56) which are presented as DEGs or overrepresented biological processes (from Gene Ontology database) that occured only in 14- vs. 4-month-old FVB mice
Supplementary files format and content: genes_and_processes_ageing_heart_FVBvs.FVB (Excel file) - file involves the number of ‘genes of ageing heart’(n=481) and ‘processes of ageing heart’ (n=55) which are presented as DEGs or overrepresented biological processes (from Gene Ontology database) that occured in 14- vs. 4-month-old FVB mice and at least in one comparison between 8-, 10-, 12- vs. 4-month-old FVB mice

source_name: heart (apex of left ventricle)

growth_protocol: Mice were fed a standard chow diet, given water ad libitum, and kept in pathogen-free conditions (22–25 °C, 45–65% humidity, 12 h light/12 h dark cycle).

extract_protocol:
Apexes of LV were dissected from hearts and homognized in TRIzol reagent. Total RNA was extracted from cardiac tissues (i.e., apex of the heart) using an RNeasy Mini Kit (Qiagen) with DNAse treatment. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared with Sense mRNA-Seq Library prep Kit v2 (Lexogen) according to the manufacturer’s protocol. Five biological replicates in each group for a total of 50 samples (5 replicates*(5 time points)*(2 strains)) were submitted for RNA sequencing.

treatment_protocol: x

value: overexpression of G{alpha}q protein

tag: disease

value: heart failure

value: female

value: 14 months

value: heart (apex of left ventricle)


title: Tgαq*44, 14 months, mouse 2

description:
48_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 14 months, mouse 4

description:
50_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 12 months, mouse 5

description:
46_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)

value: 12 months


title: Tgαq*44, 12 months, mouse 3

description:
44_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 12 months, mouse 4

description:
45_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 12 months, mouse 2

description:
43_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 14 months, mouse 3

description:
49_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 14 months, mouse 1

description:
47_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 10 months, mouse 3

description:
39_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)

value: 10 months


title: Tgαq*44, 10 months, mouse 5

description:
41_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 10 months, mouse 1

description:
37_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 12 months, mouse 1

description:
42_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 8 months, mouse 5

description:
36_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)

value: 8 months


title: Tgαq*44, 10 months, mouse 4

description:
40_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 10 months, mouse 2

description:
38_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 8 months, mouse 4

description:
35_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 8 months, mouse 3

description:
34_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 8 months, mouse 1

description:
32_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 4 months, mouse 4

description:
30_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)

value: 4 months


title: Tgαq*44, 4 months, mouse 5

description:
31_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 8 months, mouse 2

description:
33_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 4 months, mouse 3

description:
29_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: Tgαq*44, 4 months, mouse 1

description:
27_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: FVB, 14 months, mouse 2

description:
23_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)

value: FVB

value: wild-type

value: x


title: FVB, 14 months, mouse 3

description:
24_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 14 months, mouse 5

description:
26_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: Tgαq*44, 4 months, mouse 2

description:
28_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)


title: FVB, 12 months, mouse 5

description:
21_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 12 months, mouse 4

description:
19_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 12 months, mouse 3

description:
18_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 12 months, mouse 2

description:
17_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 10 months, mouse 1

description:
11_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 10 months, mouse 4

description:
14_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 10 months, mouse 2

description:
12_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 10 months, mouse 3

description:
13_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)


title: FVB, 12 months, mouse 1

description:
16_sample (column in counts_matrix)
counts_matrix (Excel file)
DEGs_FVB_vs_FVB_analysis (Excel file)
DEGs_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_Tg_vs_FVB_analysis (Excel file)
overrepresented_processes_FVB_vs_FVB_analysis (Excel file)
ageing_processes_in_HF (Tg_vs_FVB_analysis)(Excel file)
ageing_genes_in_HF (Tg_vs_FVB_analysis)(Excel file)
annotated_DEGs_to_overrepresented_processes_in_FVBvsFVB (Excel file)
annotated_DEGs_to_overrepresented_processes_in_Tgvs.FVB (Excel file)
gene_freq_in_common_overrepresented_processes_4-14_months_TgvsFVB (Excel file)
156_common_DEGs_for_4-14months_Tgvs.FVB (Excel file)
genes_and_processes_of_aged_heart_FVBvs.FVB (Excel file)
genes_and_processes_ageing_heart_FVBvs.FVB (Excel file)